Comparison of molecular evolutionary properties between mitochondrial and nuclear genes in turtles

• Project/Area Number: 15K07169
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Evolutionary biology
• Research Institution: Nagoya City University
• Principal Investigator: Kumazawa Yoshinori 名古屋市立大学, 大学院システム自然科学研究科, 教授 (60221941)
• Co-Investigator(Renkei-kenkyūsha): SHIBATA hiroki ; YABE takashi ; INOUE jun
• Research Collaborator: SUN yao ; YAMADA chiemi ; KUSUMA wahyu endra
• Project Period (FY): 2015-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2018: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2017: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2016: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2015: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: カメ / ミトコンドリア遺伝子 / 核遺伝子 / 系統的有用度 / 翻訳フレームシフト / RNAシーケンシング / 分子進化 / 系統解析 / cDNA / RNA-Seq / 分子進化速度

Outline of Final Research Achievements

In the present study, we determined complete mitochondrial DNA sequences and obtained datasets of orthologous cDNA sequences from representative turtle species. We found some new translational frameshifts in the turtle mitochondrial protein-coding genes and showed mRNA structural features at and around the frameshift site. We showed that molecular evolutionary rates are not homogeneous among turtle lineages. Most nuclear genes had much older optima in the phylogenetic informativeness profile than mitochondrial genes. We proposed more than 50 candidate single-copy nuclear genes that may be suitable for deep-branch phylogenetic analyses in turtles.

Academic Significance and Societal Importance of the Research Achievements

本研究では、様々なカメ類からミトコンドリアゲノムと核ゲノムにコードされる遺伝情報を迅速に決定して系統解析に利用する方法を探求した。分岐年代が7千万年前を超えるような高次の系統解析には、ミトコンドリア遺伝子よりも核遺伝子の方が概して有用性が高いことを示し、今後の研究で利用可能な核遺伝子の候補をいくつか提案した。核遺伝子の情報を網羅的に取得するには特定臓器を用いたRNAシーケンシングの手法が優れていることも示した。

Research Products

• [Int'l Joint Research] University of Brawijaya(インドネシア)
• [Int'l Joint Research] ブラウィジャヤ大学(インドネシア)
• [Int'l Joint Research] University of Brawijaya(インドネシア)
• [Int'l Joint Research] University of Brawijaya(インドネシア)
• [Journal Article] Karyotype analysis of four blind snake species (Reptilia: Squamata: Scolecophidia) and karyotypic changes in Serpentes (2019)
  • Author(s): Kazumi Matsubara, Yoshinori Kumazawa, Hidetoshi Ota, Chizuko Nishida, Yoichi Matsuda
  • Journal Title: Cytogenetics and Genome Research Volume: 157 Issue: 1-2 Pages: 98-106
  • DOI: 10.1159/000496554
  • Peer Reviewed
• [Journal Article] 名古屋市産淡水貝類のDNAバーコーディング (2019)
  • Author(s): 熊澤慶伯，松原美恵子，横山悠理，寺本匡寛，村瀬幸雄，那須健一郎，孫ぎょう，森山昭彦，川瀬基弘
  • Journal Title: なごやの生物多様性 Volume: 6 Pages: 1-14
  • Peer Reviewed / Open Access
• [Journal Article] The complete mitochondrial DNA sequence of Pectenocypris sp. (Actinopterygii: Cyprinidae) from Serkap River, Sumatra, Indonesia. (2018)
  • Author(s): Atminarso D., Wibowo A., Kusuma W. E., Prianto E., Ahnelt H., Vasemagi A. and Kumazawa Y.
  • Journal Title: Mitochondrial DNA Part B Volume: 3 Issue: 1 Pages: 122-124
  • DOI: 10.1080/23802359.2018.1424585
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 遺伝子解析に基づく中部・西日本産ナミギセルStereophaedusa japonica個体群の種内多様性と名古屋市の個体群の系統的位置づけ． (2018)
  • Author(s): 川瀬基弘，西尾和久，松原美恵子，市原俊，森山昭彦，熊澤慶伯
  • Journal Title: なごやの生物多様性 Volume: 5 Pages: 11-22
  • Peer Reviewed / Open Access
• [Journal Article] Complete mitogenome sequence of Rasbora argyrotaenia (Actinopterygii: Cyprinidae). (2017)
  • Author(s): Kusuma W. E., Samuel P. D., Wiadnya D. G. R., Hariati A. M. and Kumazawa Y.
  • Journal Title: Mitochondrial DNA Part B Volume: 2 Issue: 2 Pages: 373-374
  • DOI: 10.1080/23802359.2017.1347835
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing. (2017)
  • Author(s): Sun Y., Kurisaki M., Hashiguchi Y. and Kumazawa Y.
  • Journal Title: BMC Genomics Volume: 18 Issue: 1 Pages: 665-665
  • DOI: 10.1186/s12864-017-4080-0
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 名古屋市を中心とした愛知県及び近隣県産ゾウムシ類のDNAバーコーディング． (2017)
  • Author(s): 井上晶次，熊澤慶伯
  • Journal Title: なごやの生物多様性 Volume: 4 Pages: 23-29
  • Peer Reviewed / Open Access
• [Journal Article] Molecular phylogeny and historical biogeography of the Indonesian freshwater fish Rasbora lateristriata species complex (Actinopterygii: Cyprinidae): cryptic species and west-to-east divergences. (2016)
  • Author(s): Kusuma, W. E., Ratmuangkhwang, S., and Kumazawa, Y.
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 105 Pages: 212-223
  • DOI: 10.1016/j.ympev.2016.08.014
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Complete mitochondrial genome sequences of two lndonesian rasboras (Rasbora aprotaenia and Rasbora lateristriata). (2016)
  • Author(s): Kusuma, W. E. and Kumazawa, Y.
  • Journal Title: Mitochondrial DNA Volume: 印刷中 Issue: 6 Pages: 4222-4223
  • DOI: 10.3109/19401736.2015.1022749
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Sex chromosome evolution in snakes inferred from divergence patterns of two gametologous genes and chromosome distribution of sex chromosome-linked repetitive sequences. (2016)
  • Author(s): Matsubara, K., Nishida, C., Matsuda, Y., and Kumazawa, Y.
  • Journal Title: Zoological Letters Volume: 2 Issue: 1 Pages: 19-19
  • DOI: 10.1186/s40851-016-0056-1
  • Peer Reviewed / Open Access
• [Journal Article] ミトコンドリアDNA塩基配列を用いた名古屋市及び周辺地域におけるカスミサンショウウオの遺伝的多様性の研究． (2016)
  • Author(s): 藤谷武史，能登原盛弘，熊澤慶伯
  • Journal Title: 爬虫両棲類学会報 Volume: 2016 Pages: 1-12
  • NAID: 40020882167
  • Peer Reviewed
• [Presentation] Molecular phylogeny of the endemic freshwater fish Rasbora baliensis (Actinopterygii: Cyprinidae) and its taxonomic implications (2018)
  • Author(s): Wahyu Endra Kusuma and Yoshinori Kumazawa
  • Organizer: The 10th National Seminar in Fish
• [Presentation] Evolution of structural and abundancy profiles in vertebrate mitochondrial mRNAs (2018)
  • Author(s): Yao Sun, Masaki Kurisaki, Yasuyuki Hashiguchi and Yoshinori Kumazawa
  • Organizer: SMBE 2018 Yokohama Japan
  • Int'l Joint Research
• [Presentation] Genetic diversity of two new species of Rasbora sp. (Actinopterygii: Cyprinidae) from Central Java, Indonesia (2018)
  • Author(s): Wahyu Endra Kusuma and Yoshinori Kumazawa
  • Organizer: International Conference of Aquaculture Indonesia 2018
  • Int'l Joint Research
• [Presentation] Whole genome sequencing reveals subspecies taxonomic affinities for peregrine falcon (2018)
  • Author(s): Jeff A. Johnson, Bud Anderson, Doug Bell, Andrew Dixon, Yoshinori Kumazawa, Garrett Meeks, Keiya Nakajima, Ben J. Novak, Sandra Talbot, Clayton White and Xiangjiang Zhan
  • Organizer: 2018 Annual Meeting of the Raptor Research Foundation
  • Int'l Joint Research
• [Presentation] ヘビからカエルへの遺伝子水平伝播：起源系統とその伝播メカニズム (2018)
  • Author(s): 神林千晶、掛橋竜祐、佐藤祐輔、古野伸明、水野英明、大島一彦、熊澤慶伯、Zoltan T. Nagy、森哲、Allen Allison、Stephen C. Donnellan、太田英利、細将貴、柳田哲矢、佐藤宏、Miguel Vences、倉林敦
  • Organizer: 日本爬虫両棲類学会第５７回大会
• [Presentation] RNA-Seqを用いた竜弓類ミトコンドリアmRNAのpolyA付加サイトの網羅的解析 (2017)
  • Author(s): ○孫ぎょう、栗崎正希、橋口康之、熊澤慶伯
  • Organizer: 第５回NGS現場の会
• [Presentation] 脊椎動物ミトコンドリアmRNAにおけるポリアデニル化サイトの網羅的探索と分子進化 (2017)
  • Author(s): ○孫ぎょう、栗崎正希、橋口康之、熊澤慶伯
  • Organizer: 日本進化学会第１９回大会
• [Presentation] Molecular phylogeny and historical biogeography of the Indonesian rasboras, the Rasbora lateristriata species complex. (2017)
  • Author(s): ○Wahyu Endra Kusuma、Yoshinori Kumazawa
  • Organizer: ASEAN-FEN International Fisheries Symposium - 2017
  • Int'l Joint Research
• [Presentation] 単一種か種群か？インドー東南アジア地域に分布する淡水魚類の分類学の進展と今後の展望 (2016)
  • Author(s): プラチャー ムシカシントーン、熊澤慶伯、Sahat Ratmuangkhwang、Siwaphong Ekajit
  • Organizer: 日本魚類学会第４９回年会
  • Place of Presentation: 岐阜大学（岐阜市）
  • Year and Date: 2016-09-23
• [Presentation] Molecular phylogeny of Javanese freshwater Rasbora fishes (2016)
  • Author(s): Wahyu Endra Kusuma、Yoshinori Kumazawa
  • Organizer: 日本魚類学会第４９回年会
  • Place of Presentation: 岐阜大学（岐阜市）
  • Year and Date: 2016-09-23
• [Presentation] A unique gene horizontal transfer from predator to prey occurred between distinct vertebrate classes. (2016)
  • Author(s): Yusuke Sato, Hideaki Mizuno, Kazuhiko Ohshima, Yoshinori Kumazawa, Zoltan T. Nagy, Akira Mori, Allen Allison, Stephen C. Donnellan, Hidetoshi Ota, Masaki Hoso, Nobuaki Furuno, Miguel Vences, and Atsushi Kurabayashi
  • Organizer: 日本動物学会第８７回大会＆第２２回国際動物学会合同年会
  • Place of Presentation: 沖縄コンベンションセンター（宜野湾市）
  • Int'l Joint Research
• [Presentation] Molecular phylogeny and historical biogeography of some Asian vertebrates. (2015)
  • Author(s): Yoshinori Kumazawa
  • Organizer: NCU 65th Anniversary Event Symposium “Biodiversity and Environmental Medicine in South East and East Asia Based on Molecular Biology 2015”
  • Place of Presentation: Nagoya City University (Mizuho-ku, Nagoya)
  • Year and Date: 2015-07-16
  • Int'l Joint Research / Invited
• [Presentation] Molecular phylogeography of the endemic freshwater fish Rasbora baliensis. (2015)
  • Author(s): Wahyu Endra Kusuma and Yoshinori Kumazawa
  • Organizer: NCU 65th Anniversary Event Symposium “Biodiversity and Environmental Medicine in South East and East Asia Based on Molecular Biology 2015”
  • Place of Presentation: Nagoya City University (Mizuho-ku, Nagoya)
  • Year and Date: 2015-07-16
  • Int'l Joint Research
• [Presentation] The evolutionary history of Anabas based on mitochondrial and nuclear DNA sequences. (2015)
  • Author(s): Ken Ratih Probosari, Sahat Ratmuangkhwang and Yoshinori Kumazawa
  • Organizer: NCU 65th Anniversary Event Symposium “Biodiversity and Environmental Medicine in South East and East Asia Based on Molecular Biology 2015”
  • Place of Presentation: Nagoya City University (Mizuho-ku, Nagoya)
  • Year and Date: 2015-07-16
  • Int'l Joint Research
• [Book] 魚類学の百科事典 第１版 (2018)
  • Author(s): 日本魚類学会編
  • Publisher: 丸善出版
  • ISBN: 9784621303177