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Takashi Makino

Section

Graduate School of Life Sciences

Job title

Professor

Degree

博士（理学）（総合研究大学院大学）
修士（農学）（名古屋大学）

researchmap

https://researchmap.jp/read0149982

J-GLOBAL ID

201001061387304825

Committee Memberships 1

日本進化学会　代議員

2022/01 - Present

Professional Memberships 3

THE GENETICS SOCIETY OF JAPAN
THE ECOLOGICAL SOCIETY OF JAPAN
SOCIETY OF EVOLUTIONARY STUDIES, JAPAN

Research Interests 4

遺伝子発現制御の進化
Gene duplication
comparative genomics
gene duplication

Research Areas 1

Life sciences / Evolutionary biology / Molecular Evolution

Papers 78

Modification of TAWAWA1‐mediated panicle architecture by genome editing of a downstream conserved noncoding sequence in rice

Takeshi Kuroha, Fabien Lombardo, Watal M. Iwasaki, Svetlana Chechetka, Yoshihiro Kawahara, Akiko Yoshida, Takashi Makino, Hitoshi Yoshida

Plant Biotechnology Journal　2025/07

DOI： 10.1111/pbi.70043 　

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<jats:title>Summary</jats:title><jats:p>Genome editing is a promising tool to enhance plant breeding, particularly for the generation of practical quantitative traits. We focused on the rice yield-related gene<jats:italic>TAWAWA1</jats:italic>(<jats:italic>TAW1</jats:italic>) and produced various degrees of increased panicle branching phenotypes by modifying its downstream conserved noncoding sequence (CNS). Differential modification of two highly conserved regions containing putative repressive elements in this CNS caused transcriptional upregulation of<jats:italic>TAW1</jats:italic>, resulting in diverse phenotypes.</jats:p>
Genomic signature and evolutionary history of completely cleistogamous lineages in the non-photosynthetic orchid Gastrodia

Kenji Suetsugu, Shun K. Hirota, Takashi Makino, Yoshihisa Suyama, Shingo Kaneko, Kenji Fukushima

Proceedings of the Royal Society B: Biological Sciences　2025/05

DOI： 10.1098/rspb.2025.0574 　
Ancestral origin and structural characteristics of non-syntenic homologous chromosomes in abalones

Shotaro Hirase, Takashi Makino, Takeshi Takeuchi, Mitsutaka Kadota, Shigehiro Kuraku, Kiyoshi Kikuchi

2025/04/03

DOI： 10.1101/2025.04.02.641744 　
Evaluation of the conservation value and conservation difficulty of local populations of the rare plant <scp>Viola raddeana</scp> based on genetic diversity and gene expression information using next‐generation sequencers

Hiroaki Shiraishi, Yoshihisa Suyama, Takashi Makino, Shun K. Hirota, Kazuo Obata, Jung‐Hyun Lee, Hyeok Jae Choi, Yoshihiko Tsumura

Plant Species Biology　2025/02/05
Publisher: Wiley
DOI： 10.1111/1442-1984.12507 　

ISSN： 0913-557X

eISSN： 1442-1984

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Abstract Rare plant species identified in project areas where land is to be developed or altered may need to be extracted for ex situ conservation under human control. During ex situ conservation, it is important to minimize the impact of adverse factors including the potentially limited environmental adaptability of rare plants under cultivation and possible losses of genetic diversity due to inbreeding if the number of conserved individuals is low. Here we evaluate the conservation difficulty and genetic diversity of populations of the rare plant Violα raddeana at five sites based on harmful gene accumulation and gene duplication data gathered using RNA‐seq. Additionally, we evaluate the genetic diversity and structure of these populations using single‐nucleotide polymorphism (SNP) data acquired by multiplexed inter‐simple sequence repeat genotyping by sequencing (MIG‐seq). The results obtained indicate that the V. raddeana populations have declined but remain robust toward environmental changes and can undergo voluntary mating at all sites. Moreover, we observed clear genetic differentiation between two populations in close geographic proximity. We considered that if the majority of the remaining individuals of V. raddeana in each genetically related population were transplanted and cultivated, it would be possible to maintain their genetic diversity through ex situ conservation. It is important that V. raddeana be kept under ex situ conservation management. In order to achieve this, we should work with public organizations such as local government agencies and botanical gardens.
Conservation units and the origin of planted individuals of an endangered endemic species Lobelia boninensis in the Ogasawara Islands

Chikashi Hata, Chiharu Endo, Hiroshi Tanaka, Miho Hiruma, Maiko Kumamoto, Izumi Takenaka, Takashi Makino, Kento Niinaka, Yoshihisa Suyama, Shun K. Hirota, Michimasa Yamasaki, Yuji Isagi

Scientific Reports　2024/11/09

DOI： 10.1038/s41598-024-78452-w 　

ISSN： 2045-2322

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<jats:title>Abstract</jats:title><jats:p>The Ogasawara Islands, one of the UNESCO World Natural Heritage Site located about 1000 km south of Japan’s main island, harbor numerous endemic species, many of which are as endangered. One of the endemic plant species, <jats:italic>Lobelia boninensis</jats:italic>, found in the Mukojima, Chichijima, and Hahajima archipelagoes, is endangered due to predation. As part of conservation efforts, translocation is now underway, especially on Chichijima. However, we lack essential information, such as the genetic population structure, to develop appropriate translocation strategies for both wild and planted individuals. Here, we aimed to identify the conservation units and the origin of planted individuals by estimating the genetic population structure and phylogenetic relationships across all habitats of this species. We identified two distinct genetic clusters, indicating genetic differentiation between the northern and southern populations. The genetic population components detected at an isolated site on Chichijima showed a mixture of these distinct clusters, probably due to hybridization. The transplanted individuals in Chichijima were found to have originated from a population in Hahajima. These results suggest the presence of two distinct conservation units. Furthermore, the current translocation strategy poses a risk of genetic contamination between these units, highlighting the need for revised conservation management practices.</jats:p>
Expression of laccase and ascorbate oxidase affects lignin composition in Arabidopsis thaliana stems

Konan Ishida, Senri Yamamoto, Takashi Makino, Yuki Tobimatsu

Journal of Plant Research　2024/10/07
Publisher: Springer Science and Business Media LLC
DOI： 10.1007/s10265-024-01585-6 　

ISSN： 0918-9440

eISSN： 1618-0860
Dramatic evolutionary changes of conserved noncoding elements accompanied by extraordinary features ofCaenorhabditis inopinata

Katsunori Tamagawa, Shun Oomura, Asako Sugimoto, Takashi Makino

2024/09/21
Publisher: Cold Spring Harbor Laboratory
DOI： 10.1101/2024.09.18.613604 　

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Phenotypic evolution is caused by mutations in noncoding and protein-coding regions. Conserved noncoding elements (CNEs) have-at least partially-gene regulatory functions and contribute to the evolution of organisms by modifying their gene expression. While evolutionary changes of CNEs-such as loss and accelerated evolution-have been intensively studied in vertebrates, only a few studies have focused on invertebrates. The availability of detailed functional genomic information of the model nematodeCaenorhabditis elegansand recent accumulation of genome sequences within the same genus facilitate the use of these nematodes in comparative genomics focusing on CNEs. The recently discovered speciesCaenorhabditis inopinatahas several peculiar traits characterized by a larger body size than that of its close relatives and are regarded as an appropriate species that links phenotypic evolution with genomic changes. Herein, using comparative genomics and transcriptomics inC. inopinata, we analyzed the evolution of CNEs and their functions during phenotypic evolution. We detected substantial evolutionary changes in CNEs inC. inopinatacompared to other relatives-changes frequently associated with body morphology and behavior corresponding to extraordinary body size and unique life cycles. Our study revealed an association between noncoding elements and substantial phenotypic evolution in invertebrates.
Evolutionary changes of noncoding elements associated with transition of sexual mode in Caenorhabditis nematodes

Katsunori Tamagawa, Mehmet Dayi, Simo Sun, Rikako Hata, Taisei Kikuchi, Nami Haruta, Asako Sugimoto, Takashi Makino

Science Advances　10　(37)　2024/09/13
Publisher: American Association for the Advancement of Science (AAAS)
DOI： 10.1126/sciadv.adn9913 　

eISSN： 2375-2548

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The transition of the sexual mode occurs widely in animal evolution. In Caenorhabditis nematodes, androdioecy, a sexual polymorphism composed of males and hermaphrodites having the ability to self-fertilize, has evolved independently multiple times. While the modification of noncoding regulatory elements likely contributed to the evolution of hermaphroditism, little is known about these changes. Here, we conducted a genome-wide analysis of conserved noncoding elements (CNEs) focusing on the evolution of hermaphroditism in Caenorhabditis nematodes. We found that, in androdioecious nematodes, mutations rapidly accumulated in CNEs’ neighboring genes associated with sexual traits. Expression analysis indicate that the identified CNEs are involved in spermatogenesis in hermaphrodites and associated with the transition of gene expression from dioecious to androdioecious nematodes. Last, genome editing of a CNE neighboring laf-1 resulted in a change in its expression in the gonadal region undergoing spermatogenesis. Our bioinformatic and experimental analyses highlight the importance of CNEs in gene regulation associated with the development of hermaphrodites.
Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut. International-journal

Hiroki Nagai, Yuya Adachi, Tenki Nakasugi, Ema Takigawa, Junichiro Ui, Takashi Makino, Masayuki Miura, Yu-Ichiro Nakajima

BMC biology　22　(1)　157-157　2024/08/02

DOI： 10.1186/s12915-024-01956-4 　

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BACKGROUND: The remarkable regenerative abilities observed in planarians and cnidarians are closely linked to the active proliferation of adult stem cells and the precise differentiation of their progeny, both of which typically deteriorate during aging in low regenerative animals. While regeneration-specific genes conserved in highly regenerative organisms may confer regenerative abilities and long-term maintenance of tissue homeostasis, it remains unclear whether introducing these regenerative genes into low regenerative animals can improve their regeneration and aging processes. RESULTS: Here, we ectopically express highly regenerative species-specific JmjC domain-encoding genes (HRJDs) in Drosophila, a widely used low regenerative model organism. Surprisingly, HRJD expression impedes tissue regeneration in the developing wing disc but extends organismal lifespan when expressed in the intestinal stem cell lineages of the adult midgut under non-regenerative conditions. Notably, HRJDs enhance the proliferative activity of intestinal stem cells while maintaining their differentiation fidelity, ameliorating age-related decline in gut barrier functions. CONCLUSIONS: These findings together suggest that the introduction of highly regenerative species-specific genes can improve stem cell functions and promote a healthy lifespan when expressed in aging animals.
Comparative genomics reveals convergent signals associated with the high metabolism and longevity in birds and bats. International-journal

Yuki Matsuda, Takashi Makino

Proceedings. Biological sciences　291　(2029)　20241068-20241068　2024/08

DOI： 10.1098/rspb.2024.1068 　

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Birds and bats have long lifespans relative to their body size compared with non-flying animals. However, the genomic basis associated with longer lifespan of flying species despite their higher metabolism was unclear. In this study, we hypothesized that genes involved in the regulation of metabolism and lifespan changed with the acquisition of flight and searched for genes that show specific evolutionary patterns in flying species. As a result, we identified several genes that show different evolutionary rates in bird and bat lineages. Genes in pathways involved in lifespan regulation were conserved in birds, while they evolved at an accelerated rate in bats. We also searched for genes in which convergent amino acid substitutions occurred in birds and bats and found such substitutions in genes involved in cancer, reactive oxygen species control and immunity. Our study revealed genomic changes associated with the acquisition of flight in birds and bats and suggested that multiple genes involved in the regulation of lifespan and metabolism support both high metabolism and longevity in flying species.
Convergent accelerated evolution of mammal-specific conserved non-coding elements in hibernators

Daiki Nakayama, Takashi Makino

Scientific Reports　14　(1)　2024/05/23
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41598-024-62455-8 　

ISSN： 2045-2322

eISSN： 2045-2322

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Abstract Mammals maintain their body temperature, yet hibernators can temporarily lower their metabolic rate as an energy-saving strategy. It has been proposed that hibernators evolved independently from homeotherms, and it is possible that the convergent evolution of hibernation involved common genomic changes among hibernator-lineages. Since hibernation is a seasonal trait, the evolution of gene regulatory regions in response to changes in season may have been important for the acquisition of hibernation traits. High-frequency accumulation of mutations in conserved non-coding elements (CNEs) could, in principle, alter the expression of neighboring genes and thereby contribute to the acquisition of new traits. To address this possibility, we performed a comparative genomic analysis of mammals to identify accelerated CNEs commonly associated with hibernation. We found that accelerated CNEs are common to hibernator-lineages and could be involved with hibernation. We also found that common factors of genes that located near accelerated CNEs and are differentially expressed between normal and hibernation periods related to gene regulation and cell-fate determination. It suggests that the molecular mechanisms controlling hibernation have undergone convergent evolution. These results help broaden our understanding of the genetic adaptations that facilitated hibernation in mammals and may offer insights pertaining to stress responses and energy conservation.
Conserved Genes in Highly Regenerative Metazoans Are Associated with Planarian Regeneration. International-journal

Shankar C R R Chereddy, Takashi Makino

Genome biology and evolution　16　(5)　2024/05/02

DOI： 10.1093/gbe/evae082 　

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Metazoan species depict a wide spectrum of regeneration ability which calls into question the evolutionary origins of the underlying processes. Since species with high regeneration ability are widely distributed throughout metazoans, there is a possibility that the metazoan ancestor had an underlying common molecular mechanism. Early metazoans like sponges possess high regenerative ability, but, due to the large differences they have with Cnidaria and Bilateria regarding symmetry and neuronal systems, it can be inferred that this regenerative ability is different. We hypothesized that the last common ancestor of Cnidaria and Bilateria possessed remarkable regenerative ability which was lost during evolution. We separated Cnidaria and Bilateria into three classes possessing whole-body regenerating, high regenerative ability, and low regenerative ability. Using a multiway BLAST and gene phylogeny approach, we identified genes conserved in whole-body regenerating species and lost in low regenerative ability species and labeled them Cnidaria and Bilaterian regeneration genes. Through transcription factor analysis, we identified that Cnidaria and Bilaterian regeneration genes were associated with an overabundance of homeodomain regulatory elements. RNA interference of Cnidaria and Bilaterian regeneration genes resulted in loss of regeneration phenotype for HRJDa, HRJDb, DUF21, DISP3, and ARMR genes. We observed that DUF21 knockdown was highly lethal in the early stages of regeneration indicating a potential role in wound response. Also, HRJDa, HRJDb, DISP3, and ARMR knockdown showed loss of regeneration phenotype after second amputation. The results strongly correlate with their respective RNA-seq profiles. We propose that Cnidaria and Bilaterian regeneration genes play a major role in regeneration across highly regenerative Cnidaria and Bilateria.
Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards

Fuku Sakamoto, Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Yuu Ishii, Katsushi Yamaguchi, Shuji Shigenobu, Takuro Nakayama, Takashi Makino, Masakado Kawata

Ecology and Evolution　14　(3)　2024/03/07
Publisher: Wiley
DOI： 10.1002/ece3.11117 　

ISSN： 2045-7758

eISSN： 2045-7758

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Abstract Understanding the genetic basis for adapting to thermal environments is important due to serious effects of global warming on ectothermic species. Various genes associated with thermal adaptation in lizards have been identified mainly focusing on changes in gene expression or the detection of positively selected genes using coding regions. Only a few comprehensive genome‐wide analyses have included noncoding regions. This study aimed to identify evolutionarily conserved and accelerated genomic regions using whole genomes of eight Anolis lizard species that have repeatedly adapted to similar thermal environments in multiple lineages. Evolutionarily conserved genomic regions were extracted as regions with overall sequence conservation (regions with fewer base substitutions) across all lineages compared with the neutral model. Genomic regions that underwent accelerated evolution in the lineage of interest were identified as those with more base substitutions in the target branch than in the entire background branch. Conserved elements across all branches were relatively abundant in “intergenic” genomic regions among noncoding regions. Accelerated regions (ARs) of each lineage contained a significantly greater proportion of noncoding RNA genes than the entire multiple alignment. Common genes containing ARs within 5 kb of their vicinity in lineages with similar thermal habitats were identified. Many genes associated with circadian rhythms and behavior were found in hot‐open and cool‐shaded habitat lineages. These genes might play a role in contributing to thermal adaptation and assist future studies examining the function of genes involved in thermal adaptation via genome editing.
Genomic screening of fish‐specific genes in gnathostomes and their functions in fin development

Hidehiro Kudoh, Sayuri Yonei‐Tamura, Gembu Abe, Junichi Iwakiri, Masahiro Uesaka, Takashi Makino, Koji Tamura

Development, Growth & Differentiation　2024/03/04
Publisher: Wiley
DOI： 10.1111/dgd.12918 　

ISSN： 0012-1592

eISSN： 1440-169X

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Abstract In this study, we comprehensively searched for fish‐specific genes in gnathostomes that contribute to development of the fin, a fish‐specific trait. Many previous reports suggested that animal group‐specific genes are often important for group‐specific traits. Clarifying the roles of fish‐specific genes in fin development of gnathostomes, for example, can help elucidate the mechanisms underlying the formation of this trait. We first identified 91 fish‐specific genes in gnathostomes by comparing the gene repertoire in 16 fish and 35 tetrapod species. RNA‐seq analysis narrowed down the 91 candidates to 33 genes that were expressed in the developing pectoral fin. We analyzed the functions of approximately half of the candidate genes by loss‐of‐function analysis in zebrafish. We found that some of the fish‐specific and fin development‐related genes, including fgf24 and and1/and2, play roles in fin development. In particular, the newly identified fish‐specific gene qkia is expressed in the developing fin muscle and contributes to muscle morphogenesis in the pectoral fin as well as body trunk. These results indicate that the strategy of identifying animal group‐specific genes is functional and useful. The methods applied here could be used in future studies to identify trait‐associated genes in other animal groups.
Double migration of the endangered Tricyrtis formosana (Liliaceae) in Japan. International-journal

Kaori Tsunenari, Takuro Ito, Masatsugu Yokota, Mayu Shibabayashi, Chiharu Endo, Kuo-Fang Chung, Yoshihisa Suyama, Ayumi Matsuo, Atsushi Abe, Akiyo Naiki, Hiroaki Setoguchi, Takashi Makino, Yuji Isagi

Scientific reports　14　(1)　957-957　2024/01/10

DOI： 10.1038/s41598-024-51431-x 　

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The Ryukyu Islands of Japan are a biodiversity hotspot due to geographical and historical factors. Tricyrtis formosana is a perennial herbaceous plant that commonly found in Taiwan. But only a few populations have been identified in a limited habitat on Iriomote Island, while populations of unknown origin occur near human settlements in an area on the main island of Okinawa. To better understand these populations of the phylogenetic uniqueness and intrinsic vulnerability, we conducted comparative analyses including (1) phylogeny and population structure with MIG-seq data, (2) photosynthesis-related traits of plants grown under common conditions and (3) transcriptome analysis to detect deleterious variations. Results revealed that T. formosana was split into two clades by the congeners and that Iriomote and Okinawa populations independently derived from ancestral Taiwanese populations in each clade. Photosynthetic efficiency was lowest in the Iriomote population, followed by Okinawa and Taiwan. Transcriptome analysis showed that the Iriomote population accumulated more deleterious variations, suggesting intrinsic vulnerability. These results indicate that each T. formosana population in Japan is phylogenetically unique and has been independently dispersed from Taiwan, and that the Iriomote population presents a high conservation difficulty with a unique photosynthesis-related characteristic and a larger amount of deleterious variations.
Transcriptomic signatures associated with underlying rapid changes in the early phase brain of bi-directional sex change in Trimma okinawae

Katsunori Tamagawa, Tomoki Sunobe, Takashi Makino, Masakado Kawata

Royal Society Open Science　10　(12)　2023/12/06
Publisher: The Royal Society
DOI： 10.1098/rsos.231450 　

eISSN： 2054-5703

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Teleost fish exhibit remarkable sexual plasticity and divergent developmental systems, including sequential hermaphroditism. One of the more fascinating models of sexual plasticity is socially controlled sex change, which is often observed in coral reef fish. The Okinawa rubble goby, Trimma okinawae, is a bi-directional sex-changing fish. It can rapidly change sex in either direction based on social circumstances. Although behavioural and neuroendocrine sex change occurs immediately and is believed to trigger gonadal changes, the underlying mechanisms remain poorly understood. In this study, we conducted a de novo transcriptome analysis of the T. okinawae brain and identified genes that are differentially expressed between the sexes and genes that were immediately controlled by social stimulation implicating sex change. Several genes showed concordant expression shifts regardless of the sex change direction and were associated with histone modification in nerve cells. These genes are known to function in the neuroendocrine control of reproduction in nerve cells. Overall, we identified genes associated with the initiation of sex change, which provides insight into the regulation of sex change and sexual plasticity.
Genomic adaptive potential to cold environments in the invasive red swamp crayfish

Daiki X. Sato, Yuki Matsuda, Nisikawa Usio, Ryo Funayama, Keiko Nakayama, Takashi Makino

iScience　107267-107267　2023/07
Publisher: Elsevier BV
DOI： 10.1016/j.isci.2023.107267 　

ISSN： 2589-0042
RNA-seq analysis to identify genes related to resting egg production of panarctic Daphnia pulex

Natsumi Maruoka, Takashi Makino, Jotaro Urabe

BMC Genomics　24　(1)　2023/05/17
Publisher: Springer Science and Business Media LLC
DOI： 10.1186/s12864-023-09369-3 　

eISSN： 1471-2164

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Abstract Background The genus Daphnia switches its reproductive mode from subitaneous egg production to resting egg production in response to environmental stimuli. Although this life history trait is essential for surviving unsuitable environments, the molecular mechanism of resting egg production is little understood. In this study, we examined genes related to induction of resting egg production using two genotypes of panarctic Daphnia pulex, the JPN1 and JPN2 lineages, which differ genetically in the frequency of resting egg production. We reared these genotypes under high and low food levels. At the high food level, individuals of both genotypes continually produced subitaneous eggs, whereas at the low food level, only the JPN2 genotype produced resting eggs. Then, we performed RNA-seq analysis on specimens of three instars, including before and after egg production. Results These results showed that expressed genes differed significantly between individuals grown under high and low food levels and among individuals of different instars and genotypes. Among these differentially expressed genes (DEGs), we found 16 that changed expression level before resting egg production. Some of these genes showed high-level expression only before resting egg production and one gene was an ortholog of bubblegum (bgm), which is reportedly up-regulated before diapause in bumblebees. According to gene ontology (GO) enrichment analysis, one GO term annotated as long-chain fatty acid biosynthetic process was enriched among these 16 genes. In addition, GO terms related to glycometabolism were enriched among down-regulated genes of individuals holding resting eggs, compared to those before resting egg production. Conclusions We found candidate genes highly expressed only before resting egg production. Although functions of candidate genes found in this study have not been reported previously in Daphnia, catabolism of long-chain fatty acids and metabolism of glycerates are related to diapause in other organisms. Thus, it is highly probable that candidate genes identified in this study are related to the molecular mechanism regulating resting egg production in Daphnia.
Differentially expressed genes associated with body size changes and transposable element insertions between Caenorhabditis elegans and its sister species, C. inopinata.

Kazuma Kawahara, Taruho Inada, Ryusei Tanaka, Mehmet Dayi, Takashi Makino, Shinichi Maruyama, Taisei Kikuchi, Asako Sugimoto, Masakado Kawata

Genome Biology and Evolution　2023/04/18
Publisher: Oxford University Press (OUP)
DOI： 10.1093/gbe/evad063 　

eISSN： 1759-6653

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Abstract Why the recently discovered nematode Caenorhabditis inopinata differs so greatly from its sibling species Caenorhabditis elegans remains unknown. A previous study showed that C. inopinata has more transposable elements (TEs), sequences that replicate and move autonomously throughout the genome, potentially altering the expression of neighboring genes. In this study, we focused on how the body size of this species has evolved and whether TEs could affect the expression of genes related to species-specific traits such as body size. First, we compared gene expression levels between C. inopinata and C. elegans in the L4 larval and young adult stages—when growth rates differ most prominently between these species—to identify candidate genes contributing to their differences. The results showed that the expression levels of collagen genes were consistently higher in C. inopinata than in C. elegans and that some genes related to cell size were differentially expressed between the species. Then, we examined whether genes with TE insertions are differentially expressed between species. Indeed, the genes featuring C. inopinata-specific TE insertions had higher expression levels in C. inopinata than in C. elegans. These upregulated genes included those related to body size, suggesting that these genes could be candidates for artificial TE insertion to examine the role of TEs in the body size evolution of C. inopinata.
Invasions of an obligate asexual daphnid species support the nearly neutral theory

Hajime Ohtsuki, Hirotomo Norimatsu, Takashi Makino, Jotaro Urabe

Scientific Reports　12　(1)　2022/12
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41598-022-11218-4 　

eISSN： 2045-2322

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Abstract To verify the “nearly neutral theory (NNT),” the ratio of nonsynonymous to synonymous substitutions (dN/dS) was compared among populations of different species. To determine the validity of NNT, however, populations that are genetically isolated from each other but share the same selection agents and differ in size should be compared. Genetically different lineages of obligate asexual Daphnia pulex invading Japan from North America are an ideal example as they satisfy these prerequisites. Therefore, we analyzed the whole-genome sequences of 18 genotypes, including those of the two independently invaded D. pulex lineages (JPN1 and JPN2) and compared the dN/dS ratio between the lineages. The base substitution rate of each genotype demonstrated that the JPN1 lineage having a larger distribution range diverged earlier and thus was older than the JPN2 lineage. Comparisons of the genotypes within lineages revealed that changes in dN/dS occurred after the divergence and were larger in the younger lineage, JPN2. These results imply that the JPN1 lineage has been more effectively subjected to purification selections, while slightly deteriorating mutations are less purged in JPN2 with smaller population size. Altogether, the lineage-specific difference in the dN/dS ratio for the obligate asexual D. pulex was well explained by the NNT.
Transcriptomic heterochrony and completely cleistogamous flower development in the mycoheterotrophic orchidGastrodia

Kenji Suetsugu, Kenji Fukushima, Takashi Makino, Shuka Ikematsu, Tomoaki Sakamoto, Seisuke Kimura

New Phytologist　237　(1)　323-338　2022/10/17
Publisher: Wiley
DOI： 10.1111/nph.18495 　

ISSN： 0028-646X

eISSN： 1469-8137
Massive expression of cysteine-containing proteins causes abnormal elongation of yeast cells by perturbing the proteasome International-journal

Shotaro Namba, Hisaaki Kato, Shuji Shigenobu, Takashi Makino, Hisao Moriya

G3 Genes|Genomes|Genetics　12　(6)　2022/04/29
Publisher: Oxford University Press (OUP)
DOI： 10.1093/g3journal/jkac106 　

eISSN： 2160-1836

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Abstract The enhanced green fluorescent protein (EGFP) is considered to be a harmless protein because the critical expression level that causes growth defects is higher than that of other proteins. Here, we found that overexpression of EGFP, but not a glycolytic protein Gpm1, triggered the cell elongation phenotype in the budding yeast Saccharomyces cerevisiae. By the morphological analysis of the cell overexpressing fluorescent protein and glycolytic enzyme variants, we revealed that cysteine content was associated with the cell elongation phenotype. The abnormal cell morphology triggered by overexpression of EGFP was also observed in the fission yeast Schizosaccharomyces pombe. Overexpression of cysteine-containing protein was toxic, especially at high-temperature, while the toxicity could be modulated by additional protein characteristics. Investigation of protein aggregate formation, morphological abnormalities in mutants, and transcriptomic changes that occur upon overexpression of EGFP variants suggested that perturbation of the proteasome by the exposed cysteine of the overexpressed protein causes cell elongation. Overexpression of proteins with relatively low folding properties, such as EGFP, was also found to promote the formation of SHOTA (Seventy kDa Heat shock protein-containing, Overexpression-Triggered Aggregates), an intracellular aggregate that incorporates Hsp70/Ssa1, which induces a heat shock response, while it was unrelated to cell elongation. Evolutionary analysis of duplicated genes showed that cysteine toxicity may be an evolutionary bias to exclude cysteine from highly expressed proteins. The overexpression of cysteine-less moxGFP, the least toxic protein revealed in this study, would be a good model system to understand the physiological state of protein burden triggered by ultimate overexpression of harmless proteins.
Open reading frame dominance indicates protein-coding potential of RNAs. International-journal

Yusuke Suenaga, Mamoru Kato, Momoko Nagai, Kazuma Nakatani, Hiroyuki Kogashi, Miho Kobatake, Takashi Makino

EMBO reports　e54321　2022/04/19

DOI： 10.15252/embr.202154321 　

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Recent studies have identified numerous RNAs with both coding and noncoding functions. However, the sequence characteristics that determine this bifunctionality remain largely unknown. In the present study, we develop and test the open reading frame (ORF) dominance score, which we define as the fraction of the longest ORF in the sum of all putative ORF lengths. This score correlates with translation efficiency in coding transcripts and with translation of noncoding RNAs. In bacteria and archaea, coding and noncoding transcripts have narrow distributions of high and low ORF dominance, respectively, whereas those of eukaryotes show relatively broader ORF dominance distributions, with considerable overlap between coding and noncoding transcripts. The extent of overlap positively and negatively correlates with the mutation rate of genomes and the effective population size of species, respectively. Tissue-specific transcripts show higher ORF dominance than ubiquitously expressed transcripts, and the majority of tissue-specific transcripts are expressed in mature testes. These data suggest that the decrease in population size and the emergence of testes in eukaryotic organisms allowed for the evolution of potentially bifunctional RNAs.
Capturing hidden regulation based on noise change of gene expression level from single cell RNA-seq in yeast International-journal

Thoma Itoh, Takashi Makino

Scientific Reports　11　(1)　22547-22547　2021/12
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41598-021-01558-y 　

eISSN： 2045-2322

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Abstract Recent progress in high throughput single cell RNA-seq (scRNA-seq) has activated the development of data-driven inferring methods of gene regulatory networks. Most network estimations assume that perturbations produce downstream effects. However, the effects of gene perturbations are sometimes compensated by a gene with redundant functionality (functional compensation). In order to avoid functional compensation, previous studies constructed double gene deletions, but its vast nature of gene combinations was not suitable for comprehensive network estimation. We hypothesized that functional compensation may emerge as a noise change without mean change (noise-only change) due to varying physical properties and strong compensation effects. Here, we show compensated interactions, which are not detected by mean change, are captured by noise-only change quantified from scRNA-seq. We investigated whether noise-only change genes caused by a single deletion of STP1 and STP2, which have strong functional compensation, are enriched in redundantly regulated genes. As a result, noise-only change genes are enriched in their redundantly regulated genes. Furthermore, novel downstream genes detected from noise change are enriched in “transport”, which is related to known downstream genes. Herein, we suggest the noise difference comparison has the potential to be applied as a new strategy for network estimation that capture even compensated interaction.
Protein-coding potential of RNAs measured by potentially translated island scores

Yusuke Suenaga, Mamoru Kato, Momoko Nagai, Kazuma Nakatani, Hiroyuki Kogashi, Miho Kobatake, Takashi Makino

2021/04/15

DOI： 10.1101/2021.04.14.439730 　
Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species International-journal

Kanako Bessho-Uehara, Yoshiyuki Yamagata, Tomonori Takashi, Takashi Makino, Hideshi Yasui, Atsushi Yoshimura, Motoyuki Ashikari

Plants　10　(4)　725-725　2021/04/08
Publisher: MDPI AG
DOI： 10.3390/plants10040725 　

eISSN： 2223-7747

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Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species Oryza sativa ssp. japonica. Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, REGULATOR OF AWN ELONGATION 1 (RAE1) and RAE2. To understand the conserveness of RAE1 and RAE2 in wild rice relatives, we analyzed RAE1 and RAE2 sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional RAE1 and RAE2, whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of RAE1 and RAE2 were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of RAE1 and RAE2 were selected after the speciation of O. sativa, and that two-step loss of function in RAE1 and RAE2 contributed to awnlessness in Asian cultivated rice.
Significant loss of genetic diversity and accumulation of deleterious genetic variation in a critically endangered azalea species, Rhododendron boninense, growing on the Bonin Islands Peer-reviewed

Yuji Isagi, Takashi Makino, Tomoko Hamabata, Ping-Lin Cao, Satoshi Narita, Yoshiteru Komaki, Kazuki Ktuita, Akiyo Naiki, Yoshiaki Kameyama, Toshiaki Kondo, Mayu Shibabayashi

PLANT SPECIES BIOLOGY　35　(3)　166-174　2020/07

DOI： 10.1111/1442-1984.12270 　

ISSN： 0913-557X

eISSN： 1442-1984
Genetic factors for short life span associated with evolution of the loss of flight ability Peer-reviewed

Atsushi Ikemoto, Daiki X. Sato, Takashi Makino, Masakado Kawata

Ecology and Evolution　10　(12)　6020-6029　2020/05/29
Publisher: Wiley
DOI： 10.1002/ece3.6342 　

ISSN： 2045-7758

eISSN： 2045-7758
Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations Peer-reviewed

Kohta Yoshida, Mark Ravinet, Takashi Makino, Atsushi Toyoda, Tomoyuki Kokita, Seiichi Mori, Jun Kitano

Genome Biology and Evolution　2020/04/01
Publisher: Oxford University Press ({OUP})
DOI： 10.1093/gbe/evaa065 　
Sensitivity to gene dosage and gene expression affects genes with copy number variants observed among neuropsychiatric diseases. International-journal Peer-reviewed

Maria Yamasaki, Takashi Makino, Seik-Soon Khor, Hiromi Toyoda, Taku Miyagawa, Xiaoxi Liu, Hitoshi Kuwabara, Yukiko Kano, Takafumi Shimada, Toshiro Sugiyama, Hisami Nishida, Nagisa Sugaya, Mamoru Tochigi, Takeshi Otowa, Yuji Okazaki, Hisanobu Kaiya, Yoshiya Kawamura, Akinori Miyashita, Ryozo Kuwano, Kiyoto Kasai, Hisashi Tanii, Tsukasa Sasaki, Makoto Honda, Katsushi Tokunaga

BMC medical genomics　13　(1)　55-55　2020/03/29

DOI： 10.1186/s12920-020-0699-9 　

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BACKGROUND: Copy number variants (CNVs) have been reported to be associated with diseases, traits, and evolution. However, it is hard to determine which gene should have priority as a target for further functional experiments if a CNV is rare or a singleton. In this study, we attempted to overcome this issue by using two approaches: by assessing the influences of gene dosage sensitivity and gene expression sensitivity. Dosage sensitive genes derived from two-round whole-genome duplication in previous studies. In addition, we proposed a cross-sectional omics approach that utilizes open data from GTEx to assess the effect of whole-genome CNVs on gene expression. METHODS: Affymetrix Genome-Wide SNP Array 6.0 was used to detect CNVs by PennCNV and CNV Workshop. After quality controls for population stratification, family relationship and CNV detection, 287 patients with narcolepsy, 133 patients with essential hypersomnia, 380 patients with panic disorders, 164 patients with autism, 784 patients with Alzheimer disease and 1280 healthy individuals remained for the enrichment analysis. RESULTS: Overall, significant enrichment of dosage sensitive genes was found across patients with narcolepsy, panic disorders and autism. Particularly, significant enrichment of dosage-sensitive genes in duplications was observed across all diseases except for Alzheimer disease. For deletions, less or no enrichment of dosage-sensitive genes with deletions was seen in the patients when compared to the healthy individuals. Interestingly, significant enrichments of genes with expression sensitivity in brain were observed in patients with panic disorder and autism. While duplications presented a higher burden, deletions did not cause significant differences when compared to the healthy individuals. When we assess the effect of sensitivity to genome dosage and gene expression at the same time, the highest ratio of enrichment was observed in the group including dosage-sensitive genes and genes with expression sensitivity only in brain. In addition, shared CNV regions among the five neuropsychiatric diseases were also investigated. CONCLUSIONS: This study contributed the evidence that dosage-sensitive genes are associated with CNVs among neuropsychiatric diseases. In addition, we utilized open data from GTEx to assess the effect of whole-genome CNVs on gene expression. We also investigated shared CNV region among neuropsychiatric diseases.
Invasive invertebrates associated with highly duplicated gene content Peer-reviewed

Takashi Makino, Masakado Kawata

Molecular Ecology　28　1652-1663　2019/04

DOI： 10.1111/mec.15019 　
JmjC Domain-Encoding Genes Are Conserved in Highly Regenerative Metazoans and Are Associated with Planarian Whole-Body Regeneration. Peer-reviewed

Cao PL, Kumagai N, Takeshi Inoue, Kiyokazu Agata, Takashi Makino

Genome biology and evolution　11　(2)　552-564　2019/02/01

DOI： 10.1093/gbe/evz021 　

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The capacity for regeneration varies greatly among metazoans, yet little is known about the evolutionary processes leading to such different regeneration abilities. In particular, highly regenerative species such as planarians and cnidarians can regenerate the whole body from an amputated fragment; however, a common molecular basis, if any, among these species remains unclear. Here, we show that genes encoding Jumonji C (JmjC) domain-containing proteins are associated with high regeneration ability. We classified 132 fully sequenced metazoans into two groups with high or low regeneration abilities and identified 118 genes conserved in the high regenerative group that were lost in species in the low regeneration group during evolution. Ninety-six percent of them were JmjC domain-encoding genes. We denoted the candidate genes as high regenerative species-specific JmjC domain-encoding genes (HRJDs). We observed losses of HRJDs in Helobdella robusta, which lost its high regeneration ability during evolution based on phylogenetic analysis. By RNA sequencing analyses, we observed that HRJD orthologs were differentially expressed during regeneration in two Cnidarians, as well as Platyhelminthes and Urochordata, which are highly regenerative species. Furthermore, >50% of the head and tail parts of amputated planarians (Dugesia japonica) died during regeneration after RNA interference of HRJD orthologs. These results indicate that HRJD are strongly associated with a high regeneration ability in metazoans. HRJD paralogs regulate gene expression by histone demethylation; thus, HRJD may be related to epigenetic regulation controlling stem cell renewal and stem cell differentiation during regeneration. We propose that HRJD play a central role in epigenetic regulation during regeneration.
Endangered island endemic plants have vulnerable genomes. International-journal Peer-reviewed

Tomoko Hamabata, Gohta Kinoshita, Kazuki Kurita, Ping-Lin Cao, Motomi Ito, Jin Murata, Yoshiteru Komaki, Yuji Isagi, Takashi Makino

Communications biology　2　(244)　244-244　2019

DOI： 10.1038/s42003-019-0490-7 　

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Loss of genetic diversity is known to decrease the fitness of species and is a critical factor that increases extinction risk. However, there is little evidence for higher vulnerability and extinction risk in endangered species based on genomic differences between endangered and non-endangered species. This is true even in the case of functional loci, which are more likely to relate to the fitness of species than neutral loci. Here, we compared the genome-wide genetic diversity, proportion of duplicated genes (PD), and accumulation of deleterious variations of endangered island endemic (EIE) plants from four genera with those of their non-endangered (NE) widespread congeners. We focused on exhaustive sequences of expressed genes obtained by RNA sequencing. Most EIE species exhibited significantly lower genetic diversity and PD than NE species. Additionally, all endangered species accumulated deleterious variations. Our findings provide new insights into the genomic traits of EIE species.
Factors affecting interspecific differences in genetic divergence among populations of Anolis lizards in Cuba Peer-reviewed

Antonio Cádiz, Nobuaki Nagata, Luis M. Díaz, Yukari Suzuki-Ohno, Lázaro M. Echenique-Díaz, Hiroshi D. Akashi, Takashi Makino, Masakado Kawata

Zoological Letters　4　(1)　21　2018/08/09
Publisher: Springer Nature America, Inc
DOI： 10.1186/s40851-018-0107-x 　

ISSN： 2056-306X
Evolution of Gustatory Receptor Gene Family Provides Insights into Adaptation to Diverse Host Plants in Nymphalid Butterflies Peer-reviewed

Hiromu C Suzuki, Katsuhisa Ozaki, Takashi Makino, Hironobu Uchiyama, Shunsuke Yajima, Masakado Kawata

Genome Biology and Evolution　10　(6)　1351-1362　2018/06/01
Publisher: Oxford University Press ({OUP})
DOI： 10.1093/gbe/evy093 　
Comparisons of behavioural and TRPA1 heat sensitivities in three sympatric Cuban Anolis lizards Peer-reviewed

Hiroshi D. Akashi, Shigeru Saito, Antonio Cádiz Díaz, Takashi Makino, Makoto Tominaga, Masakado Kawata

Molecular Ecology　27　(9)　2234-2242　2018/05/01
Publisher: Blackwell Publishing Ltd
DOI： 10.1111/mec.14572 　

ISSN： 1365-294X 0962-1083
Elevated proportions of deleterious genetic variation in domestic animals and plants Peer-reviewed

Takashi Makino, Carl-Johan Rubin, Miguel Carneiro, Erik Axelsson, Leif Andersson, Matthew T. Webster

Genome Biology and Evolution　10　(1)　276-290　2018/01/01
Publisher: Oxford University Press
DOI： 10.1093/gbe/evy004 　

ISSN： 1759-6653
Inferring evolutionary responses of Anolis carolinensis introduced into the Ogasawara archipelago using whole genome sequence data Peer-reviewed

Satoshi Tamate, Watal M. Iwasaki, Kenneth L. Krysko, Brian J. Camposano, Hideaki Mori, Ryo Funayama, Keiko Nakayama, Takashi Makino, Masakado Kawata

SCIENTIFIC REPORTS　7　(1)　18008　2017/12

DOI： 10.1038/s41598-017-17852-7 　

ISSN： 2045-2322
Inference of Causative Genes for Alzheimer's Disease Due to Dosage Imbalance Peer-reviewed

Mizuka Sekine, Takashi Makino

MOLECULAR BIOLOGY AND EVOLUTION　34　(9)　2396-2407　2017/09

DOI： 10.1093/molbev/msx183 　

ISSN： 0737-4038

eISSN： 1537-1719
HSF1 and HSF3 cooperatively regulate the heat shock response in lizards Peer-reviewed

Ryosuke Takii, Mitsuaki Fujimoto, Yuki Matsuura, Fangxu Wu, Namiko Oshibe, Eiichi Takaki, Arpit Katiyar, Hiroshi Akashi, Takashi Makino, Masakado Kawata, Akira Nakai

PLOS ONE　12　(7)　e0180776　2017/07

DOI： 10.1371/journal.pone.0180776 　

ISSN： 1932-6203
Factors restricting the range expansion of the invasive green anole Anolis carolinensis on Okinawa Island, Japan Peer-reviewed

Yukari Suzuki-Ohno, Kenjiro Morita, Nobuaki Nagata, Hideaki Mori, Shintaro Abe, Takashi Makino, Masakado Kawata

ECOLOGY AND EVOLUTION　7　(12)　4357-4366　2017/06

DOI： 10.1002/ece3.3002 　

ISSN： 2045-7758
Physiological conditions and genetic controls of phaeomelanin pigmentation in nestling barn swallows Peer-reviewed

Emi Arai, Masaru Hasegawa, Takashi Makino, Akihiko Hagino, Yusuke Sakai, Hajime Ohtsuki, Kazumasa Wakamatsu, Masakado Kawata

BEHAVIORAL ECOLOGY　28　(3)　706-716　2017/05

DOI： 10.1093/beheco/arx012 　

ISSN： 1045-2249

eISSN： 1465-7279
The Effects of CpG Densities around Transcription Start Sites on Sex-Biased Gene Expression in Poecilia reticulata Peer-reviewed

Katsunori Tamagawa, Takashi Makino, Masakado Kawata

GENOME BIOLOGY AND EVOLUTION　9　(5)　1204-1211　2017/05

DOI： 10.1093/gbe/evx083 　

ISSN： 1759-6653
Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes Peer-reviewed

Asano Ishikawa, Makoto Kusakabe, Kohta Yoshida, Mark Ravinet, Takashi Makino, Atsushi Toyoda, Asao Fujiyama, Jun Kitano

EVOLUTION　71　(3)　565-581　2017/03

DOI： 10.1111/evo.13175 　

ISSN： 0014-3820

eISSN： 1558-5646
Accumulation of Deleterious Mutations on the Neo-Y Chromosome of Japan Sea Stickleback (Gasterosteus nipponicus) Peer-reviewed

Kohta Yoshida, Takashi Makino, Jun Kitano

JOURNAL OF HEREDITY　108　(1)　63-68　2017/01

DOI： 10.1093/jhered/esw054 　

ISSN： 0022-1503

eISSN： 1465-7333
Genetic basis for variation in salinity tolerance between stickleback ecotypes Peer-reviewed

Makoto Kusakabe, Asano Ishikawa, Mark Ravinet, Kohta Yoshida, Takashi Makino, Atsushi Toyoda, Asao Fujiyama, Jun Kitano

MOLECULAR ECOLOGY　26　(1)　304-319　2017/01

DOI： 10.1111/mec.13875 　

ISSN： 0962-1083

eISSN： 1365-294X
Organ identity specification factor WGE localizes to the histone locus body and regulates histone expression to ensure genomic stability in Drosophila Peer-reviewed

Nao Ozawa, Hirofumi Furuhashi, Keita Masuko, Eriko Numao, Takashi Makino, Tamaki Yano, Shoichiro Kurata

GENES TO CELLS　21　(5)　442-456　2016/05

DOI： 10.1111/gtc.12354 　

ISSN： 1356-9597

eISSN： 1365-2443
Differentially expressed genes associated with adaptation to different thermal environments in three sympatric Cuban Anolis lizards Peer-reviewed

Hiroshi D. Akashi, Antonio Cadiz Diaz, Shuji Shigenobu, Takashi Makino, Masakado Kawata

MOLECULAR ECOLOGY　25　(10)　2273-2285　2016/05

DOI： 10.1111/mec.13625 　

ISSN： 0962-1083

eISSN： 1365-294X
Whole-genome sequencing reveals small genomic regions of introgression in an introduced crater lake population of threespine stickleback Peer-reviewed

Kohta Yoshida, Ryutaro Miyagi, Seiichi Mori, Aya Takahashi, Takashi Makino, Atsushi Toyoda, Asao Fujiyama, Jun Kitano

ECOLOGY AND EVOLUTION　6　(7)　2190-2204　2016/04

DOI： 10.1002/ece3.2047 　

ISSN： 2045-7758
Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions Peer-reviewed

Mitsuhiko P. Sato, Takashi Makino, Masakado Kawata

BMC EVOLUTIONARY BIOLOGY　16　35　2016/02

DOI： 10.1186/s12862-016-0606-3 　

ISSN： 1471-2148
Contribution of Nonohnologous Duplicated Genes to High Habitat Variability in Mammals Peer-reviewed

Satoshi C. Tamate, Masakado Kawata, Takashi Makino

MOLECULAR BIOLOGY AND EVOLUTION　31　(7)　1779-1786　2014/07

DOI： 10.1093/molbev/msu128 　

ISSN： 0737-4038

eISSN： 1537-1719
Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species Peer-reviewed

Kohta Yoshida, Takashi Makino, Katsushi Yamaguchi, Shuji Shigenobu, Mitsuyasu Hasebe, Masakado Kawata, Manabu Kume, Seiichi Mori, Catherine L. Peichel, Atsushi Toyoda, Asao Fujiyama, Jun Kitano

PLOS GENETICS　10　(3)　e1004223　2014/03

DOI： 10.1371/journal.pgen.1004223 　

ISSN： 1553-7390

eISSN： 1553-7404
Ohnologs are overrepresented in pathogenic copy number mutations Peer-reviewed

Aoife McLysaght, Takashi Makino, Hannah M. Grayton, Maria Tropeano, Kevin J. Mitchell, Evangelos Vassos, David A. Collier

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　111　(1)　361-366　2014/01

DOI： 10.1073/pnas.1309324111 　

ISSN： 0027-8424
The neo-sex-chromosome formation drove the evolution of protein-coding sequences and transcriptome in three-spine sticklebacks Peer-reviewed

Kohta Yoshida, Takashi Makino, Katsushi Yamaguchi, Shuji Shigenobu, Mitsuyasu Hasebe, Masakado Kawata, Atsushi Toyoda, Asao Fujiyama, Jun Kitano

GENES & GENETIC SYSTEMS　88　(6)　356-356　2013/12

ISSN： 1341-7568

eISSN： 1880-5779
Genome-wide deserts for copy number variation in vertebrates Peer-reviewed

Takashi Makino, Aoife McLysaght, Masakado Kawata

NATURE COMMUNICATIONS　4　2283　2013/08

DOI： 10.1038/ncomms3283 　

ISSN： 2041-1723
Relative importance of habitat use, range expansion, and speciation in local species diversity of Anolis lizards in Cuba Peer-reviewed

Antonio Cadiz, Nobuaki Nagata, Masatoshi Katabuchi, Luis M. Diaz, Lazaro M. Echenique-Diaz, Hiroshi D. Akashi, Takashi Makino, Masakado Kawata

ECOSPHERE　4　(7)　UNSP 78　2013/07

DOI： 10.1890/ES12-00383.1 　

ISSN： 2150-8925
Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method Peer-reviewed

Koji Makanae, Reiko Kintaka, Takashi Makino, Hiroaki Kitano, Hisao Moriya

GENOME RESEARCH　23　(2)　300-311　2013/02

DOI： 10.1101/gr.146662.112 　

ISSN： 1088-9051
Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant Peer-reviewed

Takashi Makino, Aoife McLysaght

GENOME RESEARCH　22　(12)　2427-2435　2012/12

DOI： 10.1101/gr.131953.111 　

ISSN： 1088-9051

eISSN： 1549-5469
Habitat variability correlates with duplicate content of drosophila genomes Peer-reviewed

Takashi Makino, Masakado Kawata

Molecular Biology and Evolution　29　(10)　3169-3179　2012/10

DOI： 10.1093/molbev/mss133 　

ISSN： 0737-4038 1537-1719
Evolution of Vertebrate Tissues Driven by Differential Modes of Gene Duplication Peer-reviewed

Satake Masanobu, Kawata Masakado, McLysaght Aoife, Makino Takashi

DNA RESEARCH　19　(4)　305-316　2012/08

DOI： 10.1093/dnares/dss012 　

ISSN： 1340-2838
Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome Peer-reviewed

Eugenie Pessia, Takashi Makino, Marc Bailly-Bechet, Aoife McLysaght, Gabriel A. B. Marais

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　109　(14)　5346-5351　2012/04

DOI： 10.1073/pnas.1116763109 　

ISSN： 0027-8424
Comprehensive Primer Design for Analysis of Population Genetics in Non-Sequenced Organisms Peer-reviewed

Ayumi Tezuka, Noe Matsushima, Yoriko Nemoto, Hiroshi D. Akashi, Masakado Kawata, Takashi Makino

PLOS ONE　7　(2)　e32314　2012/02

DOI： 10.1371/journal.pone.0032314 　

ISSN： 1932-6203
Divergence in Sex Steroid Hormone Signaling between Sympatric Species of Japanese Threespine Stickleback Peer-reviewed

Jun Kitano, Yui Kawagishi, Seiichi Mori, Catherine L. Peichel, Takashi Makino, Masakado Kawata, Makoto Kusakabe

PLOS ONE　6　(12)　e29253　2011/12

DOI： 10.1371/journal.pone.0029253 　

ISSN： 1932-6203
Duplicability of self-interacting human genes Peer-reviewed

Asa Perez-Bercoff, Takashi Makino, Aoife McLysaght

BMC EVOLUTIONARY BIOLOGY　10　(160)　2010/05

DOI： 10.1186/1471-2148-10-160 　

ISSN： 1471-2148
Ohnologs in the human genome are dosage balanced and frequently associated with disease Peer-reviewed

Takashi Makino, Aoife McLysaght

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　107　(20)　9270-9274　2010/05

DOI： 10.1073/pnas.0914697107 　

ISSN： 0027-8424
Functional divergence of duplicated genes Peer-reviewed

Makino T, Knowles DG, McLysaght A

Evolution After Gene Duplication (Katharina Dittmar and David Liberles eds)　23-30　2010

DOI： 10.1002/9780470619902.ch2 　
The complex relationship of gene duplication and essentiality Peer-reviewed

Takashi Makino, Karsten Hokamp, Aoife McLysaght

TRENDS IN GENETICS　25　(4)　152-155　2009/04

DOI： 10.1016/j.tig.2009.03.001 　

ISSN： 0168-9525
Evolutionary Analyses of Protein Interaction Networks Peer-reviewed

Makino T, McLysaght A

Biological Data Mining in Protein Interaction Network (Xiao-Li Li, See-Kiong Ng eds)　169-181　2009

DOI： 10.4018/978-1-60566-398-2.ch010 　
The Evolution of Functional Gene Clusters in Eukaryote Genomes Peer-reviewed

Takashi Makino, Aoife McLysaght

EVOLUTIONARY BIOLOGY: CONCEPT, MODELING, AND APPLICATION　185-+　2009

DOI： 10.1007/978-3-642-00952-5_11 　
Interacting Gene Clusters and the Evolution of the Vertebrate Immune System (vol 25. pg 1855, 2007) Peer-reviewed

Takashi Makino, Aoife McLysaght

MOLECULAR BIOLOGY AND EVOLUTION　25　(12)　2771-2771　2008/12

DOI： 10.1093/molbev/msn241 　

ISSN： 0737-4038
Evolution of Pacific Ocean and the Sea of Japan populations of the gobiid species, Pterogobius elapoides and Pterogobius zonoleucus, based on molecular and morphological analyses Peer-reviewed

Akihito, Akishinonomiya Fumihito, Yuji Ikeda, Masahiro Aizawa, Takashi Makino, Yumi Umehara, Yoshiaki Kai, Yuriko Nishimoto, Masami Hasegawa, Tetsuji Nakabo, Takashi Gojobori

GENE　427　(1-2)　7-18　2008/12

DOI： 10.1016/j.gene.2008.09.026 　

ISSN： 0378-1119
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts Peer-reviewed

Chisato Yamasaki, Katsuhiko Murakami, Yasuyuki Fujii, Yoshiharu Sato, Erimi Harada, Jun-Ichi Takeda, Takayuki Taniya, Ryuichi Sakate, Shingo Kikugawa, Makoto Shimada, Motohiko Tanino, Kanako O. Koyanagi, Roberto A. Barrero, Craig Gough, Hong-Woo Chun, Takuya Habara, Hideki Hanaoka, Yosuke Hayakawa, Phillip B. Hilton, Yayoi Kaneko, Masako Kanno, Yoshihiro Kawahara, Toshiyuki Kawamura, Akihiro Matsuya, Naoki Nagata, Kensaku Nishikata, Akiko Ogura Noda, Shin Nurimoto, Naomi Saichi, Hiroaki Sakai, Ryoko Sanbonmatsu, Rie Shiba, Mami Suzuki, Kazuhiko Takabayashi, Aiko Takahashi, Takuro Tamura, Masayuki Tanaka, Susumu Tanaka, Fusano Todokoro, Kaori Yamaguchi, Naoyuki Yamamoto, Toshihisa Okido, Jun Mashima, Aki Hashizume, Lihua Jin, Kyung-Bum Lee, Yi-Chueh Lin, Asami Nozaki, Katsunaga Sakai, Masahito Tada, Satoru Miyazaki, Takashi Makino, Hajime Ohyanagi, Naoki Osato, Nobuhiko Tanaka, Yoshiyuki Suzuki, Kazuho Ikeo, Naruya Saitou, Hideaki Sugawara, Claire O'Donovan, Tamara Kulikova, Eleanor Whitfield, Brian Halligan, Mary Shimoyama, Simon Twigger, Kei Yura, Kouichi Kimura, Tomohiro Yasuda, Tetsuo Nishikawa, Yutaka Akiyama, Chie Motono, Yuri Mukai, Hideki Nagasaki, Makiko Suwa, Paul Horton, Reiko Kikuno, Osamu Ohara, Doron Lancet, Eric Eveno, Esther Graudens, Sandrine Imbeaud, Marie Anne Debily, Yoshihide Hayashizaki, Clara Amid, Michael Han, Andreas Osanger, Toshinori Endo, Michael A. Thomas, Mika Hirakawa, Wojciech Makalowski, Mitsuteru Nakao, Nam-Soon Kim, Hyang-Sook Yoo, Sandro J. De Souza, Maria de Fatima Bonaldo, Yoshihito Niimura, Vladimir Kuryshev, Ingo Schupp, Stefan Wiemann, Matthew Bellgard, Masafumi Shionyu, Libin Jia, Danielle Thierry-Mieg, Jean Thierry-Mieg, Lukas Wagner, Qinghua Zhang, Mitiko Go, Shinsei Minoshima, Masafumi Ohtsubo, Kousuke Hanada, Peter Tonellato, Takao Isogai, Ji Zhang, Boris Lenhard, Sangsoo Kim, Zhu Chen, Ursula Hinz, Anne Estreicher, Kenta Nakai, Izabela Makalowska, Winston Hide, Nicola Tiffin, Laurens Wilming, Ranajit Chakraborty, Marcelo Bento Soares, Maria Luisa Chiusano, Yutaka Suzuki, Charles Auffray, Yumi Yamaguchi-Kabata, Takeshi Itoh, Teruyoshi Hishiki, Satoshi Fukuchi, Ken Nishikawa, Sumio Sugano, Nobuo Nomura, Yoshio Tateno, Tadashi Imanishi, Takashi Gojobori

NUCLEIC ACIDS RESEARCH　36　(SI)　D793-D799　2008/01

DOI： 10.1093/nar/gkm999 　

ISSN： 0305-1048

eISSN： 1362-4962
Evolution of protein-protein interaction network Peer-reviewed

T. Makino, T. Gojobori

Genome Dynamics　3　13-29　2007

DOI： 10.1159/000107601 　

ISSN： 1660-9263
Differential evolutionary rates of duplicated genes in protein interaction network Peer-reviewed

Takashi Makino, Yoshiyuki Suzuki, Takashi Gojobori

GENE　385　57-63　2006/12

DOI： 10.1016/j.gene.2006.06.028 　

ISSN： 0378-1119
The evolutionary rate of a protein is influenced by features of the interacting partners Peer-reviewed

T Makino, T Gojobori

MOLECULAR BIOLOGY AND EVOLUTION　23　(4)　784-789　2006/04

DOI： 10.1093/molbev/msj090 　

ISSN： 0737-4038
Integrative annotation of 21,037 human genes validated by full-length cDNA clones Peer-reviewed

T Imanishi, T Itoh, Y Suzuki, C O'Donovan, S Fukuchi, KO Koyanagi, RA Barrero, T Tamura, Y Yamaguchi-Kabata, M Tanino, K Yura, S Miyazaki, K Ikeo, K Homma, A Kasprzyk, T Nishikawa, M Hirakawa, J Thierry-Mieg, D Thierry-Mieg, J Ashurst, LB Jia, M Nakao, MA Thomas, N Mulder, Y Karavidopoulou, LH Jin, S Kim, T Yasuda, B Lenhard, E Eveno, Y Suzuki, C Yamasaki, J Takeda, C Gough, P Hilton, Y Fujii, H Sakai, S Tanaka, C Amid, M Bellgard, MD Bonaldo, H Bono, SK Bromberg, AJ Brookes, E Bruford, P Carninci, C Chelala, C Couillault, SJ de Souza, MA Debily, MD Devignes, Dubchak, I, T Endo, A Estreicher, E Eyras, K Fukami-Kobayash, GR Gopinath, E Graudens, Y Hahn, M Han, ZG Han, K Hanada, H Hanaoka, E Harada, K Hashimoto, U Hinz, M Hirai, T Hishiki, Hopkinson, I, S Imbeaud, H Inoko, A Kanapin, Y Kaneko, T Kasukawa, J Kelso, P Kersey, R Kikuno, K Kimura, B Korn, Kuryshev, V, Makalowska, I, T Makino, S Mano, R Mariage-Samson, J Mashima, H Matsuda, HW Mewes, S Minoshima, K Nagai, H Nagasaki, N Nagata, R Nigam, O Ogasawara, O Ohara, M Ohtsubo, N Okada, T Okido, S Oota, M Ota, T Ota, T Otsuki, D Piatier-Tonneau, A Poustka, SX Ren, N Saitou, K Sakai, S Sakamoto, R Sakate, Schupp, I, F Servant, S Sherry, R Shiba, N Shimizu, M Shimoyama, AJ Simpson, B Soares, C Steward, M Suwa, M Suzuki, A Takahashi, G Tamiya, H Tanaka, T Taylor, JD Terwilliger, P Unneberg, Veeramachaneni, V, S Watanabe, L Wilming, N Yasuda, HS Yoo, M Stodolsky, W Makalowski, M Go, K Nakai, T Takagi, M Kanehisa, Y Sakaki, J Quackenbush, Y Okazaki, Y Hayashizaki, W Hide, R Chakraborty, K Nishikawa, H Sugawara, Y Tateno, Z Chen, M Oishi, P Tonellato, R Apweiler, K Okubo, L Wagner, S Wiemann, RL Strausberg, T Isogai, C Auffray, N Nomura, T Gojobori, S Sugano

PLOS BIOLOGY　2　(6)　856-875　2004/06

DOI： 10.1371/journal.pbio.0020162 　

ISSN： 1545-7885
Purification, characterization, and molecular cloning of acidophilic xylanase from Penicillium sp 40 Peer-reviewed

T Kimura, J Ito, A Kawano, T Makino, H Kondo, S Karita, K Sakka, K Ohmiya

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　64　(6)　1230-1237　2000/06

DOI： 10.1271/bbb.64.1230 　

ISSN： 0916-8451

eISSN： 1347-6947
Analysis of the Promoter Activity of the Taka-Amylase Gene and the Phosphoglycerate Kinase Gene in a Shoyu-koji Mold Aspergillus oryzae KBN616 Peer-reviewed

Tetsuya Kimura, Takashi Makino, Takeshi Aburatani, Shuichi Karita, Kazuo Sakka, Kunio Ohmiya

Food Science and Technology Research　6　(1)　44-47　2000
Publisher: S. Karger AG
DOI： 10.3136/fstr.6.44 　

ISSN： 1344-6606

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Misc. 12

Identification and analysis of tetrapod-specific conserved genome sequences related to limb development

工藤栄大, 上坂将弘, 牧野能士, 田村宏治

日本分子生物学会年会プログラム・要旨集(Web)　46th　2023
Comparative genomics and developmental biological approaches on morphological evolution in vertebrates

関谷洸, 宮腰拓, 米井小百合, 阿部玄武, 田中良和, 牧野能士, 田村宏治

日本分子生物学会年会プログラム・要旨集(Web)　42nd　2019
ゲノム比較と発生学的手法を用いたアプローチから脊椎動物の形態進化を考察する

関谷洸, 宮腰拓, 米井小百合, 阿部玄武, 田中良和, 牧野能士, 田村宏治

日本分子生物学会年会プログラム・要旨集(Web)　42nd　2019
イトヨの海水適応に必須な遺伝子を遺伝学的視点から探る

日下部誠, 石川麻乃, Mark Ravinet, 吉田恒太, 牧野能士, 北野潤

月刊海洋　49　(4)　187-195　2017
小笠原諸島に侵入したグリーンアノールの進化的変化の検出と集団ゲノム解析

玉手智史, 森英章, COMPOSANO Brian J., LKRYSKO Kenneth, 舟山亮, 中山啓子, 牧野能士, 河田雅圭

日本生態学会大会講演要旨(Web)　63rd　2016
小笠原諸島に侵入したグリーンアノールの進化的変化の検出と集団ゲノミクス解析

玉手智史, 森英章, KRYSKO Kenneth L., 牧野能士, 河田雅圭

日本進化学会大会プログラム・講演要旨集(Web)　17th　2015
ゲノム内の遺伝子重複の進化がもたらす生物の適応力

河田雅圭, 牧野能士

化学と生物　53　(11)　731-733　2015
Publisher: 日本農芸化学会 ; 1962-
DOI： 10.1271/kagakutoseibutsu.53.731 　

ISSN： 0453-073X
小笠原諸島に侵入したグリーンアノールの進化的変化の検出

玉手智史, 牧野能士, 森英章, KRYSKO Kenneth L., 河田雅圭

日本生態学会大会講演要旨(Web)　61st　2014
Robustness in Biological Systems Generated by Gene Duplications

牧野能士

細胞工学　33　(1)　73-78　2014
Publisher: 学研メディカル秀潤社
ISSN： 0287-3796
生物が持つ遺伝子の数の話

牧野能士

まなびの杜　70　3-4　2014
タンパク質間相互作用がタンパク質分子の進化に与える影響

牧野能士, 五條堀孝

生体の科学　58　(5)　348-351　2007
Publisher: 金原一郎記念医学医療振興財団
DOI： 10.11477/mf.2425100061 　

ISSN： 0370-9531
ゲノミクスの現状と展望

牧野能士, 五條堀孝

ファルマシア　42　(1)　17-20　2006
Publisher: 公益社団法人日本薬学会
ISSN： 0014-8601

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Books and Other Publications 2

遺伝学の百科事典 : 継承と多様性の源 = Encyclopedia of genetics : origin of inheritance and diversity

日本遺伝学会

丸善出版　2022/01

ISBN: 9784621306604
ヒトゲノム事典

井ノ上, 逸朗, 今西, 規, 河村, 正二, 斎藤, 成也, 颯田, 葉子, 田嶋, 敦

一色出版　2021/11

ISBN: 9784910389127

Presentations 6

遺伝子重複による生物進化

牧野能士

トヨタコンポン研究所探査プロジェクト未踏探索の原理と限界　2024/07/11
Evolutionary approaches to the estimation of deleterious CNVs causing diseases Invited

牧野能士

静岡がんセンター研究所リサーチカンファレンス　2022/12/21
絶滅危惧種の保全優先度評価に向けたゲノム科学的アプローチ Invited

牧野能士

水産育種研究会・定例シンポジウム　2022/12/10
希少植物の絶滅危険度はゲノムの情報から読み取ることができる Invited

牧野能士

日本生態学会企画集会　2022/03
RNA-seq解析による希少植物のゲノム診断 Invited

牧野能士

種生物学会　2021/12
低温環境に適応した侵略種アメリカザリガニのパラロガスゲノミクス

牧野能士

日本進化学会沖縄大会シンポジウム

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Research Projects 23

ダイズ遺伝子の精密発現調節技術の開発

吉田均(代表)

Offer Organization: 内閣府

System: 戦略的イノベーション創造プログラム第３期

Institution: 農研機構、東北大学

2023/07 - 2029/03
絶滅に瀕する島嶼陸産貝類の保全に向けた貝食性外来種防除技術の開発

千葉聡(代表)

Offer Organization: 環境省

System: 環境研究総合推進費

Institution: 東北大学

2024/04 - 2027/03
新たな限界発現系gTOW2.0で解き明かす発現制約メカニズムの全体像

守屋央朗, 牧野能士

Offer Organization: 日本学術振興会

System: 科学研究費助成事業基盤研究(B)

Institution: 岡山大学

2024/04 - 2027/03
Single-cell analysis to understand gene regulatory system in crops

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (A)

Institution: National Agriculture and Food Research Organization

2023/04/01 - 2026/03/31
刺胞動物エダアシクラゲにおける枝分かれ形成機構の解析

熊野岳, 牧野能士

Category: 日本学術振興会科学研究費助成事業基盤研究(B)

2023 - 2026
遺伝子近傍保存モジュールによる発現抑制機構の解明と分子育種への利用

吉田均, 黒羽剛, 川原善浩, 牧野能士

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 基盤研究(A)

Institution: 国立研究開発法人農業・食品産業技術総合研究機構

2022/04/01 - 2025/03/31
Characterizing the JmjC Domain-Encoding demethylase HRJD in highly regenerative arthropods for evolutionary insights into regenerative processes

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (B)

Institution: Tohoku University

2021/04/01 - 2025/03/31
連続するアミノ酸（PolyX）が生み出す細胞毒性のメカニズム

守屋央朗, 牧野能士, 紀藤圭治

Offer Organization: 日本学術振興会

System: 科学研究費助成事業挑戦的研究(萌芽)

Category: 挑戦的研究(萌芽)

Institution: 岡山大学

2022/06/30 - 2024/03/31
Evolutionary mechnisms for thermal niche shift in Anolis lizards

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

Institution: Tohoku University

2019/10/07 - 2023/03/31
Traits changing associated with the evolution of body size

KAWATA MASAKADO, SUGIMOTO Asako, MAKINO Takashi, MARUYAMA Shinichro, YOKOYAMA Jun

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Challenging Exploratory Research

Institution: Tohoku University

2016/04/01 - 2018/03/31

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We purpose to determine candidate genes responsible for the evolution of larger body size of C. inopinata. C. inopinata became larger during developmental L4 to adult stages comparing with C. elegans. Then, we detected 2699 genes which expression patterns differed between C. inopinata and C. elegans. We also detected 42 genes which have been subject to positive selection during the evolution of C. inopinata from other related species. Among them, daf-2 could be detected and this gene encodes the insulin-like growth factor 1 receptor and variant of def-1 in C. elegance became larger. Thus, the results suggest that daf-2 is as an important genes affecting the evolution of large body size of C. inopinata
Evolutionary mechanisms for individual variation of female choice in the guppy

KAWATA MASAKADO, MAKINO Takashi, KAWAMURA Shoji, KARINO Kenji

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (B)

Institution: Tohoku University

2015/04/01 - 2018/03/31

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We examined the effects of genotypes and DNA methylation variations on visual sensitivity and female preference to male body colors, focusing on light environments during growth and carotenoid intakes in the guppy, Poecilia reticulata. The results showed that genetic polymorphism and light environment in habitats can contribute to variation in opsin gene expression levels and subsequent visual sensitivity and female preference for male body color. The genotype and environmental interactions were partly caused by difference in DNA methylation rates of CG sequences along controlling regions of opsin genes. The whole genome bisulfie sequence analysis showed that in the brains and eyes in Guppies fed by high concentration of carotenoid foods, genes for light sensitivity and regulating synaptic membranes were detected genes with higher h DNA methylation rates.
Genetic basis for key traits of stickleback freshwater coloniztion

Kitano Jun, MAKINO TAKASHI

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (A)

Institution: National Institute of Genetics

2015/04/01 - 2018/03/31

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Our phylogenomic analysis revealed that all Japanese freshwater populations are derived from Gasterosteus aculetus rather than Gasterosteus nipponics. We found that differences in the ability to produce an poly unsaturated fatty acids and the copy number of an enzyme explains the different ability to colonize freshwater.
Analysis of mechanisms to avoid stoichiometry imbalance

Moriya Hisao

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (B)

Institution: Okayama University

2014/04/01 - 2017/03/31

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About one third of proteins function as protein complexes. Imbalances in the stoichiometry of subunits constituting protein complexes sometimes cause harmful effects on cellular functions. In this study, using budding yeast, we revealed a mechanism to avoid stoichiometry imbalances in protein complexes. We identified several proteins whose expressions were not increased as expected when their gene copy numbers were artificially increased. The buffering of protein expression was performed through active degradation of excess proteins by the ubiquitin-proteasome system.
Evolution of gene duplication and adaptive capacity; experimental evolution of Saccharomyces cerevisiae

Kawata Masakado, MAKINO TAKASHI

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Challenging Exploratory Research

Institution: Tohoku University

2014/04/01 - 2016/03/31

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We conducted evolutionary experiments using Saccharomyces cerevisiae to test a hypothesis that number of duplicated genes increased under unpredictable environmental fluctuations and organisms with larger number of duplicated genes have high adaptive capacity. Th results showed that under randomly fluctuated environmental variable, Saccharomyces cerevisiae evolved to have larger number of newly acquired duplicated genes than those under constant environments during 500 generations of evolutionary experiments. The results also showed that for evolved Saccharomyces cerevisiae, the fitness from 450th to 500th generation increased with the increased number of newly acquired duplicated genes. These results support the hypothesis.
Adaptation to new climate environments:using Cuban Anoles lizard in a semi-desert habitat

Kawata Masakado, MAKINO TAKASHI, TAMURA KOJI, TAKIMOTO GAKU, NAGATA NOBUAKI

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (B)

Institution: Tohoku University

2013/04/01 - 2016/03/31

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In Cuba, the Anolis lizard A. homolechis usually inhabits in forest edges, while we found a population where lizards inhabit in a hot and dry semi-desert habitat. The results of behavioral experiments for temperature tolerance showed that the maximum running speeds decreased from 30℃ to 35℃ conditions in the forest population, but did not decreased in semi-desert population. Using SNPs detected by RAD-seq, STRUCTURE analysis showed that the forest population (Los Cardelos) and semi-desert population showed slightly different genetic structure. Between the two populations, 5 SNPs were detected as loci that subject to divergent selection using LOSITAN. RNA-seq was conducted to detect differentially expressed genes (DGE) between 33℃ and 36℃ conditions for individuals from the forest and semi-desert populations. The results showed that 78 and 36 DGE were detected in the forest and semi-desert populations, respectively.
Development of forest paleogenetic approaches using ancient pollen grains found in an ice core from mountain glacier

Suyama Yoshihisa, NAKAZAWA Fumio, MAKINO Takashi, MATSUKI Yu

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (A)

Institution: Tohoku University

2012/04/01 - 2016/03/31

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We developed basic methods for paleogenetic approaches using conifer pollen grains found in a mountain glacier. First, we developed a protocol for single-pollen DNA analysis using whole-genome amplification (WGA) method. Second, we developed a novel approach that we termed “multiplexed ISSR genotyping by sequencing” (MIG-seq), which is a PCR-based procedure for constructing highly reduced representation libraries involving de novo SNP discovery, and their genotyping using next generation sequencing. Then we applied these methods to pollen samples found in a glacier.
Molecular mechanisms of genomic incompatibility and reproductive isolation in sticklebacks

Kitano Jun, MAKINO Takashi

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Institution: National Institute of Genetics

2011/04/01 - 2016/03/31

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To characterize the net-sex chromosomes, we conducted whole genome sequencing of the Japan Sea and Pacific Ocean sticklebacks. We also identified a candidate gene encoding a TRIM gene within the QTL causing hybrid male sterility. To investigate the patterns of sex chromosome-autosome fusions, we made a database and analyzed the patterns. To explain the observed patterns, we proposed that female meiotic drive, genetic drift and sexually antagonistic selection may drive the fusions.
Evolutionary factors affecting species range shift: using butterfly species

KAWATA Masakado, YOKOYAMA Jun, MAKINO Takashi, NAGATA Noboski

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (B)

Institution: Tohoku University

2012/04/01 - 2015/03/31

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Ranges of many species tend to move northward owing to recent global warming, but those of some species have not changed or reduced. In this study, we examined genetic population structures of 4 species in which the range boundaries recently moved to northward (north-moving species) and 3 species in which they have not changed (stationary species) over recent decades using genome-wide SNP markers. The results show that clear genetic divergence among local populations could be found in stationary species, but not in north-moving species. This indicated that the stationary species could not move to northward owing to local adaptation to factors other than temperature.
The analysis of copy number variations in the field populations for disease ecology

KAWATA Masakado, MAKINO Takashi

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Challenging Exploratory Research

Institution: Tohoku University

2012/04/01 - 2014/03/31

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Our previous study indicated that anti peptide, Temporin-1 in Rana ornativentirs shows copy-number variations. In order to determine DNA sequences in the regions including temporin-1, we created fosmid library and chose the clone libraries including temporin-1. Then we tried to determine these DNA sequences using the next generation sequencer (Ion PGM). The results showed that among about 40kbp DNA region, those in 33kbp were non-coding regions. The rest of the sequences contained at least three copies of temporin-1, including temporin-1Oj and temproin-1OC. This suggests that these copies of temporin might be tenderly repeated. At the present study, we could not determine complete sequences of these regions.
Analysis of the network constructed by dosage balanced genes in yeast

MORIYA Hisao, MAKINO Takashi

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (B)

Institution: Okayama University

2011/04/01 - 2014/03/31

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Dosage balanced gene (DBG) is a gene whose expression is balanced against more than two genes, and the perturbation of the balance causes cellular dysfunction. Using a genetic method designated "genetic tug-of-war", we have been trying to identify "dosage sensitive genes" whose minor overexpression cause cellular dysfunction. In this study, we proceeded this analysis, and identified 115 dosage sensitive genes in the budding yeast genome. We further identified 13 dosage-balanced interactions. This study is the first example for the systematic identification of dosage sensitive genes in a organism's genome, and for the identification of multiple dosage balanced genes at a time.
アノールトカゲにおける複合適応形質としての温度適応分化の遺伝的基盤の解明

牧野能士

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 新学術領域研究(研究領域提案型)

Institution: 東北大学

2011/04/01 - 2013/03/31

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キューバにおいて、木の幹や地上を主に生活場所とする種では、開けた場所に生息し高体温を維持する種（Anolis sagrei, 体温34度）、森林の縁に生息する種（たとえばAnolis homolechis, 体温30-31度）、森林内に生息し低体温を維持する種（Anolis allogus, 体温27-29度）などが共存している。しかし、様々な地域で、どのような種同士が共存しているのか、また、どのような遺伝的変化を伴って温度適応の分化が生じたのかは不明である。本研究では、キューバに生息するアノールをモデルとして体温適応という生理機能や行動形質などが複雑に関連して決まる複合適応形質の進化遺伝基盤の解明を目指し、アノールトカゲの温度センサー遺伝子および温度変化に反応する遺伝子に着目して研究を行った。キューバ産アノールトカゲ3種(A. sagrei、A. homolechis、A. allogus)の温度センサー遺伝子TRPの塩基配列を決定し種間比較を行った。その結果、TRPA1において、活性化温度に影響を与える機能ドメイン内に種間で非同義置換が観察された。また、低温適応種であるA. allogusの肝臓において特異的に、機能ドメイン中に32アミノ酸のインサーションがあることも明らかとなった。キューバにてサンプリングしたアノールトカゲ3種を5日間の温度維持実験を実施し、3組織(皮膚、肝臓、脳)における遺伝子発現量を、次世代シークエンサーを用いて推定した。異なる温度条件間、及び、体温の異なる種間において、各組織の発現量を比較し、有意に発現量差のある遺伝子の探索を行った。その結果、温度変化に対し脳においてはエネルギー生産やミトコンドリアに関する遺伝子が多数検出された。このことは、エネルギー生産が温度適応に関連していることを示唆している。
Determining adaptive traits and the candidate genes in Cuban Anolis lizards

KAWATA Masakado, MAKINO Takashi, KITANO Jun, TAMURA Koji, TAKIMOTO Gaku

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (B)

Institution: Tohoku University

2010 - 2012

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The present results suggest that the species composition and richness in local assemblages could be explained by evolutionary history (the number of speciation events and limits to range expansion) and ecological processes (habitat partitioning). The results of developmental timings for divergence of hindlimb length showed that there are several important developmental stages for differentiation of hindlimb length between twig and trunk-ground species, depending on different elements of hindlimb.
Deleterious effect to human genes by meiotic recombination

MAKINO Takashi

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Young Scientists (B)

Institution: Tohoku University

2010 - 2011

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The results in this study suggest that those functional regions of the human genome which are subject to high recombination rates may experience an elevated rate of deleterious point mutation and hence are more likely to become implicated in inherited disease, particularly in the case of those diseases that are caused by rare genomic variants.

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