Abstract
A large proportion of the genome of ‘Suli’ pear (Pyrus pyrifolia) contains long terminal repeat retrotransposons (LTR-RTs), which suggests that LTR-RTs have played important roles in the evolution of Pyrus. Further analysis of retrotransposons, particularly of high-copy-number LTR-RTs in different species, will provide new insights into the evolutionary history of Pyrus. A total of 4912 putative LTR-RTs classified into 198 subfamilies were identified in the ‘Suli’ pear genome. Six Asian pear accessions, including cultivars and wild species, were resequenced. The comparison of copy number for each LTR-RT subfamily was evaluated in Pyrus accessions, and data showed up to four-fold differences for some subfamilies. This contrast suggests different fates for retrotransposon families in the evolution of Pyrus. Fourteen high-copy-number subfamilies were identified in Asian pears, and more than 50% of the LTR-RTs in the genomes of all Pyrus accessions were from these 14 identified LTR-RT subfamilies. Their average insertion time was 3.42 million years ago, which suggests that these subfamilies were recently inserted into the genome. Many homologous and specific retrotransposon insertion sites were identified in oriental and occidental pears, suggesting that the duplication of retrotransposons has occurred throughout almost the entire origin and evolution of Pyrus species. The LTR-RTs show high heterogeneity, and their copy numbers vary in different Pyrus species. Thus, our findings suggest that LTR-RTs are an important source of genetic variation among Pyrus species.
Highlights
Transposable elements (TEs) are mobile sequences that use different enzymatic strategies, such as reverse transcriptase, transposase and helicase, to move and insert in all eukaryote genomes [1].These elements could create insertion mutations and constitute a high percentage of plant genomes [2].Two main classes have been identified: Class I retrotransposons and Class II transposons [2].Retrotransposons flanked by long terminal repeats (LTR-RTs) are Class I elements that undergo replicative transposition, and they have been widely investigated in plants due to their distribution and contributions on genome organization [3,4]
Some of them were mapped to partial sequences of reference retrotransposons (Supplementary Figure S1), which were not full-length retrotransposons. These findings indicated that the mutation of LTR-RTs in the ‘Suli’ genome was universal and variable, similar to those observed in rice, strawberry and Masson pine [36,37,38]
A large number of LTR-RTs was identified from the Pyrus genome, and fourteen high-copynumber LTR-RTs were isolated in six Asian pear accessions
Summary
Transposable elements (TEs) are mobile sequences that use different enzymatic strategies, such as reverse transcriptase, transposase and helicase, to move and insert in all eukaryote genomes [1].These elements could create insertion mutations and constitute a high percentage of plant genomes [2].Two main classes have been identified: Class I retrotransposons and Class II transposons [2].Retrotransposons flanked by long terminal repeats (LTR-RTs) are Class I elements that undergo replicative transposition, and they have been widely investigated in plants due to their distribution and contributions on genome organization [3,4]. Transposable elements (TEs) are mobile sequences that use different enzymatic strategies, such as reverse transcriptase, transposase and helicase, to move and insert in all eukaryote genomes [1]. These elements could create insertion mutations and constitute a high percentage of plant genomes [2]. In Oryza australiensis, the transposition of retrotransposons has led to a rapid two-fold increase in genome size over the last 3 million years, suggesting that the rapid amplification of LTR-RTs plays a major evolutionary role in genome expansion [5]. A larger number of partial retrotransposons have been identified in rice genomes, suggesting that some pathways (e.g., illegitimate recombination) must exist for removing retrotransposons, corresponding to a rapid reduction in genome size [6]
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