Evolution of gene regulatory network for eye diversification

• Project/Area Number: 24770002
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Genetics/Genome dynamics
• Research Institution: Nagahama Institute of Bio-Science and Technology (2013); The University of Tokushima (2012)
• Principal Investigator: OGURA Atsushi 長浜バイオ大学, バイオサイエンス学部, 准教授 (60465929)
• Project Period (FY): 2012-04-01 – 2014-03-31
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2013: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2012: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
• Keywords: 眼 / 進化 / トランスクリプトーム / 眼の多様性 / 比較トランスクリプトーム / 次世代シーケンス

Research Abstract

Eye is one of the most important organ but they are morphologically divorced among animals. To understand evolutionary process of camera eye in squid and pinhole eye in Nautilus, we have performed comparative transcriptome analysis of developing eyes of squid and Nautilus using next generation sequencer. First, six3/6 that are required for lens formation in vertebrates was not expressed in Nautilus. Many downstream target genes of six3/6 were also not expressed in Nautilus, suggesting that deregulation of the six3/6 pathway led to the pinhole eye evolution in Nautilus. We also found five types of Pax-6 splicing variants but no duplication of the Pax-6 gene in squid. Previous studies have reported that vertebrate eyes are controlled by four Pax-6 splicing variants, whereas eyes are controlled by duplicated Pax-6 genes. Cephalopods acquired Pax-6 splicing variants independent of those in vertebrates and that these variants were similarly utilized in the development of the squid eye.

Research Products

• [Journal Article] Integrative omics analysis reveals differentially dist ibuted proteins in dimorphic euspermatozoa of the squid, Loligo bleekeri (2014)
  • Author(s): Yoshida M., Yamada L , Ochi H., Iwata Y., Tamura-Nakano M., Sawada H., Sauer W.H.H., Ogura A., Hirohashi N.
  • Journal Title: BBRC
  • Peer Reviewed
• [Journal Article] Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants (2014)
  • Author(s): Yoshida M., Yura K., Ogura A.
  • Journal Title: Scientific Reports Volume: 4 Pages: 4256-4256
• [Journal Article] The complete mitochondrial genome of the pygmy squid, Idiosepius (Cephalopoda : Decapodiformes): the first representative from the family Idiosepiidae (2014)
  • Author(s): Hall NE., Hanzak J., Allcock AL., Cooke IR., Ogura A., Strugnell JM.
  • Journal Title: Mitochondrial DNA Pages: 1940-1736
• [Journal Article] Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants (2014)
  • Author(s): Yoshida MA, Yura K, Ogura A.
  • Journal Title: Scientific Reports Volume: 4 Issue: 1 Pages: 4256-4256
  • DOI: 10.1038/srep04256
  • Peer Reviewed
• [Journal Article] Transcriptome analysis of Nautilus and pygmy squid developing eye provides insights in lens and eye evolution (2013)
  • Author(s): Sousounis K, Ogura A., Tsonis PA
  • Journal Title: PLoS ONE Volume: 8(10)
• [Journal Article] Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus (2013)
  • Author(s): Ogura A., Yoshida M., Moritaki T., Okuda Y., Sese J., Shimizu KK., Sousounis K., Tsonis PA.
  • Journal Title: Scientific Reports Volume: 3 Pages: 1432-1432
• [Journal Article] Comparison of Gene Expression Profile of Epiretinal Membranes Obtained from Eyes with Proliferative Vitreoretinopathy to That of Secondary Epiretinal Membranes (2013)
  • Author(s): Asato R., Yoshida S., Ogura A., Nakama T., Ishikawa K., Nakao S., Sassa Y., Enaida H., Oshima Y., Ikeo K., Gojobori T., Kono T., Ishibashi T.
  • Journal Title: PLoS ONE Volume: 8(1)
  • NAID: 120005227330
• [Journal Article] Transcriptome analysis of Nautilus and pygmy squid developing eye provides insights in lens and eye evolution (2013)
  • Author(s): Sousounis K, *Ogura A., *Tsonis PA.
  • Journal Title: PLoS One Volume: 8(10) Issue: 10 Pages: e78054-e78054
  • DOI: 10.1371/journal.pone.0078054
  • Peer Reviewed
• [Journal Article] The complete mitochondrial genome of the pygmy squid, Idiosepius (Cephalopoda: Decapodiformes): the first representative from the family Idiosepiidae (2013)
  • Author(s): Hall NE., Hanzak J., Allcock AL., Cooke IR., Ogura A., *Strugnell JM.
  • Journal Title: Mitochondrial DNA Volume: 1940 Issue: 1 Pages: 1736-1736
  • DOI: 10.3109/19401736.2013.865180
  • Peer Reviewed
• [Journal Article] Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus (2013)
  • Author(s): Ogura A, et al.
  • Journal Title: Scientific Reports Volume: 3 Issue: 1 Pages: 1432-1432
  • DOI: 10.1038/srep01432
  • Peer Reviewed
• [Journal Article] Systematic Measurement of Missmatch Effect for Designing Inter-Species Microarray (2012)
  • Author(s): Fukuzaki M., Yoshida M., Ogura A., Sese J.
  • Journal Title: BIBM 2012 Pages: 478-481
• [Journal Article] Cephalopod Genomics : A Plan of Strategies and Organization (2012)
  • Author(s): Albertin CB, Bonnaud L, Brown CT, Crookes-Goodson WJ, da Fonseca RR, Cristo CD, Dilkes BP, Edsinger-Gonzales E, Freeman RJ, Hanlon RT, Koenig KM, Lindgren AR, Martindale MQ, Minx P, Moroz LL, Nödl MT, Nyholm SV, Ogura A., Pungor JR, Rosenthal JJC, Schwarz EM, Shigeno S, Strugnell JM, Wollesen T, Zhang G, Ragsdale CW
  • Journal Title: Stand. Genomic Sci. Volume: 7
• [Journal Article] Cephalopod Genomics: A Plan of Strategies and Organization (2012)
  • Author(s): Albertin CB., et al.
  • Journal Title: Stand. Genomic Sci. Volume: 7 Issue: 1 Pages: 175-188
  • DOI: 10.4056/sigs.3136559
  • Peer Reviewed
• [Journal Article] Systematic Measurement of Missmatch Effect for Designing Inter-Species Microarray (2012)
  • Author(s): Fukuzaki M., et al.
  • Journal Title: BIBM 2012 Volume: 2012 Pages: 478-481
  • DOI: 10.1109/bibm.2012.6392729
  • Peer Reviewed
• [Journal Article] Comparison of Gene Expression Profile of Epiretinal Membranes Obtained from Eyes with Proliferative Vitreoretinopathy to That of Secondary Epiretinal Membranes (2012)
  • Author(s): Asato R., et al.
  • Journal Title: PLoS ONE Volume: 8 (1) Issue: 2 Pages: 157-165
  • DOI: 10.1016/j.exer.2004.03.004
  • Peer Reviewed
• [Presentation] 比較ゲノム・トランスクリプトーム研究から迫る眼多様化メカニズム (2014)
  • Author(s): 小倉淳
  • Organizer: 遺伝研研究集会-ゲノム編集時代の分子進化
  • Place of Presentation: 国立遺伝学研究所
  • Year and Date: 2014-06-28
• [Presentation] 次世代シーケンス解析に基づく生物の多様性と進化メカニズムの研究 (2014)
  • Author(s): 小倉淳
  • Place of Presentation: 北海道大学
  • Year and Date: 2014-03-31
• [Presentation] Evolutionary Genomics of Cephalopods (2014)
  • Author(s): Ogura A
  • Organizer: PAG XXII
  • Place of Presentation: Sad Diego, USA
  • Year and Date: 2014-01-17
• [Presentation] Novel role of PERK-regulated non-coding RNAs in the unfolded protein response revealed by comprehensive gene expression analysis (2013)
  • Author(s): Ogura A
  • Organizer: The 24th CDB meeting
  • Place of Presentation: Kobe, Japan
  • Year and Date: 2013-06-13
• [Presentation] Comparative Transcriptomics for Eye Diversification of Cephalopod : Evolution of Camera eye and Pinhole eye (2012)
  • Author(s): Ogura A
  • Organizer: Society for Molecular Biology and Evolution 2012
  • Place of Presentation: Ireland, Dublin
  • Year and Date: 2012-06-12
• [Presentation] オウムガイおよびイカ胚の比較RNAseqに見る頭足類カメラ眼の進化メカニズム (2012)
  • Author(s): 吉田真明, 小倉淳
  • Organizer: NGS現場の会
  • Place of Presentation: 神戸
  • Year and Date: 2012-05-24
• [Presentation] Genomes of Cephalopods (2012)
  • Author(s): Ogura A
  • Organizer: NESCent meeting "Path to CephalopodGenomics"
  • Place of Presentation: Durham, USA
  • Year and Date: 2012-05-22
• [Presentation] Evolutionary Genomics of Cephalopods
  • Author(s): Ogura A.
  • Organizer: PAG XXII
  • Place of Presentation: San Diego
• [Presentation] 次世代 シーケンス解析に基づく生物の多様性と進化メカニズムの研究
  • Author(s): 小倉淳
  • Organizer: 非モデル生物のための次世代シーケンサー活用術
  • Place of Presentation: 札幌
  • Invited
• [Presentation] Genomes of Cephalopods
  • Author(s): Ogura A.
  • Organizer: NESCent meeting
  • Place of Presentation: Duke University (USA)
  • Invited
• [Presentation] Cyclops phenocopy in squids indicates common and diverged mechanisms of eye field determination
  • Author(s): Yoshida M., Gojobori T.,Ogura A.
  • Organizer: Euro Evo Devo
  • Place of Presentation: Risbon University (Portugal)
• [Presentation] Comparative Transcriptomics for Eye Diversification of Cephalopod: Evolution of Camera eye and Pinhole eye
  • Author(s): Ogura A.
  • Organizer: SMBE
  • Place of Presentation: Dublin Convention Centre (Ireland)
• [Book] Metatranscriptome"Genome Analysis : Current Procedures and Applications (2014)
  • Author(s): Ogura A
  • Publisher: Horizon press (ISBN : 978-1-908230-29-4)
• [Book] Genome Analysis: Current Procedures and Applications (2014)
  • Author(s): Ogura A
  • Total Pages: 374
  • Publisher: Horizon press
• [Book] 頭足類の比較ゲノムプラットフォームの展望, 比較生理生化学会誌 (2013)
  • Author(s): 小倉淳
• [Book] 頭足類の比較ゲノムプラットフォームの展望 (2013)
  • Author(s): 小倉淳
  • Total Pages: 7
  • Publisher: 比較生理生化学会