論文 - 松波　雅俊

Transcriptomics on Social Interactions in Termites: Effects of Soldier Presence

Matsunami M.

Frontiers in Ecology and Evolution ( Frontiers in Ecology and Evolution )  10   2022年06月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The organization of social insect colonies requires sophisticated mechanisms to regulate caste composition according to colony demands. In termites, the soldier caste is responsible for the inhibition of soldier differentiation, but the mechanism underlying the regulation of soldier differentiation is still unclear. In this study, we performed transcriptome analyses to identify genes expressed in workers that fluctuated in the presence of soldiers in the subterranean termite Reticulitermes speratus. First, soldier differentiation was artificially induced via juvenile hormone (JH) application, and the inhibitory effects of soldier differentiation on soldier presence were evaluated. Second, transcriptomes were prepared from workers with or without soldiers under JH treatment, and expression analyses were performed to identify differentially expressed genes (DEGs) for each treatment. The expression levels of several DEGs were verified by quantitative real-time PCR. The results indicated that only a small number of DEGs were upregulated by the presence of soldiers. A homology search of DEGs and gene ontology (GO) analysis of the DEGs showed that some genes were responsible for the regulation of hormone levels, social interaction, and response to xenobiotic substances, suggesting that they could be involved in developmental arrest and pheromonal regulation in workers. Moreover, GO analysis indicated that the expression of many genes, including those involved in hormone metabolic processes, fluctuated with JH application. Suppression of soldier differentiation in the presence of soldiers could be accomplished by the expression of a large number of genes required for soldier differentiation.

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Genomic and transcriptomic analyses of the subterranean termite <i>Reticulitermes speratus</i>: Gene duplication facilitates social evolution.

Shigenobu S, Hayashi Y, Watanabe D, Tokuda G, Hojo MY, Toga K, Saiki R, Yaguchi H, Masuoka Y, Suzuki R, Suzuki S, Kimura M, Matsunami M, Sugime Y, Oguchi K, Niimi T, Gotoh H, Hojo MK, Miyazaki S, Toyoda A, Miura T, Maekawa K

Proceedings of the National Academy of Sciences of the United States of America ( Proceedings of the National Academy of Sciences of the United States of America )  119 ( 3 )   2022年01月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Transcriptomic Changes in Hot Spring Frog Tadpoles (Buergeria otai) in Response to Heat Stress

Shohei Komaki, Masatoshi Matsunami, Jhan-Wei Lin, Ko-Huan Lee, Yen-Po Lin, Yu Lee, Si-Min Lin, Takeshi Igawa

Frontiers in Ecology and Evolution ( Frontiers Media SA )  9   2021年10月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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<italic>Buergeria</italic> frog tadpoles exhibit high thermal tolerance and are occasionally found in water pools that temporarily exceed 40°C. With the aim of understanding how they can cope with the severe heat stress, we performed RNA-seq of three heat-treated (38°C) and three control (25°C) tadpoles and compared their transcriptomic profiles. We identified 382 differentially expressed transcripts. A protein-protein interaction (PPI) network analysis of these transcripts further identified hub proteins involved in protein degradation, stress granule assembly, and global suppression of DNA transcription and mRNA translation. Along with the avoidance behavior against high water temperature, these endurance mechanisms potentially support tadpoles to survive in high temperatures for short periods of time. Similar mechanisms may exist in many other amphibian species whose habitats are prone to high temperatures.

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Species divergence and repeated ancient hybridization in a Sulawesian lake system.

Mandagi IF, Kakioka R, Montenegro J, Kobayashi H, Masengi KWA, Inomata N, Nagano AJ, Toyoda A, Ansai S, Matsunami M, Kimura R, Kitano J, Kusumi J, Yamahira K

Journal of evolutionary biology ( Journal of Evolutionary Biology )  34 ( 11 ) 1767 - 1780   2021年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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An increasing volume of empirical studies demonstrated that hybridization between distant lineages may have promoted speciation in various taxa. However, the timing, extent and direction of introgressive hybridization remain unknown in many cases. Here, we report a possible case in which repeated hybridization promoted divergence of Oryzias ricefishes (Adrianichthyidae) on Sulawesi, an island of Wallacea. Four Oryzias species are endemic to the Malili Lake system in central Sulawesi, which is composed of five tectonic lakes; of these, one lake is inhabited by two species. Morphological and population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that these two sympatric species are phylogenetically sister to but substantially reproductively isolated from each other. Analyses of admixture and comparison of demographic models revealed that the two sympatric species experienced several substantial introgressions from outgroup populations that probably occurred soon after they had secondary contact with each other in the lake. However, the ratio of migrants from the outgroups was estimated to be different between the two species, which is consistent with the hypothesis that these introgressions aided their divergence or prevented them from forming a hybrid swarm. Repeated lake fragmentations and fusions may have promoted diversification of this freshwater fish species complex that is endemic to this ancient lake system.

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Coevolution between MHC Class I and Antigen-Processing Genes in Salamanders

Gemma Palomar, Katarzyna Dudek, Magdalena Migalska, J W Arntzen, G Francesco Ficetola, Dušan Jelić, Elizabeth Jockusch, Inigo Martínez-Solano, Masatoshi Matsunami, H Bradley Shaffer, Judit Vörös, Bruce Waldman, Ben Wielstra, Wiesław Babik, Yuseob Kim

Molecular Biology and Evolution ( Oxford University Press ({OUP}) )  38 ( 11 ) 5092 - 5106   2021年08月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Genome-wide association studies identify two novel loci conferring susceptibility to diabetic retinopathy in Japanese patients with type 2 diabetes.

Imamura M, Takahashi A, Matsunami M, Horikoshi M, Iwata M, Araki SI, Toyoda M, Susarla G, Ahn J, Park KH, Kong J, Moon S, Sobrin L, International Diabetic Retinopathy and Genetics CONsortium (iDRAGON)., Yamauchi T, Tobe K, Maegawa H, Kadowaki T, Maeda S

Human molecular genetics ( Human Molecular Genetics )  30 ( 8 ) 716 - 726   2021年05月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Several reports have suggested that genetic susceptibility contributes to the development and progression of diabetic retinopathy. We aimed to identify genetic loci that confer susceptibility to diabetic retinopathy in Japanese patients with type 2 diabetes. We analysed 5 790 508 single nucleotide polymorphisms (SNPs) in 8880 Japanese patients with type 2 diabetes, 4839 retinopathy cases and 4041 controls, as well as 2217 independent Japanese patients with type 2 diabetes, 693 retinopathy cases, and 1524 controls. The results of these two genome-wide association studies (GWAS) were combined with an inverse variance meta-analysis (Stage-1), followed by de novo genotyping for the candidate SNP loci (p < 1.0 × 10-4) in an independent case-control study (Stage-2, 2260 cases and 723 controls). After combining the association data (Stage-1 and -2) using meta-analysis, the associations of two loci reached a genome-wide significance level: rs12630354 near STT3B on chromosome 3, p = 1.62 × 10-9, odds ratio (OR) = 1.17, 95% confidence interval (CI) 1.11-1.23, and rs140508424 within PALM2 on chromosome 9, p = 4.19 × 10-8, OR = 1.61, 95% CI 1.36-1.91. However, the association of these two loci were not replicated in Korean, European, or African American populations. Gene-based analysis using Stage-1 GWAS data identified a gene-level association of EHD3 with susceptibility to diabetic retinopathy (p = 2.17 × 10-6). In conclusion, we identified two novel SNP loci, STT3B and PALM2, and a novel gene, EHD3, that confers susceptibility to diabetic retinopathy; however, further replication studies are required to validate these associations.

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Fine-Scale Genetic Structure and Demographic History in the Miyako Islands of the Ryukyu Archipelago.

Matsunami M, Koganebuchi K, Imamura M, Ishida H, Kimura R, Maeda S

Molecular biology and evolution ( Molecular Biology and Evolution )  38 ( 5 ) 2045 - 2056   2021年05月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The Ryukyu Archipelago is located in the southwest of the Japanese islands and is composed of dozens of islands, grouped into the Miyako Islands, Yaeyama Islands, and Okinawa Islands. Based on the results of principal component analysis (PCA) on genome-wide single nucleotide polymorphisms (SNPs), genetic differentiation was observed among the island groups of the Ryukyu Archipelago. However, a detailed population structure analysis of the Ryukyu Archipelago has not yet been completed. We obtained genomic DNA samples from 1,240 individuals living in the Miyako Islands, and we genotyped 665,326 SNPs to infer population history within the Miyako Islands, including Miyakojima, Irabu and Ikema islands. The haplotype-based analysis showed that populations in the Miyako Islands were divided into three subpopulations located on Miyakojima northeast, Miyakojima southwest, and Irabu/Ikema. The results of haplotype sharing and the D statistics analyses showed that the Irabu/Ikema subpopulation received gene flows different from those of the Miyakojima subpopulations, which may be related with the historically attested immigration during the Gusuku period (900 - 500 BP). A coalescent-based demographic inference suggests that the Irabu/Ikema population firstly split away from the ancestral Ryukyu population about 41 generations ago, followed by a split of the Miyako southwest population from the ancestral Ryukyu population (about 16 generations ago), and the differentiation of the ancestral Ryukyu population into two populations (Miyako northeast and Okinawajima populations) about 7 generations ago. Such genetic information is useful for explaining the population history of modern Miyako people and must be taken into account when performing disease association studies.

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Molecular Evolution of Antigen-Processing Genes in Salamanders: Do They Coevolve with MHC Class I Genes?

Palomar G, Dudek K, Wielstra B, Jockusch EL, Vinkler M, Arntzen JW, Ficetola GF, Matsunami M, Waldman B, Těšický M, Zieliński P, Babik W

Genome biology and evolution ( Genome biology and evolution )  13 ( 2 )   2021年02月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Proteins encoded by antigen-processing genes (APGs) prepare antigens for presentation by the major histocompatibility complex class I (MHC I) molecules. Coevolution between APGs and MHC I genes has been proposed as the ancestral gnathostome condition. The hypothesis predicts a single highly expressed MHC I gene and tight linkage between APGs and MHC I. In addition, APGs should evolve under positive selection, a consequence of the adaptive evolution in MHC I. The presence of multiple highly expressed MHC I genes in some teleosts, birds, and urodeles appears incompatible with the coevolution hypothesis. Here, we use urodele amphibians to test two key expectations derived from the coevolution hypothesis: 1) the linkage between APGs and MHC I was studied in Lissotriton newts and 2) the evidence for adaptive evolution in APGs was assessed using 42 urodele species comprising 21 genera from seven families. We demonstrated that five APGs (PSMB8, PSMB9, TAP1, TAP2, and TAPBP) are tightly linked (<0.5 cM) to MHC I. Although all APGs showed some codons under episodic positive selection, we did not find a pervasive signal of positive selection expected under the coevolution hypothesis. Gene duplications, putative gene losses, and divergent allelic lineages detected in some APGs demonstrate considerable evolutionary dynamics of APGs in salamanders. Overall, our results indicate that if coevolution between APGs and MHC I occurred in urodeles, it would be more complex than envisaged in the original formulation of the hypothesis.

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Gene Structure Analysis of Chemokines and Their Receptors in Allotetraploid Frog, <i>Xenopus laevis</i>.

Fukui A, Matsunami M

Frontiers in genetics ( Frontiers in Genetics )  12   787979   2021年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Expression of Genes Involved in Offensive and Defensive Phenotype Induction in the Pituitary Gland of the Hokkaido Salamander (<i>Hynobius retardatus</i>).

Matsunami M, Miura T, Kishida O, Michimae H, Nishimura K

Zoological science ( Zoological Science )  37 ( 6 ) 563 - 574   2020年12月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Robust ridge regression for estimating the effects of correlated gene expressions on phenotypic traits

Michimae H.

Environmental and Ecological Statistics ( Environmental and Ecological Statistics )  27 ( 1 ) 41 - 72   2020年03月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Evidence for sympatric speciation in a Wallacean ancient lake.

Sutra N, Kusumi J, Montenegro J, Kobayashi H, Fujimoto S, Masengi KWA, Nagano AJ, Toyoda A, Matsunami M, Kimura R, Yamahira K

Evolution; international journal of organic evolution ( Evolution )  73 ( 9 ) 1898 - 1915   2019年09月

掲載種別: 研究論文（学術雑誌）

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A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology.

Matsunami M, Suzuki M, Haramoto Y, Fukui A, Inoue T, Yamaguchi K, Uchiyama I, Mori K, Tashiro K, Ito Y, Takeuchi T, Suzuki KT, Agata K, Shigenobu S, Hayashi T

DNA research : an international journal for rapid publication of reports on genes and genomes ( DNA research : an international journal for rapid publication of reports on genes and genomes )  26 ( 3 ) 217 - 229   2019年06月

掲載種別: 研究論文（学術雑誌）

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Termite soldier mandibles are elongated by <i>dachshund</i> under hormonal and Hox gene controls.

Sugime Y, Oguchi K, Gotoh H, Hayashi Y, Matsunami M, Shigenobu S, Koshikawa S, Miura T

Development (Cambridge, England) ( Development (Cambridge) )  146 ( 5 )   2019年03月

掲載種別: 研究論文（学術雑誌）

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Transcriptomic changes during caste development through social interactions in the termite <i>Zootermopsis nevadensis</i>.

Yaguchi H, Suzuki R, Matsunami M, Shigenobu S, Maekawa K

Ecology and evolution ( Ecology and Evolution )  9 ( 6 ) 3446 - 3456   2019年03月

掲載種別: 研究論文（学術雑誌）

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Multiple Conserved Elements Structuring Inverted Repeats in the Mammalian Coat Color-Related Gene <i>Asip</i>.

Sakuma Y, Matsunami M, Takada T, Suzuki H

Zoological science ( Zoological Science )  36 ( 1 ) 23 - 30   2019年02月

掲載種別: 研究論文（学術雑誌）

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Caste-specific microRNA expression in termites: insights into soldier differentiation

Matsunami M.

Insect Molecular Biology ( Insect Molecular Biology )  28 ( 1 ) 86 - 98   2019年02月

掲載種別: 研究論文（学術雑誌）

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Signature of positive selection in mitochondrial DNA in Cetartiodactyla.

Mori S, Matsunami M

Genes & genetic systems ( 日本遺伝学会 )  93 ( 2 ) 65 - 73   2018年09月

掲載種別: 研究論文（学術雑誌）

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<p>Acceleration of the amino acid substitution rate is a good indicator of positive selection in adaptive evolutionary changes of functional genes. Genomic information about mammals has become readily available in recent years, as many researchers have attempted to clarify the adaptive evolution of mammals by examining evolutionary rate change based on multiple loci. The order Cetartiodactyla (Artiodactyla and Cetacea) is one of the most diverse orders of mammals. Species in this order are found throughout all continents and seas, except Antarctica, and they exhibit wide variation in morphology and habitat. Here, we focused on the metabolism-related genes of mitochondrial DNA (mtDNA) in species of the order Cetartiodactyla using 191 mtDNA sequences available in databases. Based on comparisons of the <i>dN</i>/<i>dS</i> ratio (<i>ω</i>) in 12 protein-coding genes, <i>ATP8</i> was shown to have a higher <i>ω</i> value (<i>ω</i> = 0.247) throughout Cetartiodactyla than the other 11 genes (<i>ω</i> < 0.05). In a branch-site analysis of <i>ATP8</i> sequences, a markedly higher <i>ω</i> value of 0.801 was observed in the ancestral lineage of the clade of Cetacea, which is indicative of adaptive evolution. Through efforts to detect positively selected amino acids, codon positions 52 and 54 of <i>ATP8</i> were shown to have experienced positive selective pressure during the course of evolution; multiple substitutions have occurred at these sites throughout the cetacean lineage. At position 52, glutamic acid was replaced with asparagine, and, at position 54, lysine was replaced with non-charged amino acids. These sites are conserved in most Artiodactyla. These results imply that the ancestor of cetaceans underwent accelerated amino acid changes in ATP8 and replacements at codons 52 and 54, which adjusted metabolism to adapt to the marine environment.</p>

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Reconsidering the estimation of costs of phenotypic plasticity using the robust ridge estimator

Michimae H.

Ecological Informatics ( Ecological Informatics )  44   7 - 20   2018年03月

掲載種別: 研究論文（学術雑誌）

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Draft genome sequence of Japanese wood mouse, <i>Apodemus speciosus</i>.

Matsunami M, Endo D, Saitou N, Suzuki H, Onuma M

Data in brief   16   43 - 46   2018年02月

掲載種別: 研究論文（学術雑誌）

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Population Structure and Evolution after Speciation of the Hokkaido Salamander (Hynobius retardatus).

Matsunami M, Igawa T, Michimae H, Miura T, Nishimura K

PloS one   11 ( 6 ) e0156815   2016年

掲載種別: 研究論文（学術雑誌）

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Transcriptome analysis of predator- and prey-induced phenotypic plasticity in the Hokkaido salamander (Hynobius retardatus).

Matsunami M, Kitano J, Kishida O, Michimae H, Miura T, Nishimura K

Molecular ecology   24 ( 12 ) 3064 - 76   2015年06月

掲載種別: 研究論文（学術雑誌）

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Development and characterization of 12 microsatellite markers for the Hokkaido Salamander (Hynobius retardatus)

Masatoshi Matsunami, Takeshi Igawa, Masafumi Nozawa, Hirofumi Michimae, Toru Miura, Kinya Nishimura

Current Herpetology ( Herpetological Society of Japan )  34 ( 2 ) 177 - 181   2015年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The Hokkaido salamander, Hynobius retardatus (Caudata: Hynobiidae), is a common salamander species distributed throughout Hokkaido Island, Japan. Because of its regional morphological diversity and flexible phenotypic plasticity, its demographic history and the causes of its distribution patterns are of intrinsic interest to evolutionary biologists. To address these issues, a microsatellite marker is an ideal genetic marker for inferring gene flows and hybridizations between populations on a fine scale. We therefore utilized an Ion PGM™ sequencing system to screen the H. retardatus genome for microsatellite markers. As the result, we identified 12 polymorphic markers. We then tested the usefulness of these markers in H. retardatus by genotyping 20 individuals from each of two regional populations (the Erimo and Nopporo populations). The total number of alleles ranged from 3 to 8, and the expected heterozygosities per locus ranged from 0.049 to 0.803. We expect the developed markers to be useful for future studies of demography of this species.

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