研究業績

2023

• Sato DX, Matsuda Y, Usio N, Funayama R, Nakayama K, Makino T. (2023) Genomic adaptive potential to cold environments in the invasive red swamp crayfish. iScience. 26(8):107267 プレスリリース
• Maruoka N, Makino T, Urabe J. (2023) RNA-seq analysis to identify genes related to resting egg production of panarctic Daphnia pulex. BMC genomics. 24(1):1-12
• Kawahara K, Inada T, Tanaka R, Dayi M, Makino T Maruyama S, Kikuchi T, Sugimoto A, Kawata M. (2023) Differentially Expressed Genes Associated with Body Size Changes and Transposable Element Insertions between Caenorhabditis elegans and Its Sister Species, Caenorhabditis inopinata. Genome Biology and Evolution. 15(4):evad063
• 別所-上原 奏子 他 (2023)「植物に見られる多様な栄養繁殖戦略」植物科学の最前線 14:47
• Bessho-Uehara K, Masuda K, Wang DR, Angeles-Shim RB, Obara K, Nagai K, Murase R, Aoki S, Furuta T, Miura K, Wu J, Yamagata Y, Yasui H, Kantar MB, Yoshimura A, Kamura T, McCouch SR, Ashikari M. (2023) Regulator of Awn Elongation 3, an E3 ubiquitin ligase, is responsible for loss of awns during African rice domestication. PNAS. 120(4):e2207105120 プレスリリース
• Suetsugu K, Fukushima K, Makino T, Ikematsu S, Sakamoto T, Kimura S. (2023) Transcriptomic heterochrony and completely cleistogamous flower development in the mycoheterotrophic orchid Gastrodia. New Phytologist. 237(1):323-338

2022

• Ishida K and Yokoyama R. (2022) Reconsidering the function of the xyloglucan endotransglucosylase/hydrolase family. J Plant Res. 135(2):145-156
• Tamagawa K, Yoshida K, Ohrui S, Takahashi Y. (2022) Population transcriptomics reveals the effect of gene flow on the evolution of range limits. Scientific Reports 12:1318
• Bessho-Uehara K. (2022) Dawn of the Awn Regulatory Mechanism in Sorghum. Plant Cell Physiol. 63(7):886-888
• Yokoyama R, 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. Frontiers in Plant Science. 13:904313 プレスリリース
• Namba S, Kato H, Shigenobu S, Makino T, Moriya H. (2022) Massive expression of cysteine-containing proteins causes abnormal elongation of yeast cells by perturbing the proteasome. G3. 12(6):jkac106
• Ohtsuki H, Norimatsu H, Makino T, Urabe J. (2022) Invasions of an obligate asexual daphnid species support the nearly neutral theory. Scientific Reports. 12(1):1-9
• Suenaga Y, Kato M, Nagai M, Nakatani K, Kogashi H, Kobatake M, Makino T. (2022) Protein-coding potential of RNAs measured by open reading frame dominance. EMBO Reports. e54321

2021

• Itoh T and Makino T. (2021) Capturing hidden regulation based on noise change of gene expression level from single cell RNA-seq in yeast. Scientific Reports. 11:22547
• Bessho-Uehara K, Yamagata Y, Takashi T, Makino T, Yasui H, Yoshimura A, Ashikari M. (2021) Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species. Plants. 10(4):725
• Narukawa H, Yokoyama R. et al. (2021) Host-produced ethylene is required for marked cell expansion and endoreduplication in dodder search hyphae. Plant Physiology. 185(2):491-502

2020

• Yokoyama R. (2020) A Genomic Perspective on the Evolutionary Diversity of the Plant Cell Wall. Plants. 9(9):1195-1195
• Kuki H, Yokoyama R, 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. Plant. 9(5):629
• Yamasaki M, Makino T et al. (2020) Sensitivity to gene dosage and gene expression affects genes with copy number variants observed among neuropsychiatric diseases. BMC Medical Genomics. BMC Medical Genomics. 12(1):55
• Yoshida K, Ravinet M, Makino T, Toyoda A, Fujiyama A, Kokita T, Mori S, and Kitano J. (2020) Accumulation of deleterious mutations in landlocked threespine stickleback populations. Genome Biology and Evolution. 12(4):479-492
• Ishida T, Suzuki R, Nakagami S, Kuroha T, Sakamoto S, Nakata, M-T, Yokoyama R, Kimura S, Mitsuda N, Nishitani K, Sawa S. (2020) Root-knot nematodes modulate cell walls during root-knot formation in Arabidopsis roots. Journal of Plant Research. 133:419-428
• Ikemoto A, Sato DX, Makino T, and Kawata M. (2020) Genetic factors for short life span associated with evolution of the loss of flight ability. Ecology and Evolution. 10(12):6020-6029
• Isagi Y, Makino T, Hamabata T, Cao P, 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, Rhododendron boninense, growing on the Bonin Islands. Plant Species Biology. 35:166-174
• Kaga Y, Yokoyama R, 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 Cuscuta campestris. Frontiers in Plant Science. 11:193

2019

• Iwasaki WM, 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. Molecular Biology and Evolution. 37(2):355-364
• Hamabata T, Kinoshita G, Kurita K, Cao P, Ito M, Murata J, Komaki Y, Isagi Y and Makino T. (2019) Endangered island endemic plants have vulnerable genomes. Communications Biology. 2:244 Behind the paper, プレスリリース
• Makino T and Kawata M. (2019) Invasive invertebrates associated with highly duplicated gene content. Molecular Ecology. 28(7):1652-1663 プレスリリース
• Cao P, Kumagai N, Inoue T, Agata K and Makino T. (2019) JmjC domain-encoding genes are conserved in highly regenerative metazoans and are associated with planarian whole-body regeneration. Genome Biology and Evolution. 11(2):552-564 SMBE 2020 Best Student Paper Awards, Faculty Opinions(Exceptional)

2018

• Makino T, Rubin CJ, Carneiro M, Axelsson E, Andersson L and Webster MT. (2018) Elevated proportions of deleterious genetic variation in domestic animals and plants. Genome Biology and Evolution. 10(1):276-290
• Cádiz A, Nagata N, Díaz L, Suzuki-Ohno Y, Echenique-Díaz L, Akashi HD, Makino T and Kawata M. (2018) Factors affecting interspecific differences in genetic divergence among populations of Anolis lizards in Cuba. Zoological Letters, 4:21
• Suzuki, HC, Ozaki K, Makino T, 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. Genome Biology and Evolution, 10:1351–1362
• Akashi DH, Saito S, Cádiz A, Makino T, Tominaga M, Kawata M. (2018) Comparisons of behavioral and TRPA1 heat sensitivities in three sympatric Cuban Anolis lizards. Molecular Ecology, 27:2234–2242

2017

• Tamate SC, Iwasaki WM, Krysko KL, Composano B, Mori H, Funayama R, Nakayama K, Makino T and Kawata M. (2017) Inferring evolutionary responses of Anolis carolinensis introduced into the Ogasawara archipelago using whole genome sequence data. Scientific Reports. 7(1):18008.
• Sekine M and Makino T. (2017) Inference of causative genes for Alzheimer’s disease due to dosage imbalance. Molecular Biology and Evolution. 34(9):2396-2407 News, プレスリリース
• Takii R, Fujimoto M, Matsuura Y, Wu F, Oshibe N, Takaki E, Katiyar A, Akashi H, Makino T, Kawata M, and Nakai A. (2017) HSF1 and HSF3 cooperatively regulate the heat shock response in lizards. PLOS ONE. 12(7):e0180776
• Tamagawa K, Makino T, and Kawata M. (2017) The effects of CpG densities around transcription start sites on sex-biased gene expression in Poecilia reticulata. Genome Biology and Evolution. 9(5):1204-1211
• Suzuki-Ohno Y, Morita K, Nagata N, Mori H, Abe S, Makino T, and Kawata M. (2017) Factors restricting the range expansion of the invasive green anole Anolis carolinensis on Okinawa Island, Japan. Ecology and Evolution. 7(12):4357-4366
• Arai E, Hasegawa M, Makino T, Hagino A, Sakai Y, Otsuki H, Wakamatsu K, Kawata M. (2017) Physiological conditions and genetic controls of phaeomelanin pigmentation in nestling barn swallows. Behavioral Ecology. 28:706-716
• Ishikawa A, Kusakabe M, Yoshida K, Ravinet M, Makino T, Toyoda A, Fujiyama A, and Kitano J. (2017) Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes. Evolution. 71(3):565-581
• Kusakabe M, Ishikawa A, Ravinet M, Yoshida K, Makino T, Toyoda A, Fujiyama A and Kitano J. (2017) Genetic basis for variation in salinity tolerance between stickleback ecotypes. Molecular Ecology. 26(1):304-319
• Yoshida K, Makino T and Kitano J. (2017) Accumulation of deleterious mutations on the neo-Y chromosome of Japan Sea stickleback (Gasterosteus nipponicus). Journal of Heredity. 108(1):63-68

2016

• Akashi HD, Cádiz DA, Shigenobu S, Makino T and Kawata M. (2016) Differentially expressed genes associated with adaptation to different thermal environments in three sympatric Cuban Anolis lizards. Molecular Ecology. 25(10):2273-2285
• Yoshida K, Miyagi R, Mori S, Takahashi A, Makino T, 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. Ecology and Evolution. 6(7):2190–2204
• Ozawa N, Furuhashi H, Masuko K, Numao E, Makino T, Yano T, Kurata S. (2016) Organ identity specification factor WGE localizes to the histone locus body and regulates heterochromatin structure in Drosophila. Genes to Cells. 21(5):442-456
• Sato PM, Makino T 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. BMC Evolutionary Biology. 16(1):35

2014

• Tamate CS, Kawata M and Makino T. (2014) Contribution of non-ohnologous duplicated genes to high habitat variability in mammals. Molecular Biology and Evolution, 31(7):1779-1786 News, プレスリリース
• Yoshida K, Makino T, 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. PLOS Genetics. 10(3):e1004223
• McLysaght A, Makino T, Grayton H, Tropeano M, Mitchell K, Vassos E, Collier DA. (2014) Ohnologs are overrepresented in pathogenic copy number mutations. PNAS. 111(1):361-366 Faculty Opinions(very good), プレスリリース

2013

• Makino T, McLysaght A and Kawata M. (2013) Genome-wide deserts for copy number variation in vertebrates. Nature Communications. 4:2283 プレスリリース
• Cádiz, A, Nagata N, Katabuchi M, Díaz LM, LEchenique-Díaz LM, Akashi HD, Makino T and Kawata M. (2013) Relative importance of habitat use, range expansion, and speciation in local species diversity of Anolis lizards in Cuba. Ecosphere. 4:art78
• Makanae K, Kintaka R, Makino T, Kitano H and Moriya H. (2013) Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method. Genome Research. 23(2):300-311

2012

• Makino T and McLysaght A. (2012) Positionally-biased gene loss after whole genome duplication: evidence from human, yeast and plant. Genome Research. 22(12):2427-2435 プレスリリース
• Makino T and Kawata M. (2012) Habitat variability correlates with duplicate content of Drosophila genomes, Molecular Biology and Evolution. 29(10):3169-3179 プレスリリース
• Satake M, Kawata M, McLysaght A and Makino T. (2012) Evolution of vertebrate tissues driven by differential modes of gene duplication. DNA Research. 19(4):305-316
• Pessia E, Makino T, 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. PNAS. 109(14), 5144-5145 Commentary, プレスリリース
• Tezuka A, Matsushima N, Nemoto Y, Akashi HD, Kawata M and Makino T. (2012) Comprehensive Primer Design for Analysis of Population Genetics in Non-Sequenced Organisms. PLOS ONE. 7(2): e32314

2011

• Kitano J, Kawagishi Y, Mori S, Peichel CL, Makino T, Kawata M and Kusakabe M. (2011) Divergence in Sex Steroid Hormone Signaling between Sympatric Species of Japanese Threespine Stickleback. PLOS ONE. 6(12): e29253

2010

• Makino T and McLysaght A. (2010) Ohnologs in the human genome are dosage balanced and frequently associated with disease. PNAS. 107(20), 9270-9274 Faculty Opinions(very good), Commentary, Research Highlight, プレスリリース
• Perez-Bercoff A, Makino T and McLysaght A. (2010) Duplicability of self-interacting human genes. BMC Evolutionary Biology. 10:160
• Makino T, Knowles DG and McLysaght A. (2010) Functional divergence of duplicated genes, In Evolution After Gene Duplication (Katharina Dittmar and David Liberles eds): 23-30, John Wiley & Sons

2009

• Makino T, Hokamp K and McLysaght A. (2009) The complex relationship of gene duplication and essentiality. Trends in Genetics. 25(4):152-155
• Makino T and McLysaght A. (2009) The evolution of functional gene clusters in eukaryote genomes. In Evolutionary Biology from Concept to Application II (Pierre Pontarotti eds): 185-194, Springer
• Makino T and McLysaght A. (2009) Evolutionary Analyses of Protein Interaction Networks, In Biological Data Mining in Protein Interaction Network (Xiao-Li Li, See-Kiong Ng eds): 169-181, IGI Global, USA

2008

• Akihito, Fumihito A, Ikeda Y, Aizawa M, Makino T, 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. Gene. 427:7-18 宮内庁
• Makino T and McLysaght A. (2008) Interacting Gene Clusters and the Evolution of the Vertebrate Immune System. Molecular Biology and Evolution. 25:1855-1862

2007

• Makino T and Gojobori T. (2007) Evolution of protein-protein interaction network, In Genome Dynamics: Gene and protein Evolution (Jean-Nicolas Volff eds.), Vol.3:13-29, S. Karger AG, Basel

2006

• Makino T, Suzuki Y, and Gojobori T. (2006) Differential evolutionary rates of duplicated genes in protein interaction network. Gene. 385:57-63
• Makino T and Gojobori T. (2006) The evolutionary rate of a protein is influenced by features of the interacting partners. Molecular Biology and Evolution. 23:784-789

2000

• Kimura T, Makino T, 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. Food Science and Technology Research. 6(1):44-47
• Kimura T, Ito J, Kawano A, Makino T, Kondo H, Karita S, Sakka K, Ohmiya K. (2000) Purification, characterization, and molecular cloning of acidophilic xylanase from Penicillium sp.40. Bioscience, biotechnology, and biochemistry. 64(6):1230-1237