Molecular survey of the functional diversity in non-photosynthetic plastids based on comparative genomics and proteomics.

2016 Fiscal Year Annual Research Report

• Project/Area Number: 26840123
• Research Institution: National Museum of Nature and Science, Tokyo
• Principal Investigator: 谷藤 吾朗 独立行政法人国立科学博物館, 動物研究部, 研究員 (70438480)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Keywords: Cryptomonads / Nucleomorph / Plastid / Comparative Genomics / Reductive Evolution

Outline of Annual Research Achievements

光合成を失った葉緑体（白色体）の機能と進化的な経緯を明らかにすることを目指し、比較ゲノム解析とトランスクリプトーム解析を行った。材料として、葉緑体の起源となった二次共生体の痕跡的核（ヌクレオモルフ）を保持していながら光合成能力を失った種と光合成を維持している種が混在しているクリプト生物を用い、葉緑体ゲノムとヌクレオモルフゲノムの比較解析、およびトランスクリプトーム解析を行った。
葉緑体ゲノムは3種の完全長ゲノムを決定した。本研究以前に解読されたクリプト生物の葉緑体ゲノムと比較を行い、非光合成葉緑体ゲノムにおいて光合成能力を失ってから光合成関連遺伝子（e.g.,psb遺伝子ファミリー）が偽遺伝子化していく様子、完全に遺伝子が消失するまでの進化段階が明らかになった。また、遺伝子が消失していく過程でゲノムのリアレンジメントの頻度が上昇することが見出された。当初の予定にはなかった株を加えたことで、光合成機能消失の進化における様子をより詳細に把握することが出来た。研究成果は国内外学会で発表し、主要成果について現在論文として投稿準備中である。最終年度は主に、ヌクレオモルフゲノムとトランスクリプトーム解析を行った。ヌクレオモルフについては光合成種と非光合成種、各1種についてほぼ全長を決定した。さらにトランスクリプトーム・データから葉緑体に輸送されるタンパク質を推定し、本研究以前に明らかになっているクリプト生物の葉緑体タンパク質群と比較した。これらの成果についても現在投稿準備中である。

Research Products

• [Int'l Joint Research] Dalhousie University(カナダ)
  • Country Name: CANADA
  • Counterpart Institution: Dalhousie University
• [Int'l Joint Research] Philipps-Universitat Marburg(ドイツ)
  • Country Name: GERMANY
  • Counterpart Institution: Philipps-Universitat Marburg
• [Int'l Joint Research] University of South Bohemia(チェコ)
  • Country Name: CZECH
  • Counterpart Institution: University of South Bohemia
• [Int'l Joint Research] Mississippi State University(米国)
  • Country Name: U.S.A.
  • Counterpart Institution: Mississippi State University
• [Journal Article] Global Kinetoplastea phylogeny inferred from a large-scale, multi-gene alignment including parasitic species and transitions from a free-living to a parasitic lifestyle (2017)
  • Author(s): Yazaki, E., S. A. Ishikawa, K. Kume, A. Kumagai, T. Kamaishi, G. Tanifuji, T. Hashimoto and Y. Inagaki
  • Journal Title: Genes & Genetic Systems Volume: - Pages: 16-00056
  • DOI: DOI: 10.1266/ggs.16-00056
  • Peer Reviewed / Open Access
• [Journal Article] Eukaryotes lacking sterols (2017)
  • Author(s): Takishita, K., Y. Chikaraishi, G. Tanifuji, N. Ohkouchi, T. Hashimoto, K. Fujikura, A. Roger
  • Journal Title: Journal of Eukaryotic Microbiology Volume: - Pages: -
  • DOI: -
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Hyper-eccentric structural genes in the mitochondrial genome of the algal parasite Hemistasia phaeocysticola (2016)
  • Author(s): Yabuki, A., G. Tanifuji, C. Kusaka, K. Takishita and K. Fujikura
  • Journal Title: Genome Biology and Evolution Volume: - Pages: evw207
  • DOI: DOI: 10.1093/gbe/evw207
  • Peer Reviewed / Open Access
• [Journal Article] Mitochondrial genome of Palpitomonas bilix: Derived genome structure and ancestral system for cytochrome c maturation (2016)
  • Author(s): Nishimura, Y., G. Tanifuji, R. Kamikawa, A. Yabuki, T. Hashimoto and Y. Inagaki
  • Journal Title: Genome Biology and Evolution Volume: - Pages: evw217
  • DOI: https://doi.org/10.1093/gbe/evw217
  • Peer Reviewed / Open Access
• [Journal Article] Heme pathway evolution in kinetoplastid protists (2016)
  • Author(s): Cenci, U., D. Moog, B. A. Curtis, G. Tanifuji, L. Eme, J. Lukes and J. M. Archibald
  • Journal Title: BMC Evolutionary Biology Volume: 16 Pages: 109
  • DOI: DOI: 10.1186/s12862-016-0664-6
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Complex evolution of two types of cardiolipin synthase in the eukaryotic lineage stramenopiles (2016)
  • Author(s): Noguchi, F., G. Tanifuji, M. W. Brown, K. Fujikura and K. Takishita
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 101 Pages: 133-141
  • DOI: doi: 10.1016/j.ympev.2016.05.011
  • Peer Reviewed / Int'l Joint Research
• [Presentation] Plastid comparative genomics elucidates multiple independent losses of photosynthesis in Cryptomonas (Cryptophyta) (2016)
  • Author(s): Tanifuji, G., R. Kamikawa, C. E. Moore, T. Mills, Y. Inagaki, T. Hashimoto and J. M. Archibald.
  • Organizer: The 13th International Colloquim on Endocytobiology and Symbiosis
  • Place of Presentation: Kyoto Prefectural University, Kyoto, Japan.
  • Year and Date: 2016-09-10 – 2016-09-14
  • Int'l Joint Research
• [Presentation] “Uneasy” loss of the Calvin Benson cycle in nonphotosynthetic plastids. (2016)
  • Author(s): Kamikawa, R., S. Zauner, D. Moog, G. Tanifuji, K. Ishida, S. Mayama, T. Hashimoto, J. M. Archibald, A. J. Roger, U. G. Maier, H. Miyashita and Y. Inagaki
  • Organizer: The 13th International Colloquim on Endocytobiology and Symbiosis
  • Place of Presentation: Kyoto Prefectural University, Kyoto, Japan.
  • Year and Date: 2016-09-10 – 2016-09-14
  • Int'l Joint Research
• [Presentation] The role of peroxisomes in eukaryote-eukaryote endosymbiosis (2016)
  • Author(s): Moog, D., B. A. Curtis, G. Tanifuji, M. Dlutek, U. G. Maier and J.M. Archibald,
  • Organizer: The 13th International Colloquim on Endocytobiology and Symbiosis
  • Place of Presentation: Kyoto Prefectural University, Kyoto, Japan.
  • Year and Date: 2016-09-10 – 2016-09-14
  • Int'l Joint Research
• [Presentation] Gregarine-like apicomplexan parasite isolated from the intestinal tract of a centipede Scolopocryptops rubiginosus (2016)
  • Author(s): Miyata R., T. Nakayama, G. Tanifuji, Y. Chikami and Y. Inagaki
  • Organizer: The 13th International Colloquim on Endocytobiology and Symbiosis
  • Place of Presentation: Kyoto Prefectural University, Kyoto, Japan.
  • Year and Date: 2016-09-10 – 2016-09-14
  • Int'l Joint Research
• [Presentation] Phylogenetic positions of marine gregarines Selenidium terebellae and Lecudina tuzetae, and molecular evidence of their remnant nonphotosynthetic plastids (apicoplasts) (2016)
  • Author(s): Wakeman K., T. Nakayama, G. Tanifuji, E. Matsuo, B. S. Leander and Y. Inagaki
  • Organizer: The 13th International Colloquim on Endocytobiology and Symbiosis
  • Place of Presentation: Kyoto Prefectural University, Kyoto, Japan.
  • Year and Date: 2016-09-10 – 2016-09-14
  • Int'l Joint Research
• [Presentation] プロティストワールドへの招待 (2016)
  • Author(s): 谷藤吾朗
  • Organizer: 日本進化学会
  • Place of Presentation: 東京工業大学、 東京.
  • Year and Date: 2016-08-25 – 2016-08-28
  • Invited
• [Presentation] 窒素固定始めました―Rhopalodia科珪藻に見る細胞内共生進化 (2016)
  • Author(s): 中山卓郎, 神川 龍馬, 谷藤 吾朗, 稲垣 祐司
  • Organizer: 日本進化学会
  • Place of Presentation: 東京工業大学、 東京.
  • Year and Date: 2016-08-25 – 2016-08-28
  • Invited
• [Presentation] The draft genome of Kipferlia bialata reveals that a gain of function conversely contributed to reductive evolution in Metamonada (2016)
  • Author(s): Tanifuji G., S. Takabayashi, K. Kume, M. Takagi, Y. Inagaki and T. Hashimoto
  • Organizer: Protist2016
  • Place of Presentation: Moscow State University, Moscow, Russia.
  • Year and Date: 2016-06-06 – 2016-06-10
  • Int'l Joint Research
• [Presentation] An evolutionary transition of chloroplast degradation in Euglenoids: Heterotorophic digestion to secondary plastid senescence (2016)
  • Author(s): Kashiyama Y., J. Kawahara, M. Maruyama, M. Kayama, M. Nakazawa, G. Tanifuji, A. Yokoyama, T. Ishikawa, H. Tamiaki and T. Suzaki
  • Organizer: Protist2016
  • Place of Presentation: Moscow State University, Moscow, Russia.
  • Year and Date: 2016-06-06 – 2016-06-10
  • Int'l Joint Research