{"id":166,"date":"2018-09-20T10:39:49","date_gmt":"2018-09-20T01:39:49","guid":{"rendered":"http:\/\/www.lifesci.tohoku.ac.jp\/evolgenomics\/?page_id=166"},"modified":"2026-04-02T10:22:55","modified_gmt":"2026-04-02T01:22:55","slug":"publications-en","status":"publish","type":"page","link":"https:\/\/www.lifesci.tohoku.ac.jp\/evolgenomics\/publications-en\/","title":{"rendered":"Publications-EN"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Publications<\/h2>\n\n\n\n<h4 class=\"wp-block-heading\" style=\"font-size:18px\">2026<\/h4>\n\n\n\n<ul>\n<li><strong>Bessho-Uehara M<\/strong>, Yamaguchi K, Koeda K, Matsuzaki S,  Maeda T, Shigenobu S. (2026) Absence of the luciferase gene in the  genome of the kleptoprotein bioluminescent fish <em>Parapriacanthus  ransonneti<\/em>. <em>Scientific Reports<\/em>. 16:9211<\/li>\n\n\n\n<li>Murase Y, Kitamura N, Namba S, Satoh A, <strong>Makino T<\/strong>, Moriya A, Moriya H. (2026) Amino acid homorepeats act as buffers to maintain proteostasis and constrain the compatible sequence space of proteomes. <em>eLife<\/em> 15<\/li>\n\n\n\n<li><strong>Sakamoto F<\/strong>,<strong> Kanamori S<\/strong>, Rakotondraparany F, <strong>Makino T<\/strong>, Kawata M. (2026) Molecular responses to temperature changes across timescales in the Madagascar ground gecko (<em>Paroedura picta<\/em>). <em>Molecular Ecology<\/em>. 35(2):e70245<\/li>\n\n\n\n<li>Segawa T, Yoshizumi S, Toyonaga H, Shiraishi A, Sato K, Yamabe T, Takagi M, <strong>Takagawa M<\/strong>, <strong>Yokoyama R<\/strong>, Itoh T, Ono E. (2026) Chromosome-scale Genome Assemblies of Two Allopolyploid Cuscuta Species Uncover Genomic Signatures of Parasitic Lifestyle and Polyploid Evolution Available for Purchase. <em>Plant Cell Physiol.<\/em> pcag002<em>ss<\/em><\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\" style=\"font-size:18px\">2025<\/h4>\n\n\n\n<ul>\n<li>Hirase S, <strong>Makino T<\/strong>, Takeuchi T, Kadota M, Kuraku S, Kikuchi K. (2025) Ancestral origin and structural characteristics of non-syntenic homologous chromosomes in abalones (<em>Haliotis<\/em>). <em>Molecular Ecology Resources.<\/em> 26(1):e70057<\/li>\n\n\n\n<li>Kise H, <strong>Bessho-Uehara M<\/strong>, Kondo KCF, Shimoji K, Ito S, Tsuchida S, Fujiwara Y, Reimer JD. (2025) Glow in the D-ARK: a new bioluminescent species of Corallizoanthus (Anthozoa: Zoantharia: Parazoanthidae) from southern Japan. <em>R Soc Open Sci<\/em>. 12(11):250890<\/li>\n\n\n\n<li>Yang X, Ruan Z, Chen K, Gu S, Wang Y, Cai Q, Yao LA, Boorboori MR, Yasir A, Chaiwanon J, <strong>Bessho-Uehara K<\/strong>, Shin K, Wu Y, Wang W, Lin W. (2025) Meta-analysis reveals that grain quality is improved in ratoon season crop compared with main crop. <em>Frontiers in Plant Science<\/em>. 16:1604686<\/li>\n\n\n\n<li>Kitano J, Sato M, Kanbe H, Okude G, Ishikawa A, Kazeto Y, <strong>Makino T<\/strong>. (2025) Functional mutations in the thyroid-stimulating hormone receptor in  natural stickleback populations at sites identical to human  disease-causing mutations. <em>BMC Ecology and Evolution.<\/em> 25(1):98<\/li>\n\n\n\n<li>Isagi Y, Shimizu T, Kobayashi Y, Suyama Y, Tokuhiro C, Kokubugata G, Abe A, Ito T, <strong>Makino T<\/strong>, Yamasaki M. (2025) Genomic analysis highlights the conservation significance of Torenia concolor (Linderniaceae) from the periphery of its distribution range. <em>Journal of Plant Research<\/em>. doi:10.1007\/s10265-025-01659-z<\/li>\n\n\n\n<li><strong>Bessho-Uehara K<\/strong>, <strong>Takara R<\/strong>, <strong>Sano K<\/strong>, Tamura K. (2025) Plant organ modulates morphological constraints of insect-induced galls: evidence from citizen science data. <em>Scientific reports<\/em>. 15(1):30433<\/li>\n\n\n\n<li><strong>Udandarao NJ<\/strong>, <strong>Yamashita Y<\/strong>, Ushima R, Tsuchida T, <strong>Bessho-Uehara K<\/strong>. (2025) Parasitic-Plant Parasite Rewires Flowering Pathways to Induce Stem-Derived Galls. <em>Plant Direct<\/em> 9(8):e70099.<\/li>\n\n\n\n<li><strong>Bessho-Uehara K<\/strong>, Omori T, Reuscher S, Nagai K, Agata A,  Kojima M, Takebayashi Y, Suzuki T, Sakakibara H, Ashikari M and Hobo T.  (2025) Spatio-Temporal Regulation of Gibberellin Biosynthesis  Contributes to Optimal Rhizome Bud Development. <em>Rice<\/em>. 24;18(1):39.<\/li>\n\n\n\n<li><strong>Takagawa M <\/strong>and <strong>Yokoyama R<\/strong>. (2025) Current understanding of the role of the cell wall in <em>Cuscuta<\/em> parasitism. <em>Plant Biol<\/em>., doi: 10.1111\/plb.70059<\/li>\n\n\n\n<li><strong>Bessho-Uehara M<\/strong>, Kato T, Ohira A, Nakamori T, Oba Y. (2025) Biochemical basis of endogenous bioluminescent springtail Lobella sauteri (Collembola). <em>Biol Open<\/em>. 14(5):bio061829. <\/li>\n\n\n\n<li>Suetsugu K, Hirota SK, <strong>Makino T<\/strong>, Suyama Y, Kaneko S,  Fukushima K. (2025) Genomic signature and evolutionary history of  completely cleistogamous lineages in the non-photosynthetic orchid  Gastrodia. <em>Proceedings of the Royal Society B<\/em>. 292(2047):20250574.<\/li>\n\n\n\n<li>Kuroha T, Lombardo F, <strong>Iwasaki WM<\/strong>, Chechetka S, Kawahara Y, Yoshida A, <strong>Makino T<\/strong>  and Yoshida H. (2025) Modification of TAWAWA1-mediated panicle  architecture by genome editing of a downstream conserved noncoding  sequence in rice. <em>Plant Biotechnology Journal. <\/em>23(7):2667-2669<\/li>\n\n\n\n<li>Shiraishi H, Suyama Y, <strong>Makino T<\/strong>, Hirota SK, Obata K,   Lee JH, Cho HJ, Tsumura Y. (2025) Evaluation of the conservation value   and conservation difficulty of local populations of the rare plant Viola   raddeana based on genetic diversity and gene expression information using next-generation sequencers. <em>Plant Species Biology<\/em>.<\/li>\n\n\n\n<li><strong>Bessho-Uehara K<\/strong>. and Obayashi T. (2025) Evolutionary approaches for narrowing down the candidate genes from the unannotated gene list. <em>Plant and Cell Physiology<\/em>. pcaf003<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\" style=\"font-size:18px\">2024<\/h4>\n\n\n\n<ul>\n<li>Hata C, Endo C, Tanaka H, Hiruma M, Kumamoto M, Takenaka I, <strong>Makino T<\/strong>, <strong>Niinaka K<\/strong>,  Suyama Y, Hirota S, Yamasaki M, Isagi Y. (2024) Conservation units and  the origin of planted individuals of an endangered endemic species  Lobelia boninensis in the Ogasawara Islands. <em>Scientific reports<\/em>. 14:27410 <\/li>\n\n\n\n<li>Ishida K, Yamamoto S, <strong>Makino T<\/strong>, Tobimatsu Y. (2024) Expression of laccase and ascorbate oxidase affects lignin composition in Arabidopsis thaliana stems. <em>Journal of Plant Research.<\/em><\/li>\n\n\n\n<li><strong>Tamagawa K<\/strong>, Dayi M, Sun S, Hata R, Kikuchi T, Haruta N, Sugimoto A and <strong>Makino T<\/strong>. (2024)             Evolutionary changes of noncoding elements associated with transition of sexual mode in <em>Caenorhabditis <\/em>nematodes<style>@font-face {font-family:\"MS Mincho\"; panose-1:2 2 6 9 4 2 5 8 3 4; mso-font-alt:\"\uff2d\uff33 \u660e\u671d\"; mso-font-charset:128; mso-generic-font-family:modern; mso-font-pitch:fixed; mso-font-signature:-536870145 1791491579 134217746 0 131231 0;}@font-face {font-family:Century; panose-1:2 4 6 4 5 5 5 2 3 4; mso-font-charset:0; mso-generic-font-family:roman; mso-font-pitch:variable; mso-font-signature:647 0 0 0 159 0;}@font-face {font-family:\"Cambria Math\"; panose-1:2 4 5 3 5 4 6 3 2 4; mso-font-charset:0; mso-generic-font-family:roman; mso-font-pitch:variable; mso-font-signature:-536870145 1107305727 0 0 415 0;}@font-face {font-family:\"\\@MS Mincho\"; panose-1:2 2 6 9 4 2 5 8 3 4; mso-font-charset:128; mso-generic-font-family:modern; mso-font-pitch:fixed; mso-font-signature:-536870145 1791491579 134217746 0 131231 0;}p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-unhide:no; mso-style-qformat:yes; mso-style-parent:\"\"; margin:0cm; text-align:justify; text-justify:inter-ideograph; mso-pagination:none; mso-hyphenate:none; font-size:10.5pt; mso-bidi-font-size:12.0pt; font-family:\"Century\",serif; mso-fareast-font-family:\"MS Mincho\"; mso-bidi-font-family:\"Times New Roman\"; mso-font-kerning:.5pt; mso-ansi-language:EN-US; mso-fareast-language:AR-SA;}.MsoChpDefault {mso-style-type:export-only; mso-default-props:yes; font-size:10.0pt; mso-ansi-font-size:10.0pt; mso-bidi-font-size:10.0pt; mso-fareast-font-family:\"MS Mincho\"; mso-font-kerning:0pt; mso-ligatures:none;}div.WordSection1 {page:WordSection1;}<\/style>.<em> Science Advances<\/em>. 10(37):eadn9913 <\/li>\n\n\n\n<li><strong>Matsuda Y<\/strong> and <strong>Makino T<\/strong>. (2024) Comparative genomics reveals convergent signals associated with the high metabolism and longevity in birds and bats. <em>Proceedings of the Royal Society B<\/em>.        291(2029):20241068<\/li>\n\n\n\n<li>Nagai H, Adachi Y, Takigawa E, Ui J, <strong>Makino T<\/strong>, Miura M and Nakajima Y. (2024) Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut. <em>BMC Biology<\/em>. 22(1):157<\/li>\n\n\n\n<li>Mizutani M, Murase R, Aoki S, Sato Y, Yamagata Y, Yasui H, Yoshimura A, Ashikari M, <strong>Bessho-Uehara K<\/strong>. (2024) Identification of <em>An7<\/em> as a positive awn regulator from two wild rice species. <em>Breeding Science<\/em>. 74(3):247-25<\/li>\n\n\n\n<li><strong>Nakayama D<\/strong> and <strong>Makino T<\/strong>. (2024) Convergent accelerated evolution of mammal-specific conserved non-coding elements in hibernators. <em>Scientific reports.<\/em> 14(1):11754 <\/li>\n\n\n\n<li><strong>Chereddy CRRS<\/strong> and <strong>Makino T<\/strong>. (2024) Conserved Genes in Highly Regenerative Metazoans Are Associated with Planarian Regeneration. <em>Genome Biology and Evolution.<\/em> 16(5):evae082 <style>@font-face {font-family:\"MS Mincho\"; panose-1:2 2 6 9 4 2 5 8 3 4; mso-font-alt:\"\uff2d\uff33 \u660e\u671d\"; mso-font-charset:128; mso-generic-font-family:modern; mso-font-pitch:fixed; mso-font-signature:-536870145 1791491579 134217746 0 131231 0;}@font-face {font-family:Century; panose-1:2 4 6 4 5 5 5 2 3 4; mso-font-charset:0; mso-generic-font-family:roman; mso-font-pitch:variable; mso-font-signature:647 0 0 0 159 0;}@font-face {font-family:\"Cambria Math\"; panose-1:2 4 5 3 5 4 6 3 2 4; mso-font-charset:0; mso-generic-font-family:roman; mso-font-pitch:variable; mso-font-signature:-536870145 1107305727 0 0 415 0;}@font-face {font-family:\"\\@MS Mincho\"; panose-1:2 2 6 9 4 2 5 8 3 4; mso-font-charset:128; mso-generic-font-family:modern; mso-font-pitch:fixed; mso-font-signature:-536870145 1791491579 134217746 0 131231 0;}p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-unhide:no; mso-style-qformat:yes; mso-style-parent:\"\"; margin:0cm; text-align:justify; text-justify:inter-ideograph; mso-pagination:none; mso-hyphenate:none; font-size:10.5pt; mso-bidi-font-size:12.0pt; font-family:\"Century\",serif; mso-fareast-font-family:\"MS Mincho\"; mso-bidi-font-family:\"Times New Roman\"; mso-font-kerning:.5pt; mso-ansi-language:EN-US; mso-fareast-language:AR-SA;}.MsoChpDefault {mso-style-type:export-only; mso-default-props:yes; font-size:10.0pt; mso-ansi-font-size:10.0pt; mso-bidi-font-size:10.0pt; mso-fareast-font-family:\"MS Mincho\"; mso-font-kerning:0pt; mso-ligatures:none;}div.WordSection1 {page:WordSection1;}<\/style><\/li>\n\n\n\n<li>Kudoh H, Yonei-Tamura S, Abe G, Iwakiri J, Uesaka M, <strong>Makino T <\/strong>and Tamura, K. (2024). Genomic screening of fish-specific genes in gnathostomes and their functions in fin development. <em>Development, Growth &amp; Differentiation<\/em>. 66(3):235-247<\/li>\n\n\n\n<li><strong>Sakamoto F<\/strong>, Kanamori S, D\u00edaz LM, C\u00e1diz A, Ishii Y, Yamaguchi K, Shigenobu S, Nakayama T, <strong>Makino T<\/strong>, and Kawata M. (2024) Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards. <em>Ecology and Evolution<\/em>. 14(3):e11117<\/li>\n\n\n\n<li>Tsunenari K, Ito T, Yokota M, Shibabayashi M, Chung K, Suyama Y, Matsuo A, Abe A, Naiki A, Setoguchi H, <strong>Makino T<\/strong>, Isagi Y. (2024) Double migration of the endangered <em>Tricyrtis formosana <\/em>(Liliaceae) in Japan. <em>Scientific reports<\/em>. 14(1):957<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2023<\/h4>\n\n\n\n<ul reversed>\n<li><strong>Tamagawa K<\/strong>, Sunobe T, <strong>Makino T<\/strong>, Kawata M. (2023) Transcriptome analysis reveals the mechanism underlying rapid changes in the early phase brain of bi-directional sex change in Trimma okinawae. <em>Royal Society Open Science<\/em>. 10(12):231450 <style>@font-face {font-family:\"MS Mincho\"; panose-1:2 2 6 9 4 2 5 8 3 4; mso-font-alt:\"\uff2d\uff33 \u660e\u671d\"; mso-font-charset:128; mso-generic-font-family:modern; mso-font-pitch:fixed; mso-font-signature:-536870145 1791491579 134217746 0 131231 0;}@font-face {font-family:Century; panose-1:2 4 6 4 5 5 5 2 3 4; mso-font-charset:0; mso-generic-font-family:roman; mso-font-pitch:variable; mso-font-signature:647 0 0 0 159 0;}@font-face {font-family:\"Cambria Math\"; panose-1:2 4 5 3 5 4 6 3 2 4; mso-font-charset:0; mso-generic-font-family:roman; mso-font-pitch:variable; mso-font-signature:-536870145 1107305727 0 0 415 0;}@font-face {font-family:\"\\@MS Mincho\"; panose-1:2 2 6 9 4 2 5 8 3 4; mso-font-charset:128; mso-generic-font-family:modern; mso-font-pitch:fixed; mso-font-signature:-536870145 1791491579 134217746 0 131231 0;}p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-unhide:no; mso-style-qformat:yes; mso-style-parent:\"\"; margin:0cm; text-align:justify; text-justify:inter-ideograph; mso-pagination:none; mso-hyphenate:none; font-size:10.5pt; mso-bidi-font-size:12.0pt; font-family:\"Century\",serif; mso-fareast-font-family:\"MS Mincho\"; mso-bidi-font-family:\"Times New Roman\"; mso-font-kerning:.5pt; mso-ansi-language:EN-US; mso-fareast-language:AR-SA;}.MsoChpDefault {mso-style-type:export-only; mso-default-props:yes; font-size:10.0pt; mso-ansi-font-size:10.0pt; mso-bidi-font-size:10.0pt; mso-fareast-font-family:\"MS Mincho\"; mso-font-kerning:0pt; mso-ligatures:none;}div.WordSection1 {page:WordSection1;}ol {margin-bottom:0cm;}ul {margin-bottom:0cm;}<\/style><\/li>\n\n\n\n<li>Sato DX, <strong>Matsuda Y<\/strong>, Usio N, Funayama R, Nakayama K, <strong>Makino T<\/strong>. (2023) Genomic adaptive potential to cold environments in the invasive red swamp crayfish. <em>iScience<\/em>. 26(8):107267<\/li>\n\n\n\n<li>Maruoka N, <strong>Makino T<\/strong>, Urabe J. (2023) RNA-seq analysis to identify genes related to resting egg production of panarctic Daphnia pulex. <em>BMC genomics<\/em>. 24(1):1-12<\/li>\n\n\n\n<li>Kawahara K, Inada T, Tanaka R, Dayi M, <strong>Makino T<\/strong> Maruyama S, Kikuchi T, Sugimoto A, Kawata M. (2023) Differentially Expressed Genes Associated with Body Size Changes and Transposable Element Insertions between <em>Caenorhabditis elegans<\/em> and Its Sister Species, <em>Caenorhabditis inopinata<\/em>. <em>Genome Biology and Evolution<\/em>. 15(4):evad063<\/li>\n\n\n\n<li><strong>Bessho-Uehara K<\/strong>, Masuda K,&nbsp;Wang DR,&nbsp;Angeles-Shim RB,&nbsp;Obara K,&nbsp;Nagai K,&nbsp;Murase R,&nbsp;Aoki S,&nbsp;Furuta T,&nbsp;Miura K,&nbsp;Wu J,&nbsp;Yamagata Y,&nbsp;Yasui H,&nbsp;Kantar MB,&nbsp;Yoshimura A,&nbsp;Kamura T,&nbsp;McCouch SR,&nbsp;Ashikari M. (2023) <em>Regulator of Awn Elongation 3<\/em>, an E3 ubiquitin ligase, is responsible for loss of awns during African rice domestication. <em>PNAS<\/em>. 120(4):e2207105120<\/li>\n\n\n\n<li>Suetsugu K, Fukushima K, <strong>Makino T<\/strong>, Ikematsu S, Sakamoto T, Kimura S. (2023) Transcriptomic heterochrony and completely cleistogamous flower development in the mycoheterotrophic orchid <em>Gastrodia<\/em>. <em>New Phytologist<\/em>. 237(1):323-338<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2022<\/h4>\n\n\n\n<ul reversed>\n<li>Ishida K and <strong>Yokoyama R<\/strong>. (2022) Reconsidering the function of the xyloglucan endotransglucosylase\/hydrolase family. <em>J Plant Res<\/em>. 135(2):145-156<\/li>\n\n\n\n<li><strong>Tamagawa K<\/strong>, Yoshida K, Ohrui S, Takahashi Y. (2022) Population transcriptomics reveals the effect of gene flow on the evolution of range limits. <em>Scientific Reports<\/em> 12:1318<\/li>\n\n\n\n<li><strong>Bessho-Uehara K<\/strong>. (2022) Dawn of the Awn Regulatory Mechanism in Sorghum. <em>Plant Cell Physiol<\/em>. 63(7):886-888<\/li>\n\n\n\n<li><strong>Yokoyama R<\/strong>, Yokoyama T, Kuroha T, Park J, Aoki K, Nishitani K. (2022) Regulatory modules involved in the degradation and modification of host cell walls during Cuscuta campestris invasion. <em>Frontiers in Plant Science<\/em>. 13:904313<\/li>\n\n\n\n<li>Namba S, Kato H, Shigenobu S, <strong>Makino T<\/strong>, Moriya H. (2022) Massive expression of cysteine-containing proteins causes abnormal elongation of yeast cells by perturbing the proteasome. <em>G3<\/em>. 12(6):jkac106<\/li>\n\n\n\n<li>Ohtsuki H, Norimatsu H, <strong>Makino T<\/strong>, Urabe J. (2022) Invasions of an obligate asexual daphnid species support the nearly neutral theory. <em>Scientific Reports<\/em>. 12(1):1-9<\/li>\n\n\n\n<li>Suenaga Y, Kato M, Nagai M, Nakatani K, Kogashi H, Kobatake M, <strong>Makino T<\/strong>. (2022) Protein-coding potential of RNAs measured by open reading frame dominance. <em>EMBO Reports<\/em>. e54321<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2021<\/h4>\n\n\n\n<ul reversed>\n<li><strong>Itoh T<\/strong> and <strong>Makino T<\/strong>. (2021) Capturing hidden regulation based on noise change of gene expression level from single cell RNA-seq in yeast. <em>Scientific Reports<\/em>. 11:22547<\/li>\n\n\n\n<li><strong>Bessho-Uehara K<\/strong>, Yamagata Y, Takashi T, <strong>Makino T<\/strong>, Yasui H, Yoshimura A, Ashikari M. (2021) Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species. <em>Plants<\/em>. 10(4):725<\/li>\n\n\n\n<li>Narukawa H, <strong>Yokoyama R<\/strong>. et al. (2021) Host-produced ethylene is required for marked cell expansion and endoreduplication in dodder search hyphae. <em>Plant Physiology<\/em>. 185(2):491-502<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2020<\/h4>\n\n\n\n<ul reversed>\n<li><strong>Yokoyama R<\/strong>. (2020) A Genomic Perspective on the Evolutionary Diversity of the Plant Cell Wall. <em>Plants<\/em>. 9(9):1195-1195<\/li>\n\n\n\n<li>Kuki H, <strong>Yokoyama R<\/strong>, Kuroha T, Nishitani K. (2020) Xyloglucan Is Not Essential for the Formation and Integrity of the Cellulose Network in the Primary Cell Wall Regenerated from Arabidopsis Protoplasts. <em>Plant<\/em>. 9(5):629<\/li>\n\n\n\n<li>Yamasaki M, <strong>Makino T<\/strong> <em>et al<\/em>. (2020) Sensitivity to gene dosage and gene expression affects genes with copy number variants observed among neuropsychiatric diseases. BMC Medical Genomics. <em>BMC Medical Genomics<\/em>. 12(1):55<\/li>\n\n\n\n<li>Yoshida K, Ravinet M, <strong>Makino T<\/strong>, Toyoda A, Fujiyama A, Kokita T, Mori S, and Kitano J. (2020) Accumulation of deleterious mutations in landlocked threespine stickleback populations. <em>Genome Biology and Evolution<\/em>. 12(4):479-492<\/li>\n\n\n\n<li>Ishida T, Suzuki R, Nakagami S, Kuroha T, Sakamoto S, Nakata, M-T, <strong>Yokoyama R<\/strong>, Kimura S, Mitsuda N, Nishitani K, Sawa S. (2020) Root-knot nematodes modulate cell walls during root-knot formation in Arabidopsis roots. <em>Journal of Plant Research<\/em>. 133:419-428<\/li>\n\n\n\n<li>Ikemoto A, Sato DX, <strong>Makino T<\/strong>, and Kawata M. (2020) Genetic factors for short life span associated with evolution of the loss of flight ability. <em>Ecology and Evolution<\/em>. 10(12):6020-6029<\/li>\n\n\n\n<li>Isagi Y, <strong>Makino T<\/strong>, Hamabata T, <strong>Cao P<\/strong>, Narita S, Komaki Y, Kurita K, Naiki A, Kaneyama Y, Kondo T, Shibabayashi M. (2020) Significant loss of genetic diversity and accumulation of deleterious genetic variation in a critically endangered azalea species, <em>Rhododendron boninense<\/em>, growing on the Bonin Islands. <em>Plant Species Biology<\/em>. 35:166-174<\/li>\n\n\n\n<li>Kaga Y, <strong>Yokoyama R<\/strong>, Sano R, Ohtani M, Demura T, Kuroha T, Shinohara N and Kazuhiko Nishitani K. (2020) Interspecific Signaling Between the Parasitic Plant and the Host Plants Regulate Xylem Vessel Cell Differentiation in Haustoria of <em>Cuscuta campestris<\/em>. <em>Frontiers in Plant Science<\/em>. 11:193<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2019<\/h4>\n\n\n\n<ul reversed>\n<li><strong>Iwasaki WM<\/strong>, Kijima TE and Innan H. (2019) Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. II. Accumulation of Variation and Evolution of a New Subfamily. <em>Molecular Biology and Evolution<\/em>. 37(2):355-364<\/li>\n\n\n\n<li><strong>Hamabata T<\/strong>, Kinoshita G, Kurita K, <strong>Cao P<\/strong>, Ito M, Murata J, Komaki Y, Isagi Y and <strong>Makino T<\/strong>. (2019) Endangered island endemic plants have vulnerable genomes. <em>Communications Biology<\/em>. 2:244 <a href=\"https:\/\/communities.springernature.com\/posts\/vulnerable-genomes-of-endangered-species\" data-type=\"link\" data-id=\"https:\/\/communities.springernature.com\/posts\/vulnerable-genomes-of-endangered-species\">Behind the paper<\/a><\/li>\n\n\n\n<li><strong>Makino T <\/strong>and Kawata M. (2019) Invasive invertebrates associated with highly duplicated gene content. <em>Molecular Ecology<\/em>. 28(7):1652-1663<\/li>\n\n\n\n<li><strong>Cao P<\/strong>, Kumagai N, Inoue T, Agata K and <strong>Makino<\/strong><strong> T<\/strong>. (2019) JmjC domain-encoding genes are conserved in highly regenerative metazoans and are associated with planarian whole-body regeneration. <em>Genome Biology and Evolution<\/em><em>. <\/em>11(2):552-564 <a href=\"https:\/\/www.smbe.org\/smbe\/FEATUREDNEWS\/TabId\/343\/ArtMID\/1390\/ArticleID\/94\/Congratulations-to-the-winners-of-the-SMBE-2020-Best-Student-Paper-Awards-for-papers-published-in-2019-in-MBE-and-GBE.aspx\">SMBE 2020 Best Student Paper Awards<\/a>, <a href=\"https:\/\/facultyopinions.com\/article\/734951954\">Faculty Opinions(Exceptional)<\/a><\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2018<\/h4>\n\n\n\n<ul reversed>\n<li><strong>Makino T<\/strong>, Rubin CJ, Carneiro M, Axelsson E, Andersson L and Webster MT. (2018) Elevated proportions of deleterious genetic variation in domestic animals and plants. <em>Genome Biology and Evolution<\/em>. 10(1):276-290<\/li>\n\n\n\n<li>C\u00e1diz A, Nagata N, D\u00edaz L, Suzuki-Ohno Y, Echenique-D\u00edaz L, Akashi HD, <strong>Makino T<\/strong> and Kawata M. (2018) Factors affecting interspecific differences in genetic divergence among populations of Anolis lizards in Cuba. <em>Zoological Letters<\/em>, 4:21<\/li>\n\n\n\n<li>Suzuki, HC, Ozaki K, <strong>Makino T<\/strong>, Uchiyama H, Yajima S and Kawata M. (2018) Evolution of gustatory receptor gene family provides insights into adaptation to diverse host plants in nymphalid butterflies. <em>Genome Biology and Evolution<\/em>, 10:1351\u20131362<\/li>\n\n\n\n<li>Akashi DH, Saito S, C\u00e1diz A, <strong>Makino T<\/strong>, Tominaga M, Kawata M. (2018) Comparisons of behavioral and TRPA1 heat sensitivities in three sympatric Cuban Anolis lizards. <em>Molecular Ecology<\/em>, 27:2234\u20132242<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2017<\/h4>\n\n\n\n<ul reversed>\n<li>Tamate SC, Iwasaki WM, Krysko KL, Composano B, Mori H, Funayama R, Nakayama K, <strong>Makino T<\/strong> and Kawata M. (2017) Inferring evolutionary responses of Anolis carolinensis introduced into the Ogasawara archipelago using whole genome sequence data. <em>Scientific Reports<\/em>. 7(1):18008.<\/li>\n\n\n\n<li><strong>Sekine M<\/strong> and <strong>Makino T<\/strong>. (2017) Inference of causative genes for Alzheimer\u2019s disease due to dosage imbalance. <em>Molecular Biology and Evolution<\/em>. 34(9):2396-2407 <a href=\"https:\/\/academic.oup.com\/mbe\/article\/34\/9\/2425\/4093849\" target=\"_blank\" rel=\"noreferrer noopener\">News<\/a><\/li>\n\n\n\n<li>Takii R, Fujimoto M, Matsuura Y, Wu F, Oshibe N, Takaki E, Katiyar A, Akashi H, <strong>Makino T<\/strong>, Kawata M, and Nakai A. (2017) HSF1 and HSF3 cooperatively regulate the heat shock response in lizards. <em>PLOS ONE<\/em>. 12(7):e0180776<\/li>\n\n\n\n<li>Tamagawa K, <strong>Makino T<\/strong>, and Kawata M. (2017) The effects of CpG densities around transcription start sites on sex-biased gene expression in Poecilia reticulata. <em>Genome Biology and Evolution<\/em>. 9(5):1204-1211<\/li>\n\n\n\n<li>Suzuki-Ohno Y, Morita K, Nagata N, Mori H, Abe S, <strong>Makino T<\/strong>, and Kawata M. (2017) Factors restricting the range expansion of the invasive green anole Anolis carolinensis on Okinawa Island, Japan. <em>Ecology and Evolution<\/em>. 7(12):4357-4366<\/li>\n\n\n\n<li>Arai E, Hasegawa M, <strong>Makino T<\/strong>, Hagino A, Sakai Y, Otsuki H, Wakamatsu K, Kawata M. (2017) Physiological conditions and genetic controls of phaeomelanin pigmentation in nestling barn swallows. <em>Behavioral Ecology<\/em>. 28:706-716<\/li>\n\n\n\n<li>Ishikawa A, Kusakabe M, Yoshida K, Ravinet M, <strong>Makino T<\/strong>, Toyoda A, Fujiyama A, and Kitano J. (2017) Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes. <em>Evolution<\/em>. 71(3):565-581<\/li>\n\n\n\n<li>Kusakabe M, Ishikawa A, Ravinet M, Yoshida K, <strong>Makino T<\/strong>, Toyoda A, Fujiyama A and Kitano J. (2017) Genetic basis for variation in salinity tolerance between stickleback ecotypes. <em>Molecular Ecology<\/em>. 26(1):304-319<\/li>\n\n\n\n<li>Yoshida K, <strong>Makino T<\/strong> and Kitano J. (2017) Accumulation of deleterious mutations on the neo-Y chromosome of Japan Sea stickleback (Gasterosteus nipponicus). <em>Journal of Heredity<\/em>. 108(1):63-68<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2016<\/h4>\n\n\n\n<ul reversed>\n<li>Akashi HD, C\u00e1diz DA, Shigenobu S, <strong>Makino T<\/strong> and Kawata M. (2016) Differentially expressed genes associated with adaptation to different thermal environments in three sympatric Cuban Anolis lizards. <em>Molecular Ecology<\/em>. 25(10):2273-2285<\/li>\n\n\n\n<li>Yoshida K, Miyagi R, Mori S, Takahashi A, <strong>Makino T<\/strong>, Toyoda A, Fujiyama A, and Kitano J. (2016) Whole-genome sequencing reveals small genomic regions of introgression in an introduced crater lake population of threespine stickleback. <em>Ecology and Evolution<\/em>. 6(7):2190\u20132204<\/li>\n\n\n\n<li>Ozawa N, Furuhashi H, Masuko K, Numao E, <strong>Makino T<\/strong>, Yano T, Kurata S. (2016) Organ identity specification factor WGE localizes to the histone locus body and regulates heterochromatin structure in Drosophila. <em>Genes to Cells<\/em>. 21(5):442-456<\/li>\n\n\n\n<li>Sato PM, <strong>Makino T<\/strong> and Kawata M. (2016) Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions. <em>BMC Evolutionary Biology<\/em>. 16(1):35<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2014<\/h4>\n\n\n\n<ul reversed>\n<li><strong>Tamate CS<\/strong>, Kawata M and <strong>Makino T<\/strong>. (2014) Contribution of non-ohnologous duplicated genes to high habitat variability in mammals. <em>Molecular Biology and Evolution<\/em>, 31(7):1779-1786 <a href=\"https:\/\/academic.oup.com\/mbe\/article\/31\/7\/1938\/2925886\" target=\"_blank\" rel=\"noreferrer noopener\">News<\/a><\/li>\n\n\n\n<li>Yoshida K, <strong>Makino T<\/strong>, Yamaguchi K, Shigenobu S, Hasebe M, Kawata M, Kume M, Mori S, Peichel CL, Toyoda A, Fujiyama A, and Kitano J. (2014) Sex chromosome turnover contributes to genomic divergence between incipient stickleback species. <em>PLOS Genetics<\/em>. 10(3):e1004223<\/li>\n\n\n\n<li>McLysaght A, <strong>Makino T<\/strong>, Grayton H, Tropeano M, Mitchell K, Vassos E, Collier DA. (2014) Ohnologs are overrepresented in pathogenic copy number mutations. <em>PNAS<\/em>. 111(1):361-366 <a href=\"https:\/\/facultyopinions.com\/article\/718218053\">Faculty Opinions(very good)<\/a><\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2013<\/h4>\n\n\n\n<ul reversed>\n<li><strong>Makino T<\/strong>, McLysaght A and Kawata M. (2013) Genome-wide deserts for copy number variation in vertebrates. <em>Nature Communications<\/em>. 4:2283<\/li>\n\n\n\n<li>C\u00e1diz, A, Nagata N, Katabuchi M, D\u00edaz LM, LEchenique-D\u00edaz LM, Akashi HD, <strong>Makino T<\/strong> and Kawata M. (2013) Relative importance of habitat use, range expansion, and speciation in local species diversity of Anolis lizards in Cuba. <em>Ecosphere<\/em>. 4:art78<\/li>\n\n\n\n<li>Makanae K, Kintaka R, <strong>Makino T<\/strong>, Kitano H and Moriya H. (2013) Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method. <em>Genome Research<\/em>. 23(2):300-311<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2012<\/h4>\n\n\n\n<ul reversed>\n<li><strong>Makino T<\/strong> and McLysaght A. (2012) Positionally-biased gene loss after whole genome duplication: evidence from human, yeast and plant. <em>Genome Research<\/em>. 22(12):2427-2435<\/li>\n\n\n\n<li><strong>Makino T<\/strong> and Kawata M. (2012) Habitat variability correlates with duplicate content of Drosophila genomes, <em>Molecular Biology and Evolution<\/em>. 29(10):3169-3179<\/li>\n\n\n\n<li>Satake M, Kawata M, McLysaght A and <strong>Makino T<\/strong>. (2012) Evolution of vertebrate tissues driven by differential modes of gene duplication. <em>DNA Research<\/em>. 19(4):305-316<\/li>\n\n\n\n<li>Pessia E, <strong>Makino T<\/strong>, Bailly-Bechet M, McLysaght A and Marais GAB. (2012) Mammalian X Chromosome Inactivation evolved as a dosage compensation mechanism for dosage-sensitive genes on the X chromosome. <em>PNAS<\/em>. 109(14), 5144-5145 <a href=\"http:\/\/www.pnas.org\/content\/109\/14\/5144\" target=\"_blank\" rel=\"noreferrer noopener\">Commentary<\/a><\/li>\n\n\n\n<li>Tezuka A, Matsushima N, Nemoto Y, Akashi HD, Kawata M and <strong>Makino T<\/strong>. (2012) Comprehensive Primer Design for Analysis of Population Genetics in Non-Sequenced Organisms. <em>PLOS ONE<\/em>. 7(2): e32314<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2011<\/h4>\n\n\n\n<ul reversed>\n<li>Kitano J, Kawagishi Y, Mori S, Peichel CL, <strong>Makino T<\/strong>, Kawata M and Kusakabe M. (2011) Divergence in Sex Steroid Hormone Signaling between Sympatric Species of Japanese Threespine Stickleback. <em>PLOS ONE<\/em>. 6(12): e29253<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2010<\/h4>\n\n\n\n<ul reversed>\n<li><strong>Makino T<\/strong> and McLysaght A. (2010) Ohnologs in the human genome are dosage balanced and frequently associated with disease. <em>PNAS<\/em>. 107(20), 9270-9274 <a href=\"https:\/\/facultyopinions.com\/article\/3176957\">Faculty Opinions(very good)<\/a>, <a href=\"http:\/\/www.pnas.org\/content\/109\/14\/5144\" target=\"_blank\" rel=\"noreferrer noopener\">Commentary<\/a>, <a href=\"http:\/\/www.nature.com\/nrg\/journal\/v11\/n7\/full\/nrg2816.html\" target=\"_blank\" rel=\"noreferrer noopener\">Research Highlight<\/a><\/li>\n\n\n\n<li>Perez-Bercoff A, <strong>Makino T<\/strong> and McLysaght A. (2010) Duplicability of self-interacting human genes. <em>BMC Evolutionary Biology<\/em>. 10:160<\/li>\n\n\n\n<li><strong>Makino T<\/strong>, Knowles DG and McLysaght A. (2010) Functional divergence of duplicated genes, <em>In Evolution After Gene Duplication (Katharina Dittmar and David Liberles eds)<\/em>: 23-30, John Wiley &amp; Sons<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2009<\/h4>\n\n\n\n<ul reversed>\n<li><strong>Makino T<\/strong>, Hokamp K and McLysaght A. (2009) The complex relationship of gene duplication and essentiality. <em>Trends in Genetics.<\/em> 25(4):152-155<\/li>\n\n\n\n<li><strong>Makino T<\/strong> and McLysaght A. (2009) The evolution of functional gene clusters in eukaryote genomes. <em>In Evolutionary Biology from Concept to Application II (Pierre Pontarotti eds)<\/em>: 185-194, Springer<\/li>\n\n\n\n<li><strong>Makino T<\/strong> and McLysaght A. (2009) Evolutionary Analyses of Protein Interaction Networks, <em>In Biological Data Mining in Protein Interaction Network (Xiao-Li Li, See-Kiong Ng eds)<\/em>: 169-181, IGI Global, USA<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2008<\/h4>\n\n\n\n<ul reversed>\n<li>Akihito, Fumihito A, Ikeda Y, Aizawa M, <strong>Makino T<\/strong>, Umehara Y, Kai Y, Hasegawa M, Nakabo T and Gojobori T. (2008) 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. <em>Gene<\/em>. 427:7-18<\/li>\n\n\n\n<li><strong>Makino T<\/strong> and McLysaght A. (2008) Interacting Gene Clusters and the Evolution of the Vertebrate Immune System. <em>Molecular Biology and Evolution<\/em>. 25:1855-1862<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2007<\/h4>\n\n\n\n<ul reversed>\n<li><strong>Makino T<\/strong> and Gojobori T. (2007) Evolution of protein-protein interaction network, In Genome Dynamics: <em>Gene and protein Evolution (Jean-Nicolas Volff eds.)<\/em>, Vol.3:13-29, S. Karger AG, Basel<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2006<\/h4>\n\n\n\n<ul reversed>\n<li><strong>Makino T<\/strong>, Suzuki Y, and Gojobori T. (2006) Differential evolutionary rates of duplicated genes in protein interaction network. <em>Gene<\/em>. 385:57-63<\/li>\n\n\n\n<li><strong>Makino T<\/strong> and Gojobori T. (2006) The evolutionary rate of a protein is influenced by features of the interacting partners. <em>Molecular Biology and Evolution<\/em>. 23:784-789<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\">2000<\/h4>\n\n\n\n<ul reversed>\n<li>Kimura T, <strong>Makino T<\/strong>, Aburatani T, Kondo H, Karita S, Sakka K, Ohmiya K. (2000) Analysis of the Promoter Activity of the Taka-Amylase Gene and the Phosphoglycerate Kinase Gene in a Shoyu-koji Mold Aspergillus oryzae KBN616. <em>Food Science and Technology Research<\/em>. 6(1):44-47<\/li>\n\n\n\n<li>Kimura T, Ito J, Kawano A, <strong>Makino T<\/strong>, Kondo H, Karita S, Sakka K, Ohmiya K. (2000) Purification, characterization, and molecular cloning of acidophilic xylanase from Penicillium sp.40. <em>Bioscience, biotechnology, and biochemistry<\/em>. 64(6):1230-1237<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Publications 2026 2025 2024 2023 2022 2021 2020 2019 2018 2017 2016 2014 2013 20 &#8230; <\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":8,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"_links":{"self":[{"href":"https:\/\/www.lifesci.tohoku.ac.jp\/evolgenomics\/wp-json\/wp\/v2\/pages\/166"}],"collection":[{"href":"https:\/\/www.lifesci.tohoku.ac.jp\/evolgenomics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.lifesci.tohoku.ac.jp\/evolgenomics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.lifesci.tohoku.ac.jp\/evolgenomics\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.lifesci.tohoku.ac.jp\/evolgenomics\/wp-json\/wp\/v2\/comments?post=166"}],"version-history":[{"count":105,"href":"https:\/\/www.lifesci.tohoku.ac.jp\/evolgenomics\/wp-json\/wp\/v2\/pages\/166\/revisions"}],"predecessor-version":[{"id":1143,"href":"https:\/\/www.lifesci.tohoku.ac.jp\/evolgenomics\/wp-json\/wp\/v2\/pages\/166\/revisions\/1143"}],"wp:attachment":[{"href":"https:\/\/www.lifesci.tohoku.ac.jp\/evolgenomics\/wp-json\/wp\/v2\/media?parent=166"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}