Isolation and characterization of putative functional long terminal repeat retrotransposons in the Pyrus genome. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Jiang, Shuang; Cai, Danying; Sun, Yongwang; Teng, Yuanwen
• Is Part Of: Mobile DNA. Volume 7:Issue 1(2016)
• Page Start: 1
• Page End: 10
• Publication Date: 2016-12
• Subjects: Retrotransposons -- Insertion time -- Distribution -- Genetic diversity -- Pyrus; Mobile genetic elements -- Periodicals; Genomics -- Periodicals; 572.869
• DOI: 10.1186/s13100-016-0058-8
• Languages: English
• ISSNs: 1759-8753

Abstract

Abstract Background 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 inPyrus evolution. Therefore, further analysis of retrotransposons will enhance our understanding of the evolutionary history ofPyrus . Results We 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 ofPyrus species showed that LTR-retrotransposons were expressed in the buds and fruit ofPyrus . 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 inPyrus . These families were rarely found in the genomes ofMalus andPrunus, but were distributed extensively inPyrus and abundance varied between species. Conclusions We 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 betweenPyrus species suggests that the transposition of retrotransposons is an important evolutionary force driving the genetic divergence of species within the genus.