Molecular phylogeny of geckos using new mitogenomic approaches

• Project/Area Number: 20370033
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biodiversity/Systematics
• 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)
• Research Collaborator: HASHIGUCHI Yasuyuki 大阪医科大学, 医学部, 助教 (70436517) ; YAMADA Chiemi 名古屋市立大学, 大学院・システム自然科学研究科, 研究員 ; JONNIAUX Pierre 名古屋市立大学, 大学院・システム自然科学研究科, 研究員
• Project Period (FY): 2008 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥17,810,000 (Direct Cost: ¥13,700,000、Indirect Cost: ¥4,110,000); Fiscal Year 2011: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000); Fiscal Year 2010: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2009: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2008: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
• Keywords: 爬虫類 / ヤモリ / ミトコンドリア / 分子系統 / 次世代シーケンサー / 次世代シーケンサ

Research Abstract

We established a method to sequence multiple complete mitochondrial genomes in parallel with the high-throughput sequencer. The efficiency and accuracy in the sequencing was confirmed using several reptilian individuals that had been sequenced for their mitogenomes manually. We have obtained dozens of complete or nearly complete mitogenomes to find new examples of gene rearrangements, as well as phylogenetic relationships of geckos.

Research Products

• [Journal Article] Mitochondrial genomes of two African geckos of genus Hemitheconyx(Squamata : Eublepharidae) (2012)
  • Author(s): Jonniaux P and Kumazawa Y
  • Journal Title: Mitochondrial DNA Volume: (印刷中) Issue: 4 Pages: 278-279
  • DOI: 10.3109/19401736.2012.668898
  • Peer Reviewed
• [Journal Article] Characterization of squamate olfactory receptor genes and their transcripts by the high-throughput sequencing approach (2012)
  • Author(s): Dehara Y, Hashiguchi Y, Matsubara K, Yanai T, Kubo M and Kumazawa Y
  • Journal Title: Genome Biology and Evolution Volume: 4(4) Issue: 4 Pages: 602-616
  • DOI: 10.1093/gbe/evs041
  • Peer Reviewed
• [Journal Article] Mitochondrial DNA variability within Uromastyx ornata philbyi(Agamidae : Squamata) from southwestern Saudi Arabia (2012)
  • Author(s): Amer SAM, Mohamed MA, Wilms TM, Shobrak M and Kumazawa Y
  • Journal Title: Comparative and Functional Genomics Volume: 2012 Pages: 851379-851379
  • DOI: 10.1155/2012/851379
  • Peer Reviewed
• [Journal Article] Mitochondrial genomes of two African geckos of genus Hemitheconyx (Squamata : Eublepharidae) (2012)
  • Author(s): Jonniaux P, Hashiguchi Y, Kumazawa Y
  • Journal Title: Mitochondrial DNA Volume: (印刷中)
  • Peer Reviewed
• [Journal Article] Preliminary molecular variability within Uromastyx aegyptia microlepis(Reptilia : Agamidae) inhabiting Saudi Arabia (2011)
  • Author(s): Amer SAM, Montaser MM and Kumazawa Y
  • Journal Title: World Applied Sciences Journal Volume: 12 Pages: 1955-1961
  • Peer Reviewed
• [Journal Article] Preliminary molecular variability within Uromastyx aegyptia microlepis (Reptilia : Agamidae) inhabiting Saudi Arabia (2011)
  • Author(s): Amer SAM, Montaser MM, Kumazawa Y
  • Journal Title: World Applied Sciences Journal Volume: 12 Pages: 1955-1961
  • Peer Reviewed
• [Journal Article] Mitochondrial genomes of acrodont lizards : timing of gene rearrangements and phylogenetic and biogeographic implications (2010)
  • Author(s): Okajima Y and Kumazawa Y
  • Journal Title: BMC Evolutionary Biology Volume: 10 Issue: 1 Pages: 141-141
  • DOI: 10.1186/1471-2148-10-141
  • Peer Reviewed
• [Journal Article] Mitochondrial genomes of acrodont lizards : timing of gene rearrangements and phylogenetic and biogeographic implications. (2010)
  • Author(s): Okajima, Y., Kumazawa, Y.
  • Journal Title: BMC Evolutionary Biology 10 Pages: 141-141
  • Peer Reviewed
• [Journal Article] Mitochondrial genomes of acrodont lizards : timing of gene rearrangements and phylogenetic and biogeographic implications. (2010)
  • Author(s): Okajima, Y., Kumazawa, Y.
  • Journal Title: BMC Evolutionary Biology Volume: 10 Pages: 141-141
  • Peer Reviewed
• [Journal Article] 進化学のすすめ (2010)
  • Author(s): 熊澤慶伯
  • Journal Title: Annual Review 2009. Graduate School of Natural Sciences, Nagoya City University Volume: 14 Pages: 35-43
  • NAID: 120006682500
• [Journal Article] Mitogenomic perspectives into iguanid phylogeny and biogeography : Gondwanan vicariance for the origin of Madagascan oplurines (2009)
  • Author(s): Okajima Y and Kumazawa Y
  • Journal Title: Gene Volume: 441 Issue: 1-2 Pages: 28-35
  • DOI: 10.1016/j.gene.2008.06.011
  • Peer Reviewed
• [Journal Article] Mitogenomic perspectives into iguanid phylogeny and biogeography : Gondwanan vicariance for the origin of Madagascan oplurines. (2009)
  • Author(s): Okajima, Y., Kumazawa, Y.
  • Journal Title: Gene 441 Pages: 28-35
  • Peer Reviewed
• [Journal Article] Molecular affinity of Somali and Egyptian mastigures among the Afro-Arabian Uromastyx. (2009)
  • Author(s): Amer, S.A.M., Kumazawa, Y.
  • Journal Title: Egyptian Journal of Experimental Biology (Zoology) 5 Pages: 1-7
  • Peer Reviewed
• [Journal Article] Mitogenomic perspectives into iguanid phylogeny and biogeography : Gondwanan vicariance for the origin of Madagascan oplurines (2009)
  • Author(s): Okajima, Y., Kumazawa, Y.
  • Journal Title: Gene 441 Pages: 28-35
  • Peer Reviewed
• [Journal Article] The historical biogeography of the freshwater knifefishes using mitogenomic approaches : A Mesozoic origin of the Asian notopterids(Actinopterygii : Osteoglossomorpha) (2009)
  • Author(s): Inoue, J.G., Kumazawa, Y., Miya, M., Nishida, M.
  • Journal Title: Molecular Phylogenetics and Evolution 51 Pages: 486-499
  • Peer Reviewed
• [Journal Article] Complete sequence of the mitochondrial genome of the endangered Nile soft-shelled turtle Trionyx triunguis (2009)
  • Author(s): Amer, S.A.M., Kumazawa, Y.
  • Journal Title: Egyptian Journal of Experimental Biology(Zoology) 5 Pages: 43-50
  • Peer Reviewed
• [Journal Article] Molecular affinity of Somali and Egyptian mastigures among the Afro-Arabian Uromastyx (2009)
  • Author(s): Amer, S.A.M., Kumazawa, Y.
  • Journal Title: Egyptian Journal of Experimental Biology(Zoology) 5 Pages: 1-7
  • Peer Reviewed
• [Journal Article] (2009)
  • Author(s): 熊澤慶伯
  • Journal Title: 第7章:分子データを用いた魚類の分岐年代の推定. 海洋生命系のダイナミクス-第1巻、海洋の生命史-生命は海でどう進化したか-(西田睦編)(東海大学出版会)
• [Journal Article] Molecular phylogenetic and dating analyses using mitochondrial DNA sequences of eyelid geckos(Squamata : Eublepharidae) (2008)
  • Author(s): Jonniaux P and Kumazawa Y
  • Journal Title: Gene Volume: 407 Issue: 1-2 Pages: 105-115
  • DOI: 10.1016/j.gene.2007.09.023
  • Peer Reviewed
• [Journal Article] Timing of a mtDNA gene rearrangement and intercontinental dispersal of varanid lizards. (2008)
  • Author(s): Amer, S.A.M., Kumazawa, Y.
  • Journal Title: Genes and Genetic Systems 83 Pages: 275-280
  • NAID: 10024396354
  • Peer Reviewed
• [Journal Article] Molecular phylogenetic and dating analyses using mitochondrial DNA sequences of eyelid geckos (Squamata : Eublepharidae). (2008)
  • Author(s): Jonniaux, P., Kumazawa, Y.
  • Journal Title: Gene 407 Pages: 105-115
  • Peer Reviewed
• [Journal Article] Timing of a mtDNA gene rearrangement and intercontinental dispersal of varanid lizards. (2008)
  • Author(s): Amer, S. A. M., Kumazawa, Y
  • Journal Title: Genes and Genetic Systems 83 Pages: 275-280
  • NAID: 10024396354
  • Peer Reviewed
• [Journal Article] Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences. (2008)
  • Author(s): Azuma, Y., Kumazawa, Y., Miya, M., Mabuchi, K., Nishida, M.
  • Journal Title: BMC Evolutionary Biology 8 Pages: 215-215
  • Peer Reviewed
• [Journal Article] Molecular phylogenetic and dating analyses using mitochondrial DNA sequences of eyelid geckos (Squamata : Eublepharidae). (2008)
  • Author(s): Jonniaux, P., Kumazawa. Y.
  • Journal Title: Gene 407 Pages: 105-115
  • Peer Reviewed
• [Presentation] 次世代シーケンシングによる新規ミトコンドリアゲノム配列決定の効率性と正確性 (2011)
  • Author(s): 熊澤慶伯
  • Organizer: 日本進化学会第13回大会
  • Place of Presentation: 京都大学(京都市)
  • Year and Date: 2011-08-30
• [Presentation] ヤモリ類の系統関係とミトコンドリアゲノムの遺伝子配置の変動 (2011)
  • Author(s): 熊澤慶伯、三浦沙綾、ピエールジョニオ、山田知江美、橋口康之
  • Organizer: 日本進化学会第13回大会
  • Place of Presentation: 京都大学(京都市)
  • Year and Date: 2011-08-30
• [Presentation] カメ類のミトコンドリアゲノムにおける分子進化速度の不均一性 (2011)
  • Author(s): 山田知江美、柴田弘紀、熊澤慶伯
  • Organizer: 日本進化学会第13回大会
  • Place of Presentation: 京都大学(京都市)
  • Year and Date: 2011-08-30
• [Presentation] 次世代シーケンシングニヨルによる新規ミトコンドリアゲノム配列決定の効率性と正確性 (2011)
  • Author(s): 熊澤慶伯、橋口康之
  • Organizer: 日本進化学会第13回大会
  • Place of Presentation: 京都大学(京都市)
  • Year and Date: 2011-08-30
• [Presentation] 有鱗目におけるトランスクリプトームプロファイル:核遺伝子を用いた系統解析を目指して (2011)
  • Author(s): 栗崎政希、松原和純、鳥羽通久、熊澤慶伯
  • Organizer: 日本進化学会第13回大会
  • Place of Presentation: 京都大学(京都市)
  • Year and Date: 2011-08-30
• [Presentation] W染色体反復配列の比較染色体マッピングと性染色体連鎖遺伝子の系統解析から推定されたヘビにおける性染色体の分化過程 (2010)
  • Author(s): 松原和純、鳥羽通久、山田和彦、西田千鶴子、松田洋一、熊澤慶伯
  • Organizer: 第61回染色体学会年会
  • Place of Presentation: 東邦大学(船橋市)
  • Year and Date: 2010-11-07
• [Presentation] ヘビ亜目における性染色体の分化過程 (2010)
  • Author(s): 松原和純、鳥羽通久、樽井寛、山田和彦、西田千鶴子、阿形清和、松田洋一、熊澤慶伯
  • Organizer: 日本遺伝学会第82回大会
  • Place of Presentation: 北海道大学(札幌市)
  • Year and Date: 2010-09-22
• [Presentation] 中-新生代の大陸移動と爬虫類の進化 (2010)
  • Author(s): 熊澤慶伯
  • Organizer: 日本進化学会第12回大会「大陸移動と動物の進化2億年」シンポジウム
  • Place of Presentation: 東京工業大学(東京都)
  • Year and Date: 2010-08-05
• [Presentation] 中-新生代の大陸移動と爬虫類の進化 (2010)
  • Author(s): 熊澤慶伯
  • Organizer: 第12回日本進化学会シンポジウム「大陸移動と動物の進化2億年」
  • Place of Presentation: 東京工業大学(東京)
  • Year and Date: 2010-08-05
• [Presentation] 中-新生代の大陸移動と爬虫類の進化 (2010)
  • Author(s): 熊澤慶伯
  • Organizer: 日本進化学会第12回大会・シンポジウム「大陸移動と動物の進化2億年」
  • Place of Presentation: 東京工業大学大岡山キャンパス(東京都)
  • Year and Date: 2010-08-05
• [Presentation] cDNAマッピングとGC3含量にもとづくヘビゲノムにおけるモザイク構造の推定 (2010)
  • Author(s): 松原和純、工樂樹洋、樽井寛、西村理、西田千鶴子、阿形清和、松田洋一、熊澤慶伯
  • Organizer: 日本進化学会第12回大会
  • Place of Presentation: 東京工業大学大岡山キャンパス(東京都)
  • Year and Date: 2010-08-05
• [Presentation] 小笠原固有種ネブトクワガタはどこから来たか? (2010)
  • Author(s): 松浦宏典、川添和英、熊澤慶伯
  • Organizer: 日本進化学会第12回大会
  • Place of Presentation: 東京工業大学大岡山キャンパス(東京都)
  • Year and Date: 2010-08-04
• [Presentation] A phylogeographic analysis of the air sac catfishes of the Heteropneustes fossilis species complex (Heteropneustidae : Siluriformes) (2010)
  • Author(s): Ratmuangkhwang S., Musikasinthorn P., Kumazawa Y.
  • Organizer: The International Symposium on Biodiversity Sciences 2010 "Genome, Evolution and Environment"
  • Place of Presentation: ルブラ王山ホテル(名古屋市)
  • Year and Date: 2010-08-02
• [Presentation] Molecular phylogeny and biogeography of lizards (2010)
  • Author(s): Kumazawa Y and Okajima Y
  • Organizer: The International Symposium on Biodiversity Sciences 2010 "Genome, Evolution and Environment"
  • Place of Presentation: ルブラ王山ホテル(名古屋市)
  • Year and Date: 2010-08-01
• [Presentation] Molecular phylogeny and biogeography of lizards. (2010)
  • Author(s): 熊澤慶伯, Okajima, Y.
  • Organizer: The International Symposium on Biodiversity Sciences 2010 "Genome, Evolution and Environment"
  • Place of Presentation: ルブラ王山ホテル(名古屋)
  • Year and Date: 2010-08-01
• [Presentation] Molecular phylogeny and biogeography of lizards. (2010)
  • Author(s): Kumazawa Y., Okajima Y.
  • Organizer: The International Symposium on Biodiversity Sciences 2010 "Genome, Evolution and Environment"
  • Place of Presentation: ルブラ王山ホテル(名古屋市)
  • Year and Date: 2010-08-01
• [Presentation] Sex chromosome evolution in snakes (2010)
  • Author(s): Matsubara K., Toriba M., Tarui H., Yamada K., Nishida C., Agata K., Matsuda Y., Kumazawa Y.
  • Organizer: The International Symposium on Biodiversity Sciences 2010 "Genome, Evolution and Environment"
  • Place of Presentation: ルブラ王山ホテル(名古屋市)
  • Year and Date: 2010-08-01
• [Presentation] DNA barcode of the Japanese click beetles (Coleoptera : Elateridae) (2010)
  • Author(s): Oba Y., Ohira H., Moriyama A., Kumazawa Y.
  • Organizer: The International Symposium on Biodiversity Sciences 2010 "Genome, Evolution and Environment"
  • Place of Presentation: ルブラ王山ホテル(名古屋市)
  • Year and Date: 2010-08-01
• [Presentation] W染色体ヘテロクロマチンの反復配列の比較染色体マッピングと性染色体上の遺伝子の系統解析によるヘビ類における性染色体の分化過程の推定 (2009)
  • Author(s): 松原和純, 鳥羽通久, 樽井寛, 山田和彦, 西田千鶴子, 阿形清和, 松田洋一, 熊澤慶伯
  • Organizer: 日本分子生物学会第32回大会
  • Place of Presentation: パシフィコ横浜(横浜市)
  • Year and Date: 2009-12-11
• [Presentation] cDNAマッピングとGC3含量にもとづくヘビゲノムにおけるモザイク構造の推定 (2009)
  • Author(s): 松原和純, 工樂樹洋, 樽井寛, 西田千鶴子, 阿形清和, 松田洋一, 熊澤慶伯
  • Organizer: 第60回年会染色体学会
  • Place of Presentation: くにびきメッセ(松江市)
  • Year and Date: 2009-11-14
• [Presentation] 爬虫類の高次系統と生物地理 (2009)
  • Author(s): 熊澤慶伯
  • Organizer: 日本進化学会第11回大会「脊椎動物の高次系統と分子進化」ワークショップ
  • Place of Presentation: 北海道大学(札幌市)
  • Year and Date: 2009-09-03
• [Presentation] 爬虫類の高次系統と生物地理 (2009)
  • Author(s): 熊澤慶伯
  • Organizer: 第11回日本進化学会ワークショップ「脊椎動物の高次系統と分子進化」
  • Place of Presentation: 北海道大学(北海道)
  • Year and Date: 2009-09-03
• [Presentation] 爬虫類の高次系統と生物地理 (2009)
  • Author(s): 熊澤慶伯
  • Organizer: 日本進化学会第11回大会
  • Place of Presentation: 北海道大学(札幌市)
  • Year and Date: 2009-09-03
• [Presentation] シマヘビ嗅覚受容体遺伝子群のクローニングおよび系統解析 (2009)
  • Author(s): 出原由季, 橋口康之, 松原和純, 熊澤慶伯
  • Organizer: 日本進化学会第11回大会
  • Place of Presentation: 北海道大学(札幌市)
  • Year and Date: 2009-09-03
• [Presentation] ヘビ亜目における性染色体の分化過程 (2009)
  • Author(s): 松原和純, 樽井寛, 鳥羽通久, 山田和彦, 西田千鶴子, 熊澤慶伯, 阿形清和, 松田洋一
  • Organizer: 日本進化学会第11回大会
  • Place of Presentation: 北海道大学(札幌市)
  • Year and Date: 2009-09-03
• [Presentation] 生物多様性科学とDNA解析 (2008)
  • Author(s): 熊澤慶伯
  • Organizer: 遺伝子実験施設シンポジウム「新たなDNA解析次世代DNA解析のすべてとDNA解析の新分野への展開」
  • Place of Presentation: 名古屋大学(名古屋)
  • Year and Date: 2008-12-17
• [Presentation] 生物多様性科学とDNA解析 (2008)
  • Author(s): ○熊澤慶伯
  • Organizer: 遺伝子実験施設シンポジウム「新たなDNA解析-次世代DNA解析のすべてとDNA解析の新分野への展開」
  • Place of Presentation: 名古屋大学(名古屋市)
  • Year and Date: 2008-12-17
• [Presentation] Reptilian phylogenetics using mitochondrial genomes (2008)
  • Author(s): Kumazawa Y
  • Organizer: The first international symposium of the Korean Tree of Life(KTOL) research group "Genomics and Phylogenetics"
  • Place of Presentation: Korea University, Seoul, Korea
  • Year and Date: 2008-12-05
• [Presentation] Reptilian phylogenetics using mitochondrial genomes. (2008)
  • Author(s): ○ Kumazavva, Y.
  • Organizer: The first international symposium of the Korean Tree of Life (KTOL) research group“Genomics and Phylogenetics"
  • Place of Presentation: Korea University, Seoul, Korea
  • Year and Date: 2008-12-05
• [Presentation] カメレオン類ミトコンドリアゲノムの構造的特徴と系統解析 (2008)
  • Author(s): 岡島泰久、熊澤慶伯
  • Organizer: 日本進化学会第10回大会
  • Place of Presentation: 東京大学(東京都)
  • Year and Date: 2008-08-22
• [Presentation] Molecular phylogenetic and dating analyses using mitochondrial DNA sequences of eyelid geckos (2008)
  • Author(s): Pierre Jonniaux and Yoshinori Kumazawa
  • Organizer: 日本進化学会第10回大会
  • Place of Presentation: 東京大学(東京都)
  • Year and Date: 2008-08-22
• [Presentation] Molecular phylogenetic and dating analyses using mitochondrial DNA sequences of eyelid geckos. (2008)
  • Author(s): Jonniaux, P., 熊澤慶伯
  • Organizer: 第10回日本進化学会
  • Place of Presentation: 東京大学(東京)
  • Year and Date: 2008-08-22
• [Presentation] Molecular phylogenetic and dating analyses using mitochondrial DNA sequences of eyelid geckos. (2008)
  • Author(s): ○Jonniaux, P., Kumazawa. Y.
  • Organizer: 日本進化学会第IO回大会
  • Place of Presentation: 東京大学(東京都)
  • Year and Date: 2008-08-22
• [Presentation] 硬骨魚類の分岐年代推定におけるシクリッド系統地理の有効性 (2008)
  • Author(s): ○東陽一郎, 熊澤慶伯, 宮正樹, 馬渕浩司, 西田睦
  • Organizer: 日本進化学会第10回大会
  • Place of Presentation: 東京大学(東京都)
  • Year and Date: 2008-08-22
• [Presentation] Molecular evolution of mitochondrial genomes and phylogenetics in reptiles (2008)
  • Author(s): Kumazawa Y
  • Organizer: Symposium "Innovations in Immunologicals and Animal Toxins"
  • Place of Presentation: Instituto Butantan, San Paulo, Brazil
  • Year and Date: 2008-08-01
• [Presentation] Molecular evolution of mitochondrial genomes and phylogenetics in reptiles. (2008)
  • Author(s): ○ Kumazawa, Y.
  • Organizer: Symposium“Innovations in Immunologicals and Animal Toxins"
  • Place of Presentation: Instituto Butantan, San Paulo, Brazil
  • Year and Date: 2008-08-01
• [Book] 第2版古生物学事典、日本古生物学会編 (2010)
  • Author(s): 熊澤慶伯
  • Publisher: 朝倉書店
• [Book] 第1版生物の事典、石原勝敏・末光隆志編 (2010)
  • Author(s): 熊澤慶伯
  • Publisher: 朝倉書店
• [Book] 生物の事典 (2010)
  • Author(s): 熊澤慶伯
  • Publisher: 朝倉書店
• [Book] 古生物学事典第2版 (2010)
  • Author(s): 熊澤慶伯
  • Total Pages: 211
  • Publisher: 朝倉書店
• [Book] 古生物学事典 第2版 (2010)
  • Author(s): 熊澤慶伯
  • Publisher: 朝倉書店
• [Book] 海洋の生命史 (2009)
  • Author(s): 熊澤慶伯
  • Publisher: 東海大学出版会
• [Remarks]
• [Remarks]
  • URL: http://www.nsc.nagoya-cu.ac.jp/~kuma/index.html
• [Remarks] ホームページ
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