東北大学研究者紹介

研究者詳細

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マキノ　タカシ

牧野　能士

Takashi Makino

所属

大学院生命科学研究科　分子化学生物学専攻　分子ネットワーク講座（進化ゲノミクス分野）

職名

教授

学位

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

委員歴 1

日本進化学会　代議員

2022年1月～継続中

所属学協会 3

日本遺伝学会
日本生態学会
日本進化学会

研究キーワード 4

遺伝子発現制御の進化
重複遺伝子の進化
分子進化学
比較ゲノム学

研究分野 1

ライフサイエンス / 進化生物学 / 分子進化学

論文 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年7月

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年5月

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年4月3日

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年2月5日
出版者・発行元： 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年11月9日

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年10月7日
出版者・発行元： 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年9月21日
出版者・発行元： 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年9月13日
出版者・発行元： 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. 国際誌

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

BMC biology　22　(1)　157-157　2024年8月2日

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. 国際誌

Yuki Matsuda, Takashi Makino

Proceedings. Biological sciences　291　(2029)　20241068-20241068　2024年8月

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年5月23日
出版者・発行元： 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. 国際誌

Shankar C R R Chereddy, Takashi Makino

Genome biology and evolution　16　(5)　2024年5月2日

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年3月7日
出版者・発行元： 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年3月4日
出版者・発行元： 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. 国際誌

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年1月10日

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年12月6日
出版者・発行元： 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年7月
出版者・発行元： 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年5月17日
出版者・発行元： 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年4月18日
出版者・発行元： 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年12月
出版者・発行元： 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年10月17日
出版者・発行元： 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 国際誌

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

G3 Genes|Genomes|Genetics　12　(6)　2022年4月29日
出版者・発行元： 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. 国際誌

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

EMBO reports　e54321　2022年4月19日

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 国際誌

Thoma Itoh, Takashi Makino

Scientific Reports　11　(1)　22547-22547　2021年12月
出版者・発行元： 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年4月15日

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

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

Plants　10　(4)　725-725　2021年4月8日
出版者・発行元： 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 査読有り

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年7月

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 査読有り

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

Ecology and Evolution　10　(12)　6020-6029　2020年5月29日
出版者・発行元： Wiley
DOI： 10.1002/ece3.6342 　

ISSN：2045-7758

eISSN：2045-7758
Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations 査読有り

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

Genome Biology and Evolution　2020年4月1日
出版者・発行元： 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. 国際誌査読有り

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年3月29日

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 査読有り

Takashi Makino, Masakado Kawata

Molecular Ecology　28　1652-1663　2019年4月

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

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

Genome biology and evolution　11　(2)　552-564　2019年2月1日

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. 国際誌査読有り

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年

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 査読有り

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年8月9日
出版者・発行元： 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 査読有り

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

Genome Biology and Evolution　10　(6)　1351-1362　2018年6月1日
出版者・発行元： Oxford University Press ({OUP})
DOI： 10.1093/gbe/evy093 　
Comparisons of behavioural and TRPA1 heat sensitivities in three sympatric Cuban Anolis lizards 査読有り

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

Molecular Ecology　27　(9)　2234-2242　2018年5月1日
出版者・発行元： Blackwell Publishing Ltd
DOI： 10.1111/mec.14572 　

ISSN：1365-294X 0962-1083
Elevated proportions of deleterious genetic variation in domestic animals and plants 査読有り

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

Genome Biology and Evolution　10　(1)　276-290　2018年1月1日
出版者・発行元： 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 査読有り

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年12月

DOI： 10.1038/s41598-017-17852-7 　

ISSN：2045-2322
Inference of causative genes for Alzheimer’s disease due to dosage imbalance 査読有り

Sekine M, Makino T

Molecular Biology and Evolution　34　(9)　2396-2407　2017年9月

DOI： 10.1093/molbev/msx183 　

ISSN：0737-4038

eISSN：1537-1719
HSF1 and HSF3 cooperatively regulate the heat shock response in lizards 査読有り

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年7月

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 査読有り

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

ECOLOGY AND EVOLUTION　7　(12)　4357-4366　2017年6月

DOI： 10.1002/ece3.3002 　

ISSN：2045-7758
Physiological conditions and genetic controls of phaeomelanin pigmentation in nestling barn swallows 査読有り

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

BEHAVIORAL ECOLOGY　28　(3)　706-716　2017年5月

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 査読有り

Katsunori Tamagawa, Takashi Makino, Masakado Kawata

GENOME BIOLOGY AND EVOLUTION　9　(5)　1204-1211　2017年5月

DOI： 10.1093/gbe/evx083 　

ISSN：1759-6653
Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes 査読有り

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

EVOLUTION　71　(3)　565-581　2017年3月

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) 査読有り

Kohta Yoshida, Takashi Makino, Jun Kitano

JOURNAL OF HEREDITY　108　(1)　63-68　2017年1月

DOI： 10.1093/jhered/esw054 　

ISSN：0022-1503

eISSN：1465-7333
Genetic basis for variation in salinity tolerance between stickleback ecotypes 査読有り

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

MOLECULAR ECOLOGY　26　(1)　304-319　2017年1月

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 査読有り

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

GENES TO CELLS　21　(5)　442-456　2016年5月

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 査読有り

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

MOLECULAR ECOLOGY　25　(10)　2273-2285　2016年5月

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 査読有り

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

ECOLOGY AND EVOLUTION　6　(7)　2190-2204　2016年4月

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 査読有り

Mitsuhiko P. Sato, Takashi Makino, Masakado Kawata

BMC EVOLUTIONARY BIOLOGY　16　35　2016年2月

DOI： 10.1186/s12862-016-0606-3 　

ISSN：1471-2148
Contribution of Nonohnologous Duplicated Genes to High Habitat Variability in Mammals 査読有り

Satoshi C. Tamate, Masakado Kawata, Takashi Makino

MOLECULAR BIOLOGY AND EVOLUTION　31　(7)　1779-1786　2014年7月

DOI： 10.1093/molbev/msu128 　

ISSN：0737-4038

eISSN：1537-1719
Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species 査読有り

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年3月

DOI： 10.1371/journal.pgen.1004223 　

ISSN：1553-7390

eISSN：1553-7404
Ohnologs are overrepresented in pathogenic copy number mutations 査読有り

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年1月

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 査読有り

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年12月

ISSN：1341-7568

eISSN：1880-5779
Genome-wide deserts for copy number variation in vertebrates 査読有り

Takashi Makino, Aoife McLysaght, Masakado Kawata

NATURE COMMUNICATIONS　4　2283　2013年8月

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 査読有り

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年7月

DOI： 10.1890/ES12-00383.1 　

ISSN：2150-8925
Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method 査読有り

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

GENOME RESEARCH　23　(2)　300-311　2013年2月

DOI： 10.1101/gr.146662.112 　

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

Takashi Makino, Aoife McLysaght

GENOME RESEARCH　22　(12)　2427-2435　2012年12月

DOI： 10.1101/gr.131953.111 　

ISSN：1088-9051

eISSN：1549-5469
Habitat variability correlates with duplicate content of drosophila genomes 査読有り

Takashi Makino, Masakado Kawata

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

DOI： 10.1093/molbev/mss133 　

ISSN：0737-4038 1537-1719
Evolution of Vertebrate Tissues Driven by Differential Modes of Gene Duplication 査読有り

Satake Masanobu, Kawata Masakado, McLysaght Aoife, Makino Takashi

DNA RESEARCH　19　(4)　305-316　2012年8月

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 査読有り

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年4月

DOI： 10.1073/pnas.1116763109 　

ISSN：0027-8424
Comprehensive Primer Design for Analysis of Population Genetics in Non-Sequenced Organisms 査読有り

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

PLOS ONE　7　(2)　e32314　2012年2月

DOI： 10.1371/journal.pone.0032314 　

ISSN：1932-6203
Divergence in Sex Steroid Hormone Signaling between Sympatric Species of Japanese Threespine Stickleback 査読有り

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

PLOS ONE　6　(12)　e29253　2011年12月

DOI： 10.1371/journal.pone.0029253 　

ISSN：1932-6203
Duplicability of self-interacting human genes 査読有り

Asa Perez-Bercoff, Takashi Makino, Aoife McLysaght

BMC EVOLUTIONARY BIOLOGY　10　(160)　2010年5月

DOI： 10.1186/1471-2148-10-160 　

ISSN：1471-2148
Ohnologs in the human genome are dosage balanced and frequently associated with disease 査読有り

Takashi Makino, Aoife McLysaght

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　107　(20)　9270-9274　2010年5月

DOI： 10.1073/pnas.0914697107 　

ISSN：0027-8424
Functional divergence of duplicated genes 査読有り

Makino T, Knowles DG, McLysaght A

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

DOI： 10.1002/9780470619902.ch2 　
The complex relationship of gene duplication and essentiality 査読有り

Takashi Makino, Karsten Hokamp, Aoife McLysaght

TRENDS IN GENETICS　25　(4)　152-155　2009年4月

DOI： 10.1016/j.tig.2009.03.001 　

ISSN：0168-9525
Evolutionary Analyses of Protein Interaction Networks 査読有り

Makino T, McLysaght A

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

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

Takashi Makino, Aoife McLysaght

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

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) 査読有り

Takashi Makino, Aoife McLysaght

MOLECULAR BIOLOGY AND EVOLUTION　25　(12)　2771-2771　2008年12月

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 査読有り

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年12月

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 査読有り

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年1月

DOI： 10.1093/nar/gkm999 　

ISSN：0305-1048

eISSN：1362-4962
Evolution of protein-protein interaction network 査読有り

T. Makino, T. Gojobori

Genome Dynamics　3　13-29　2007年

DOI： 10.1159/000107601 　

ISSN：1660-9263
Differential evolutionary rates of duplicated genes in protein interaction network 査読有り

Takashi Makino, Yoshiyuki Suzuki, Takashi Gojobori

GENE　385　57-63　2006年12月

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 査読有り

T Makino, T Gojobori

MOLECULAR BIOLOGY AND EVOLUTION　23　(4)　784-789　2006年4月

DOI： 10.1093/molbev/msj090 　

ISSN：0737-4038
Integrative annotation of 21,037 human genes validated by full-length cDNA clones 査読有り

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年6月

DOI： 10.1371/journal.pbio.0020162 　

ISSN：1545-7885
Purification, characterization, and molecular cloning of acidophilic xylanase from Penicillium sp 40 査読有り

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年6月

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 査読有り

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

Food Science and Technology Research　6　(1)　44-47　2000年
出版者・発行元： S. Karger AG
DOI： 10.3136/fstr.6.44 　

ISSN：1344-6606

︎全件表示 ︎最初の5件までを表示

MISC 12

四肢発生に関わる四足動物特異的な保存ゲノム配列の探索と解析

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年
脊椎動物における形態進化に関する比較ゲノミクスおよび発生生物学的解析

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年
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年
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年
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年
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年
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年
出版者・発行元：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年
重複遺伝子が生み出す生命システムのロバストネス

牧野能士

細胞工学　33　(1)　73-78　2014年
出版者・発行元：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年
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年
出版者・発行元：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年
出版者・発行元：公益社団法人日本薬学会
ISSN： 0014-8601

︎全件表示 ︎最初の5件までを表示

書籍等出版物 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年1月

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年11月

ISBN: 9784910389127

講演・口頭発表等 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年7月11日
Evolutionary approaches to the estimation of deleterious CNVs causing diseases 招待有り

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年12月21日
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招待有り

牧野能士

水産育種研究会・定例シンポジウム　2022年12月10日
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招待有り

牧野能士

日本生態学会企画集会　2022年3月
RNA-seq解析による希少植物のゲノム診断招待有り

牧野能士

種生物学会　2021年12月
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

︎全件表示 ︎最初の5件までを表示

共同研究・競争的資金等の研究課題 23

ダイズ遺伝子の精密発現調節技術の開発

吉田均(代表)

2023年7月～ 2029年3月
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)

2024年4月～ 2027年3月
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

2024年4月～ 2027年3月
シングルセル解析による作物の転写制御システムの解明

内藤健, 牧野能士, 川勝泰二, 黒羽剛

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Scientific Research (A)

研究機関：National Agriculture and Food Research Organization

2023年4月1日～ 2026年3月31日
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

2023年～ 2026年
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

2022年4月1日～ 2025年3月31日
胴体切断可能な節足動物の再生過程におけるHRJDの機能解明

牧野能士, 熊野岳

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Scientific Research (B)

研究機関：Tohoku University

2021年4月1日～ 2025年3月31日

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節足動物の胴体を切断すると死亡する。ところが、例外的に一部の鋏角類の動物(ウミグモやサソリ)は胴体を切断後も生存が可能であり、ウミグモにおいては胴体切断部位からの再生が可能である。節足動物であるウミグモやサソリが胴体を切断後も生存できるのはなぜだろうか。我々は、比較ゲノム解析によりプラナリアなどの再生能力が高い生物だけが持つ遺伝子HRJDを発見し、プラナリアのHRJDの発現を抑制すると再生せずに死亡することを見出した。節足動物にはHRJDが保存されていないと考えられていたが、近年、ウミグモやサソリなどの一部の鋏角類にHRJDが存在していることを突き止めた。本年度は、ウミグモとサソリの飼育条件の検討と胴体切断後の再生過程の観察および再生過程における遺伝子発現解析の準備を行った。 2021年10月に青森市の浅虫海洋生物学教育研究センターにおいて共同研究者とともにシマウミグモのサンプリングを実施し、100匹程度の個体の採集に成功した。研究室においてシマウミグモの飼育条件の検討を行った結果、人工海水、水温18度、刺胞動物を餌として与えることで研究室での飼育が可能となった。続いて飼育中の複数のシマウミグモの胴体を中央部で切断して経過観察を行った。口の無い胴体下部は切断後しばらくして死亡したが、胴体上部は長期間に渡り生存した。また、胴体上部の切断部分から脚の再生を確認した。研究室で飼育していた複数のヤエヤマサソリの腸管の通った後腹部を切断し、経過観察を行った。切断により死亡した個体が多かったものの、脱皮後に後腹部を再生する個体を確認した。
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

2022年6月30日～ 2024年3月31日
アノールトカゲを用いた温度ニッチシフトの進化機構の解明

河田雅圭, 赤司寛志, 牧野能士

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

研究機関：Tohoku University

2019年10月7日～ 2023年3月31日

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本年度は、キューバ自然史博物館のLuis Cadiz博士らと共同で、6種のキューバアノールトカゲにおいて決定した全ゲノム配列を用いて、温度適応に関わるゲノムの特徴の解析を行った。ゲノム内容をアメリカ本土のアノールトカゲのものと比較し、アノールトカゲの多様化の過程で出現・蓄積された遺伝的変異を推定した。遺伝子重複解析の結果、重複する遺伝子の割合が高温開環境と相関している可能性が示唆された。さらに、過去の有効人口を推定した結果、それぞれの種の人口規模がキューバの地史に影響された可能性が示唆された。また、これまでの研究で、TRPA1が温度感知に関与しており、Anolis allogus TRPA1の活性化温度はA. homolechisやA. sagreiよりも低いことを明らかにした。そこで、Georgia大学のMenke博士と共同で、TRPA1のCRISPR/Cas9による遺伝子編集実験の計画を検討した。またTRPA1と行動的熱感受性の関係の一般性を調べるため、TRPA1と行動的熱反応に関するメタ解析を行ったところ、多様な外温動物種で一貫した関係が見られた。このような温度感受性の違いは、トカゲの生息地の分化に重要な役割を果たすと考えられるが、生息地の分化に関わる分子基盤は不明であった。そこで、Tulane大学のGunderson博士との共同で、これまで行ったキューバのアノールトカゲに加えて、プエルトリコのアノールトカゲ（A. cristatellusとA. krugi）でRNA-seqを行い、温度感受性遺伝子を解析した。後者2種は、A. allogusと同様に比較的涼しい場所に生息している。その結果、860個の遺伝子の発現レベルが種間で有意に異なることが示され、6個の遺伝子が特に発現変動遺伝子として重要であると検出された。
体サイズの進化に伴って変化する性質と独立な性質：遺伝子改変線虫を用いて

河田雅圭, 杉本亜砂子, 牧野能士, 丸山真一朗, 横山潤

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Challenging Exploratory Research

研究機関：Tohoku University

2016年4月1日～ 2018年3月31日

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近年発見されたC. elegans の姉妹種であるC. inopinataを用いて、体長の進化に寄与した遺伝子を特定することを目的とした。二種間で大きな体長の差が生じるL4幼虫期と成虫期で、発現パターンが、種間で異なる遺伝子として2699遺伝子が検出された。6種の線虫のうち、C. inopinataの系統でのみ正の選択圧が42の遺伝子で検出され、その中に、daf-2があった。daf-2は細胞膜で発現するインスリン受容体で、C. elegansの変異体は体サイズが大きくなることが知られ、daf-2遺伝子の進化が体サイズの進化に対して大きな影響をもつ可能性が示唆された。
グッピーにおける雌配偶者選好性の個体間変異と可塑性の進化機構の解明

河田雅圭, 牧野能士, 河村正二, 狩野賢司

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Scientific Research (B)

研究機関：Tohoku University

2015年4月1日～ 2018年3月31日

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グッピーを用いて、成育時の光環境とカロテノイドの影響に焦点を当て、遺伝子型の変異とDNAメチル化によるエピジェネティックな変異が雄の体色に対する雌の配偶者選好性の個体間変異に与える影響を調べた。オプシン遺伝子の発現量は、光感受性と雄体色に対する雌の選好性に影響し、その発現量は、成育時の光環境とオプシン遺伝子LWS-1の遺伝子型との交互作用によって影響されることがわかった。またオプシン遺伝子の発現量の遺伝子と環境との交互作用は、DNAメチル化率によるものと示唆された。βカロテン高摂取により、目では、光順応に関する遺伝子が、脳では、神経伝達に関係する遺伝子においてDNAメチル化が増加した。
トゲウオ淡水進出の鍵形質の遺伝基盤

北野潤, 牧野能士

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Scientific Research (A)

研究機関：National Institute of Genetics

2015年4月1日～ 2018年3月31日

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本研究室に存在するイトヨの全集団のddRAD解析を実施し、これまでに本研究室で採集した全ての淡水イトヨは、ニホンイトヨ系統でなく、イトヨ系統から由来していることを確認した。ついで、ある不飽和脂肪酸代謝酵素のコピー数がイトヨにて高いこと、当該遺伝子発現量もイトヨにて高いこと、ある不飽和脂肪酸合成能力もイトヨで高いことを見出した。そこで、淡水餌からの不飽和脂肪酸合成能力の違いが、淡水進出能力を規定していると考えられた。
化学量不均衡を避けるメカニズムの解明

守屋央朗, 牧野能士

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Scientific Research (B)

研究機関：Okayama University

2014年4月1日～ 2017年3月31日

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細胞内のタンパク質は複数のサブユニットからなる複合体を形成していることが多い。複合体の量比が乱れた状態は、細胞にとって様々な悪影響となることが知られている。本研究では、出芽酵母を研究材料として、複合体の量比の乱れを回避する一般的なメカニズムを明らかにした。具体的には、遺伝子のコピー数の上昇を人工的に起こした際に、タンパク質発現量の上昇に結びつかないタンパク質を複数同定し、それらの「量の緩衝」が、ユビキチン－プロテアソーム系による余剰なタンパク質の積極的な分解により行われている事を明らかにした。
遺伝子重複と生物の適応力の進化；酵母の進化実験系の確立による検証

河田雅圭, 牧野能士

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Challenging Exploratory Research

研究機関：Tohoku University

2014年4月1日～ 2016年3月31日

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予測できない変動環境が遺伝子の重複を増加させ、保持し、そのような変動環境下で進化したゲノムは、適応力や進化可能性が高いという仮説を検証するために、出芽酵母(Saccharomyces cerevisiae)を用いて、変動環境下で進化させ、全ゲノム配列をモニタリングする進化実験を行った。進化実験終了後の解析の結果、RAD27変異株では３種の不規則変動環境条件と高負荷の6環境をランダム変動させる条件において、最適一定環境条件と比較して新規重複領域数が有意に増加した。また、450世代から500世代までの平均適応度は、RAD27変異株において、新規重複領域数が多いほど適応度が高い傾向を示した。
新たな気候帯への適応進化機構の解明：半砂漠地帯のキューバアノールトカゲを用いて

河田雅圭, 牧野能士, 田村宏治, 瀧本岳, 長太伸章

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Scientific Research (B)

研究機関：Tohoku University

2013年4月1日～ 2016年3月31日

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走行力測定による温度耐性実験の結果、森林集団のA. homolechisは30度に比べ35度で最高走行速度が低下したのに対し、半砂漠集団のA. homolechisは、走行速度が低下しなかった。RAD-seqにより検出されたSNPでの遺伝的構造解析では、2つの集団間に違いが観察された。LOSITANによる自然選択を受けている領域の検出では5つのSNPを検出した。33度および36度の温度環境で5日間飼育したのち脳を抽出し、RNA-seq解析を行い発現変動遺伝子の検出を行った。33度および36度で発現量が有意に異なった遺伝子は、森林集団のA. homolechisで78、半砂漠集団で43であった。
山岳氷河の掘削試料から得られた樹木花粉のＤＮＡ分析による古森林遺伝学的研究

陶山佳久, 中澤文男, 牧野能士, 松木悠

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Scientific Research (A)

研究機関：Tohoku University

2012年4月1日～ 2016年3月31日

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山岳氷河から得られた雪氷試料中に存在する花粉のDNA分析によって、過去に分布した樹木の遺伝的情報を直接取得し、樹木個体群の分布変遷史を時空間的に明らかにしようとする研究のための基礎技術開発を行った。まず、花粉一粒ずつに含まれるゲノムDNAを全ゲノム増幅法によって増幅して、ゲノム内の複数領域のDNA分析に用いるための技術を完成させた。また、次世代シーケンサーを用いてゲノム全体から網羅的に塩基配列を得る新たな手法を開発し、MIG-seq法として発表した。これらの技術を氷河から得られた花粉の分析に応用した。
異種トゲウオ間のゲノム不適合と生殖隔離の分子機構

北野潤, 牧野能士

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

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

研究機関：National Institute of Genetics

2011年4月1日～ 2016年3月31日

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転座領域におけるゲノム上の特徴を明らかにするために、日本海イトヨと太平洋イトヨのゲノムを解読し、ネオ性染色体上のゲノム配列の特徴を明らかにした。また、近縁のイトヨ種間の雑種不妊の候補遺伝子として修飾ヒストンに結合するTRIM類の遺伝子を発見した。この遺伝子は、種間で異なるタイプの修飾ヒストンに結合する。この候補遺伝子の遺伝子操作イトヨの作出に成功した。性染色体融合がどの程度普遍的な現象であるのかを明らかにするために、データベースを作出し解析するとともに、その原因として、メス減数分裂ドライブ、有害融合のdriftと性的葛藤選択の可能性を提唱した。
分布停滞および拡大に関わる進化的要因：チョウ類を用いての検証

河田雅圭, 横山潤, 牧野能士, 長太伸章

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Scientific Research (B)

研究機関：Tohoku University

2012年4月1日～ 2015年3月31日

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地球温暖化による気温の上昇とともに多くの種が分布北限を北上させていることが報告されているが、北上せず停滞していたり、逆に縮小している種も多く存在する。本研究では東北地方に分布北限があるチョウのうち、この数十年分布を大きく北上させている4種と、分布が停滞している3種を用い、遺伝的集団構造をゲノムワイドなSNPを用いて解明した。その結果、停滞している3種は地域集団間での分化を伴う遺伝的集団構造がみられたが、拡大している4種ではみられなかった。分布域の拡大が停滞している種は温度以外の要因に局所適応しているために、北上させることが困難であると示唆された。
遺伝子コピー数変異の野外集団解析による新たな疾病生態学の開拓

河田雅圭, 牧野能士

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Challenging Exploratory Research

研究機関：Tohoku University

2012年4月1日～ 2014年3月31日

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ヤマアカガエルの抗菌ペプチドのコピー数変異のゲノムでの重複の状態を調べるため、フォスミドライブラリーを作成し、抗菌ペプチドを含むクローンの配列を十世代シークエンサーでの決定を試みた。次世代シークエンサーで解読したリードを複数のアセンブラでアセンブルした結果、約40kbpの配列のうち33kbはtemporinを含まない非コード領域で、残りの配列の中に、temporin-1Ojと1Ocを含む少なくとも3コピーの配列があることが明らかになった。今回得られたコンティグの情報では、temporin-1O遺伝子の詳細のゲノム上の位置を断定することはできなかった。
酵母の量的均衡遺伝子が作るネットワークの全容解明

守屋央朗, 牧野能士

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Scientific Research (B)

研究機関：Okayama University

2011年4月1日～ 2014年3月31日

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量的均衡遺伝子とは、2つ以上の遺伝子の発現量が互いに均衡しており、そのバランスが乱れた時に、細胞機能に異常をもたらす遺伝子のことを言う。私たちは、これまでに「遺伝子つなひき法」という実験手法を用いて、わずかに遺伝子コピー数を上げただけで細胞機能が破たんする遺伝子（量感受性遺伝子）の同定を試みてきた。本研究ではこれを進め、出芽酵母の115個の量感受性遺伝子を同定するとともに、これらのうち、13の量的均衡関係を見出した。この研究は、ゲノム上の量感受性遺伝子の組織的同定としては、あらゆる生物で初めてのことであり、複数の量的均衡遺伝子を一度に同定した初めての例である。
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

2011年4月1日～ 2013年3月31日

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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。
キューバにおけるアノールトカゲの適応形質部位特定とその候補遺伝子探索

河田雅圭, 牧野能士, 北野潤, 田村宏治, 瀧本岳, 北野潤, 田村宏治

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Scientific Research (B)

研究機関：Tohoku University

2010年～ 2012年

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本研究で、同所的に生息するTrunk-Ground型(幹から地面に生息する)の種数は、異なる温度環境場所に生息できる種数とその地域で何種が種分化によって起源しているかによって決まっていることを明らかにした。また、後肢長の長いTrunk-Ground型のA.sagreiと短いTwig型のA.angusticepsの間では、発生の複数の段階で後肢長に違いが生じることを明らかにし、今後の遺伝的解析の基盤を得た。
相同組替えがヒト遺伝子に与える有害な影響

牧野能士

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Young Scientists (B)

研究機関：Tohoku University

2010年～ 2011年

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相同組替えは遺伝的多様性を生み出す重要な機構であるが、同時にエラーを起こし突然変異を生じさせやすい。本研究により、高い組替え率をもつヒトゲノム上の領域では有害な突然変異が起きやすく、そのためそのような領域が原因となって遺伝子的疾患を起こしやすいことが明らかとなった。特に、このような疾患と原因となる突然変異は極めて希な遺伝的変異であることも分かった。

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