Abstract
Long terminal repeat (LTR) retrotransposon is the most abundant DNA component and is largely responsible for plant genome size variation. Although it has been studied in plant species, very limited data is available for cotton, the most important fiber and texture crop. In this study, we performed a comprehensive analysis of LTR retrotransposon families across four cotton species. In tetraploid Gossypium species, LTR retrotransposon families from the progenitor D genome had more copies in D-subgenome, and families from the progenitor A genome had more copies in A-subgenome. Some LTR retrotransposon families that insert after polyploid formation may still distribute the majority of its copies in one of the subgenomes. The data also shows that families of 10~200 copies are abundant and they have a great influence on the Gossypium genome size; on the contrary, a small number of high copy LTR retrotransposon families have less contribution to the genome size. Kimura distance distribution indicates that high copy number family is not a recent outbreak, and there is no obvious relationship between family copy number and the period of evolution. Further analysis reveals that each LTR retrotransposon family may have their own distribution characteristics in cotton.
Highlights
As the maternal parent[8,9]
In addition to Arabidopsis[41], great progress has been made in Long terminal repeat (LTR) retrotransposon studies in corn[37], soybean[42] and tomato[43]
We identified and classified LTR retrotransposon from genomes of G. barbadense, G. hirsutum, G. arboreum and G. raimondii
Summary
As the maternal parent[8,9]. Gossypium has undergone a threefold increase in genome size due to the accumulation of LTR retrotransposons since its origin[10]. Recent whole genome sequencing of two cultivated tetraploid species, island cotton (Gossypium barbadense)[13] and upland cotton (G. hirsutum)[14], and their two diploid ancestors G. arboretum[15], and G. raimondii[16,17] make it possible for detailed discovery and cross-species comparison of LTR retrotransposons elements at the whole genome level[13,15,16,17,18,19,20]. We annotated the LTR retrotransposon of four Gossypium species (G. barbadense, G. hirsutum, G. arboreum and G. raimondii) by using multiple de novo repeat prediction pipelines with a combination of known repeat elements from the RepBase database[21]. Our results led to the identification of several previously unknown features of Gossypium LTR retrotransposon families associating with copy number, genomic distribution, average element size, and the correlation with the genes. Our results highlight the importance of distinguishing LTR retrotransposon families instead of super families when assessing their impact on gene and genome evolution
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