Rapid Genome Evolution and Adaptation of Thlaspi arvense Mediated by Recurrent RNA-Based and Tandem Gene Duplications

• DOI: 10.3389/fpls.2021.772655
• Publication Date: 2022-01-04T08:20:00Z
• Authors: Yanting Hu; Xiaopei Wu; Guihua Jin; Junchu Peng; Rong Leng; Ling Li; Daping Gui; Chuanzhu Fan; Chengjun Zhang
• Keywords: Retrotransposon

Retrotransposons are the most abundant group of transposable elements (TEs) in plants, providing an extraordinarily versatile source genetic variation. Thlaspi arvense, a close relative model plant Arabidopsis thaliana with worldwide distribution, thrives from sea level to above 4,000 m elevation Qinghai-Tibet Plateau (QTP), China. Its strong adaptability renders it ideal system for studying adaptation extreme environments. However, how retrotransposons affect T. arvense genome evolution and is largely unknown. We report high-quality chromosome-scale assembly scaffold N50 59.10 Mb. Long terminal repeat (LTR-RTs) account 56.94% assembly, Gypsy superfamily TEs. The amplification LTR-RTs last six million years primarily contributed size expansion arvense. identified 351 retrogenes 303 genes flanked by LTRs, respectively. A comparative analysis showed that orthogroups containing those LTRs have higher percentage significantly expanded (SEOs), these SEOs possess more recent tandem duplicated genes. All present results indicate RNA-based gene duplication (retroduplication) accelerated subsequent homologous resulting family expansions, families were implicated growth, development, stress responses, which one pivotal factors arvense's harsh environment QTP regions. In conclusion, provides insights into retroduplication mediated mechanism