Evolution of visual opsin gene expression through gene duplication manifested in fish and primates

• Project/Area Number: 23657164
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Physical anthropology
• Research Institution: The University of Tokyo
• Principal Investigator: KAWAMURA Shoji 東京大学, 大学院・新領域創成科学研究科, 教授 (40282727)
• Project Period (FY): 2011 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2012: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2011: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: オプシン / 視物質 / ゼブラフィッシュ / グッピー / トランスジェニック / 発現制御領域 / 霊長類 / 国際情報交換 / メダカ / 遺伝子重複 / 発現分化 / 発現制御 / 小型魚類

Research Abstract

Functional differentiation of visual opsin genes through gene duplication was investigated for fish and primates as a study model, in terms of differentiation in gene expression and absorption spectra. We contributed to understanding of retinal development by visualizing a subset of photoreceptor cells through opsin-class-specific promoters. We found that guppy LWS opsin genes have undergone genetic differentiation among wild populations. We showed that L and M opsin genes of primates have experienced homogenization between them by gene conversion in introns and hybridization, while spectral difference between L and M opsins appear to have been maintained by purifying selection.

Research Products

• [Journal Article] Characterization of transgenic zebrafish lines that express GFP in the retina, pineal gland, olfactory bulb, hatching gland, and optic tectum. (2013)
  • Author(s): Fang, W., Bonaffini, S., Zou, J., Wang, X., Zhang, C., Tsujimura, T., Kawamura, S. and Wei, X.
  • Journal Title: Gene Expression Patterns Volume: 13(5-6) Pages: 150-159
  • URL: http://dx.doi.org/10.1016/j.gep.2013.02.006
  • Peer Reviewed
• [Journal Article] Characterization of transgenic zebrafish lines that express GFP in the retina, pineal gland, olfactory bulb, hatching gland, and optic tectum (2013)
  • Author(s): Fang, W., Bonaffini, S., Zou, J., Wang, X., Zhang, C., Tsujimura, T., Kawamura, S. and Wei, X.
  • Journal Title: Gene Expression Patterns Volume: 13 Issue: 5-6 Pages: 150-159
  • DOI: 10.1016/j.gep.2013.02.006
  • Peer Reviewed
• [Journal Article] Bipolar cell-photoreceptor connectivity in the zebrafish (Danio rerio) retina. (2012)
  • Author(s): Li, Y. N., Tsujimura, T., Kawamura, S. and Dowling, J. E.
  • Journal Title: The Journal of Comparative Neurology Volume: 520(16) Pages: 3786-3802
  • URL: http://dx.doi.org/10.1002/cne.23168
  • Peer Reviewed
• [Journal Article] 視覚センサー遺伝子の適応と進化多様性:魚類から霊長類まで (2012)
  • Author(s): 河村正二
  • Journal Title: 化学と生物 Volume: 50(5) Pages: 325-336
  • NAID: 10030819632
  • Peer Reviewed
• [Journal Article] Bipolar cell-photoreceptor connectivity in the zebrafish (Danio rerio) retina (2012)
  • Author(s): Li, Y.N., Tsujimura, T., Kawamura, S. and Dowling, J.E.
  • Journal Title: The Journal of Comparative Neurology Volume: 520 Issue: 16 Pages: 3786-3802
  • DOI: 10.1002/cne.23168
  • Peer Reviewed
• [Journal Article] 視覚センサー遺伝子の適応と進化多様性：魚類から霊長類まで (2012)
  • Author(s): 河村正二
  • Journal Title: 化学と生物 Volume: 50 Pages: 325-336
  • NAID: 10030819632
  • Peer Reviewed
• [Journal Article] A population genetic study on the relationship between medaka fish and the spread of wet-rice cultivation across the Japanese archipelago (2012)
  • Author(s): Katsumura, T., Oda, S., Tsukamoto, K., Sekiya, Y., Yamashita, T., Aso, M., Hata, M., Nonaka, M., Mano, S., Ishida, H., Mitani, H., Kawamura, S., Oota, H.
  • Journal Title: Anthropological Science Volume: 120 Issue: 1 Pages: 81-89
  • DOI: 10.1537/ase.110525
  • NAID: 10030738530
  • ISSN: 0918-7960, 1348-8570
  • Peer Reviewed
• [Journal Article] Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes. (2011)
  • Author(s): Hiwatashi, T., Mikami, A., Katsumura, T., Suryobroto, B., Perwitasari-Farajallah, D., Malaivijitnond, S., Siriaroonrat, B., Oota, H., Goto, S. and Kawamura, S.
  • Journal Title: BMC Evolutionary Biology Volume: 11 Pages: 312-312
  • URL: http://dx.doi.org/10.1186/1471-2148-11-312
  • Peer Reviewed
• [Presentation] 魚類をモデルとした色覚進化の適応的柔軟性の検討 (2013)
  • Author(s): 河村正二
  • Organizer: 三重大学COE-A(世界に誇れる世界トップレベルの研究拠点)「魚類をモデルとした生物多様性と次世代型ポストゲノム教育研究拠点」シンポジウム「色覚・光受容機能の多様性・環境応答とその応用」
  • Place of Presentation: 三重大学生物資源学部、津
  • Year and Date: 2013-01-23
• [Presentation] マツカワおよびヒラメの眼球に発現する視物質遺伝子の機能解析 (2013)
  • Author(s): 笠木聡、矢野尚紀、水澤寛太、村上直人、安藤忠、河村正二、高橋明義
  • Organizer: 平成25年度日本水産学会春季大会
  • Place of Presentation: 東京海洋大学、品川
• [Presentation] 魚類をモデルとした色覚進化の適応的柔軟性の検討 (2013)
  • Author(s): 河村正二
  • Organizer: 三重大学COE-A（世界に誇れる世界トップレベルの研究拠点）「魚類をモデルとした生物多様性と次世代型ポストゲノム教育研究拠点」シンポジウム 「色覚・光受容機能の多様性・環境応答とその応用」
  • Place of Presentation: 三重大学生物資源学部、津
  • Invited
• [Presentation] 魚類と霊長類の研究から見えてきた色覚進化の秘密 (2012)
  • Author(s): 河村正二
  • Organizer: 日本塗装技術協会第27回塗料・塗装研究発表会、東京大学生産技術研究所、駒場リサーチキャンパス・コンベンションホール
  • Place of Presentation: 駒場
  • Year and Date: 2012-03-09
• [Presentation] Molecular mechanism and adaptive significance of evolutionary diversification of visual opsins (2012)
  • Author(s): Kawamura, S.
  • Organizer: The 89th Annual Meeting of the Physiological Society of Japan: Symposium 38: Functional evolution of sensing receptors: Toward the comprehensive understanding by fusion of research in the different fields (Organized by Makoto Tominaga and Hioo Imai), Shinshu University Matsumoto Campus, Matsumoto, Japan
  • Place of Presentation: (Oral) (Invited)
• [Presentation] ヒトとメダカ共通に観察された地域集団間の性的二型の程度の違いに関与する遺伝的多型 (2012)
  • Author(s): 勝村啓史、尾田正二、三谷啓志、埴原恒彦、河村正二、太田博樹
  • Organizer: 第66回日本人類学会
  • Place of Presentation: 慶應義塾大学日吉キャンパス、横浜市
• [Presentation] グッピーにおけるLWSオプシン遺伝子の多型と遺伝子発現量及び長波長光感受性との関連 (2012)
  • Author(s): 酒井祐輔、大槻朝、手塚あゆみ、笠木 聡、河村正二、河田雅圭
  • Organizer: 第14回日本進化学会
  • Place of Presentation: 首都大学東京南大沢キャンパス、八王子
• [Presentation] Medaka (Oryzias latipes) as a population model for studying functional differences between the alleles of human polymorphisms (2012)
  • Author(s): Katsumura, T., Oda, S., Mitani, H., Kawamura, S. and Oota, H.
  • Organizer: The 20th Annual Meeting of the Society for Molecular Biology and Evolution 2012 (SMBE 2012)
  • Place of Presentation: The Convention Centre Dublin, Ireland
• [Presentation] 魚類と霊長類の研究から見えてきた色覚進化の秘密 (2012)
  • Author(s): 河村正二
  • Organizer: 日本塗装技術協会 第27回塗料･塗装研究発表会(招待講演)
  • Place of Presentation: 東京大学生産技術研究所、駒場リサーチキャンパス･コンベンションホール、駒場
• [Presentation] Molecular mechanism and adaptive significance of evolutionary diversification of visual opsins (2012)
  • Author(s): Kawamura, S.
  • Organizer: The 89th Annual Meeting of the Physiological Society of Japan(招待講演)
  • Place of Presentation: Shinshu University Matsumoto Campus, Matsumoto
• [Presentation] 色覚進化研究の人類学的展開:魚類と霊長類に見られる視覚光センサーの進化多様性を通して (2011)
  • Author(s): 河村正二
  • Organizer: 北里大学海洋分子生物学特別セミナー
  • Place of Presentation: 北里大学相模原キャンパス、神奈川
  • Year and Date: 2011-12-02
• [Presentation] Evolution of visual opsin genes in fish and primates (2011)
  • Author(s): Kawamura, S.
  • Organizer: 15th Evolutionary Biology Meeting at Marseilles (15th EBM), Regional Center of Educational Documentation ("Centre Regional de Documentation Pedagogique")
  • Place of Presentation: Marseilles, France
• [Presentation] Evolutionary study of vertebrate color vision: from fish transgenesis to field primatology, and to human variation (2011)
  • Author(s): Kawamura, S.
  • Organizer: Annual Conference of Soceity for Molecular Biology and Evolution2011 (SMBE 2011)
  • Place of Presentation: Kyoto University (Clock Tower Centennial Hall and Shiran Kaikan) and Miyako Messe, Kyoto, Japan
• [Presentation] Comparison of gene organization and expression of blue-sensitive (SWS2) opsins among medaka fish species (2011)
  • Author(s): Aso, M., Takishima, N., Matsumoto, Y., Oda, S., Mitani, H. and Kawamura, S.
  • Organizer: Annual Conference of Soceity for Molecular Biology and Evolution 2011 (SMBE 2011)
  • Place of Presentation: Kyoto University (Clock Tower Centennial Hall and Shiran Kaikan) and Miyako Messe, Kyoto
• [Presentation] Exploration of regulatory region for differential expression of duplicated red-sensitive opsin genes in zebrafish (2011)
  • Author(s): Ashino, R., Tsujimura, T., Hoyoya, T. and Kawamura, S.
  • Organizer: Annual Conference of Soceity for Molecular Biology and Evolution 2011 (SMBE 2011)
  • Place of Presentation: Kyoto University (Clock Tower Centennial Hall and Shiran Kaikan) and Miyako Messe, Kyoto
• [Presentation] Allelic variations of cytochrome P450 genes in wild medaka populations: a parallelism to human alleles (2011)
  • Author(s): Katsumura, T., Oda, S., Mitani, H., Kawamura, S. and Oota, H.
  • Organizer: Annual Conference of Soceity for Molecular Biology and Evolution 2011 (SMBE 2011)
  • Place of Presentation: Kyoto University (Clock Tower Centennial Hall and Shiran Kaikan) and Miyako Messe, Kyoto
• [Presentation] Spectral characterization of guppy visual opsins (2011)
  • Author(s): Kasagi, S., Tezuka, A., Kawata, M. and Kawamura, S.
  • Organizer: Annual Conference of Soceity for Molecular Biology and Evolution 2011 (SMBE 2011)
  • Place of Presentation: Kyoto University (Clock Tower Centennial Hall and Shiran Kaikan) and Miyako Messe, Kyoto
• [Presentation] Evolutionary study of vertebrate color vision: from fish transgenesis to field primatology, and to human variation (2011)
  • Author(s): Kawamura, S.
  • Organizer: Annual Conference of Soceity for Molecular Biology and Evolution 2011 (SMBE 2011)(招待講演)
  • Place of Presentation: Kyoto University (Clock Tower Centennial Hall and Shiran Kaikan) and Miyako Messe, Kyoto
• [Presentation] Comparison of gene organization and expression of blue-sensitive (SWS2) opsins among medaka fish species (2011)
  • Author(s): Aso, M., Takishima, N., Matsumoto, Y., Oda, S., Mitani, H. and Kawamura, S.
  • Organizer: 17th Japanese Medaka and Zebrafish Meeting
  • Place of Presentation: Toray Human Resource Development Center, Mishima
• [Presentation] Identification of regulatory region for differential expression of duplicated red sensitive opsin genes in zebrafish (2011)
  • Author(s): Ashino, R., Tsujimura, T., Hoyoya, T. and Kawamura, S.
  • Organizer: 17th Japanese Medaka and Zebrafish Meeting
  • Place of Presentation: Toray Human Resource Development Center, Mishima
• [Presentation] 単一制御領域によるゼブラフィッシュ重複赤型オプシン遺伝子の発現分化制御 (2011)
  • Author(s): 蘆野龍一、辻村太郎、細谷知広、河村正二
  • Organizer: 第83回日本遺伝学会
  • Place of Presentation: 京都大学吉田キャンパス北部構内、京都
• [Presentation] Allelic variations of cytochrome P450 genes in wild medaka populations: curious similarities to humans' polymorphisms and their functions (2011)
  • Author(s): Katsumura, T., Oda, S., Mitani, H., Kawamura, S. and Oota, H.
  • Organizer: Isogenic Medaka Workshop
  • Place of Presentation: European Bioinformatics Institute (EBI), Hinxton, UK
• [Presentation] Evolution of visual opsin genes in fish and primates (2011)
  • Author(s): Kawamura, S.
  • Organizer: 15th Evolutionary Biology Meeting at Marseilles (15th EBM)(招待講演)
  • Place of Presentation: Regional Center of Educational Documentation, Marseilles, France
• [Presentation] 色覚進化研究の人類学的展開：魚類と霊長類に見られる視覚光センサーの進化多様性を通して (2011)
  • Author(s): 河村正二
  • Organizer: 北里大学海洋分子生物学特別セミナー(招待講演)
  • Place of Presentation: 北里大学相模原キャンパス、神奈川
• [Presentation] ゼブラフィッシュ重複赤型オプシン遺伝子の発現分化制御領域の探索 (2011)
  • Author(s): 蘆野龍一、辻村太郎、細谷知広、河村正二
  • Organizer: 第34回日本分子生物学会
  • Place of Presentation: パシフィコ横浜、横浜
• [Book] Polymorphism and adaptation of primate colour vision. In: Evolutionary Biology Mechanisms and Trends (Pontarotti, P. ed.) (2012)
  • Author(s): *Melin, A. D., Hiramatsu, C., Fedigan, L.M., Schaffner, C. M, Aureli, F. and*Kawamura, S.
  • Publisher: Springer-Verlag, Berlin Heidelberg.
  • URL: http://dx.doi.org/10.1007/978-3-642-30425-5_13
• [Book] 原著:Carl Zimmer (2010). The Tangled Bank: An Introduction to Evolution, Roberts and Company Publishers, Greenwood Village, Colorado.第 8 章コラム:霊 長類型 3 色型色覚をめぐる「謎」. In:進化:生命のたどる道 (長谷川眞理子 日本語版監修) (2012)
  • Author(s): *河村正二
  • Publisher: 岩波書店
  • URL: http://www.iwanami.co.jp/moreinfo/0054670/top.html
• [Book] Polymorphic color vision in primates: evolutionary considerations. In: Post-Genome Biology of Primates (2012)
  • Author(s): *Kawamura, S., Hiramatsu, C., Melin, A.D., Schaffner, C. M, Aureli, F. and Fedigan, L. M.
  • Publisher: Hirai, H., Imai, H. and Go, Y. eds.
  • URL: http://dx.doi.org/10.1007/978-4-431-54011-3_7
• [Remarks]
  • URL: http://www.jinrui.ib.k.u-tokyo.ac.jp/kawamura-home.htmlhttp://www.jinrui.ib.k.u-tokyo.ac.jp/kawamura-home-E.html
• [Remarks] 河村正二研究室ホームページ
  • URL: http://www.jinrui.ib.k.u-tokyo.ac.jp/kawamura-home.html
• [Remarks] Shoji Kawamura Lab Home Page
  • URL: http://www.jinrui.ib.k.u-tokyo.ac.jp/kawamura-home-E.html
• [Remarks]
  • URL: http://www.jinrui.ib.k.u-tokyo.ac.jp/kawamura-home.html