The role of non-allelic gene conversion in the evolution of Transposable Elements

• Project/Area Number: 20K06761
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 45010:Genetics-related
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: FAWCETT JEFFREY 国立研究開発法人理化学研究所, 数理創造プログラム, 上級研究員 (50727394)
• Co-Investigator(Kenkyū-buntansha): 印南 秀樹 総合研究大学院大学, 先導科学研究科, 教授 (90444140)
• Project Period (FY): 2020-04-01 – 2024-03-31
• Project Status: Completed (Fiscal Year 2023)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2023: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2022: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2021: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2020: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
• Keywords: Transposable Elements / gene conversion / genome evolution / Transposable Element / Gene conversion / evolution

Outline of Research at the Start

We will test the role of non-allelic gene conversion between Transposable Elements (TEs) in the evolution of TEs, and in the evolution of regulatory networks using computer simulation and genomic data analyses.

Outline of Annual Research Achievements

Transposable Elements are thought to be key drivers of evolution and have most likely contributed to various evolutionary processes such as the rewiring of regulatory networks. We previously discussed how processes such as selection within TEs and non-allelic gene conversion between TEs contribute to the evolution of TEs and the evolution of host species. The drastic increase in whole-genome sequence data of various different species in the recent years provides the opportunity to understand the evolution of TEs and their contribution to genome evolution, in great detail that was not possible before. One of the major achievement has been our results on the evolution of TEs and their contribution to genome size evolution and centromere evolution in buckwheat species. We found that the differential activity of a small number of LTR retrotransposon families account for ~500 Mb difference in genome size between closely related species. We also found that the species specific activity of a particular LTR retrotransposon family of the CRM clade is associated with neocentromere, suggesting its role in speciation via centromere turnover. We are currently investigating the role of positive selection within this TE family that allowed its proliferation and association with centromeres, and the role of non-allelic gene conversion using molecular evolutionary analyses and by collaboration with experimental biologists.

Research Products

• [Journal Article] Genome sequencing reveals the genetic architecture of heterostyly and domestication history of common buckwheat (2023)
  • Author(s): Fawcett JA, Takeshima R, Kikuchi S, Yazaki E, Katsube-Tanaka T, Dong Y, Li M, Hunt HV, Jones MK, Lister DL, Ohsako T, Ogiso-Tanaka E, Fujii K, Hara T, Matsui K, Mizuno N, Nishimura K, Nakazaki T, Saito H, Takeuchi N, Ueno M, Matsumoto D, Norizuki M, Shirasawa K, Li C, Hirakawa H, Ota T, Yasui Y.
  • Journal Title: Nature Plants Volume: 9 Issue: 8 Pages: 1236-1251
  • DOI: 10.1038/s41477-023-01474-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] The role of gene conversion between Transposable Elements in rewiring regulatory systems (2021)
  • Author(s): Jeffrey Fawcett, Hideki Innan
  • Organizer: Annual Meeting of the Molecular Biology Society of Japan
  • Invited