Journal
GENOMICS PROTEOMICS & BIOINFORMATICS
Volume 18, Issue 3, Pages 321-332Publisher
ELSEVIER
DOI: 10.1016/j.gpb.2018.07.009
Keywords
Brassicaceae; Comparative genomics; Gypsy retrotransposon; Copia retrotransposon; Genome size evolution
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Funding
- Innovation Project for the Postdoctoral Researchersin China
- Open Research Fund Program of Beijing Key Lab of Plant Resource Research and Development, Beijing Technology and Business University
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The dynamic activity of transposable elements (TEs) contributes to the vast diversity of genome size and architecture among plants. Here, we examined the genomic distribution and transposition activity of long terminal repeat retrotransposons (LTR-RTs) in Arabidopsis thaliana (Ath) and three of its relatives, Arabidopsis lyrata (Aly), Eutrema salsugineum (Esa), and Schrenkiella parvula (Spa), in Brassicaceae. Our analyses revealed the distinct evolutionary dynamics of Gypsy retrotransposons, which reflects the different patterns of genome size changes of the four species over the past million years. The rate of Gypsy transposition in Aly is approximately five times more rapid than that of Ath and Esa, suggesting an expanding Aly genome. Gypsy insertions in Esa are strictly confined to pericentromeric heterochromatin and associated with dramatic centromere expansion. In contrast, Gypsy insertions in Spa have been largely suppressed over the last million years, likely as a result of a combination of an inherent molecular mechanism of preferential DNA removal and purifying selection at Gypsy elements. Additionally, species-specific clades of Gypsy elements shaped the distinct genome architectures of Aly and Esa.
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