Genome-wide characteristics and evolution analysis of long terminal repeat retrotransposons in Phyllostachys edulis

Abstract

Objective This study aims to analyze the characteristics of long terminal repeat retrotransposons (LTR-REs) in moso bamboo genome, so as to promote the research on the function of LTR-REs in moso bamboo genome and the genetic diversity of bamboo resources. Method Based on bioinformatics methods, LTR retrotransposons in the second edition of moso bamboo genome were annotated and classified by LTRharvest and RepeatMakser software, and the distribution characteristics, evolution characteristics and insertion time of the obtained LTR retrotransposons were analyzed. Result A total of 1 014 565 LTR retrotransposons and 1 562 families were identified, accounting for 54.97% of moso bamboo genome. Among them, the ratio of solo LTR retrotransposons to intact LTR retrotransposons (S/F) was relatively high (about 1.77∶1.00), indicating that a higher frequency of illegitimate recombination and unbalanced recombination might have occurred in the LTR-REs of moso bamboo genome. LTR retrotransposons were divided into Ty1-copia and Ty3-gypsy superfamilies, and ten lineages included Tork, Reftrofit, Sire, Oryco, Del, Reina, Crm, Tat, Galadriel, and Athila. The preference of Ty1-copia and Ty3-gypsy superfamiles for PBS sites showed an opposite tendency. The longer LTR retrotransposons had longer LTR sequences and more complete structures. The insertion time of LTR retrotransposon in moso bamboo was mainly concentrated in the 0−2.0 Ma region, and it was still in a state of slow growth. Conclusion The high-quality assembly of the second edition of moso bamboo genome can better annotate and analyze the LTR retrotransposons in moso bamboo genome. The LTR harvest method based on structure prediction can more accurately predict the LTR retrotransposons of moso bamboo. The LTR retrotransposons of different lineages have different differentiation and amplification activities during evolution. LTR retrotransposons are generally in a state of continuous amplification, which is one of the reasons for the large genome of moso bamboo. [Ch, 3 fig. 3 tab. 52 ref.]