Abstract
BackgroundLong terminal repeat (LTR)-retrotransposons constitute 42.4 % of the genome of the ‘Suli’ pear (Pyrus pyrifolia white pear group), implying that retrotransposons have played important roles in Pyrus evolution. Therefore, further analysis of retrotransposons will enhance our understanding of the evolutionary history of Pyrus.ResultsWe identified 1836 LTR-retrotransposons in the ‘Suli’ pear genome, of which 440 LTR-retrotransposons were predicted to contain at least two of three gene models (gag, integrase and reverse transcriptase). Because these were most likely to be functional transposons, we focused our analyses on this set of 440. Most of the LTR-retrotransposons were estimated to have inserted into the genome less than 2.5 million years ago. Sequence analysis showed that the reverse transcriptase component of the identified LTR-retrotransposons was highly heterogeneous. Analyses of transcripts assembled from RNA-Seq databases of two cultivars of Pyrus species showed that LTR-retrotransposons were expressed in the buds and fruit of Pyrus. A total of 734 coding sequences in the ‘Suli’ genome were disrupted by the identified LTR-retrotransposons. Five high-copy-number LTR-retrotransposon families were identified in Pyrus. These families were rarely found in the genomes of Malus and Prunus, but were distributed extensively in Pyrus and abundance varied between species.ConclusionsWe identified potentially functional, full-length LTR-retrotransposons with three gene models in the ‘Suli’ genome. The analysis of RNA-seq data demonstrated that these retrotransposons are expressed in the organs of pears. The differential copy number of LTR-retrotransposon families between Pyrus species suggests that the transposition of retrotransposons is an important evolutionary force driving the genetic divergence of species within the genus.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-016-0058-8) contains supplementary material, which is available to authorized users.
Highlights
Long terminal repeat (LTR)-retrotransposons constitute 42.4 % of the genome of the ‘Suli’ pear (Pyrus pyrifolia white pear group), implying that retrotransposons have played important roles in Pyrus evolution
Our predictions focused on the existence of rt gene in LTR retrotransposons, which is essential for retrotransposon transposition
Our results showed that the copy number of retrotransposon families varied among Pyrus species
Summary
Long terminal repeat (LTR)-retrotransposons constitute 42.4 % of the genome of the ‘Suli’ pear (Pyrus pyrifolia white pear group), implying that retrotransposons have played important roles in Pyrus evolution. Repetitive sequences make up a large proportion of plant genomes. Jiang et al Mobile DNA (2016) 7:1 hypothesized to activate retrotransposons and induce duplication events in the genome [11,12,13]. Retrotransposons can insert within or near transcriptionally active regions and can cause mutations by disrupting genes, altering gene expression levels, or by driving genomic rearrangements [16, 17]. An autonomous retrotransposon is composed of two nearly sister LTR sequences flanked by target site duplications of usually 4–6 bp [1]. LTR-retrotransposons can be subdivided into the Ty1-copia and the Ty3-gypsy groups based on the order of the domains encoded within pol genes. The order in the Ty3-gypsy group is PR-RT-INT, and that in the Ty1-copia group is PR-INT-RT [2]
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