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Isolation and characterization of putative functional long terminal repeat retrotransposons in the Pyrus genome

文献类型： 外文期刊

作者： Jiang, Shuang 1 ; Cai, Danying 3 ; Sun, Yongwang 1 ; Teng, Yuanwen 1 ;

作者机构： 1.Zhejiang Univ, Dept Hort, Hangzhou 310058, Zhejiang, Peoples R China

2.Shanghai Acad Agr Sci, Forest & Fruit Tree Inst, Shanghai 201403, Peoples R China

3.Zhejiang Acad Agr Sci, Inst Hort, Hangzhou 310021, Zhejiang, Peoples R China

4.Minist Agr China, Key Lab Hort Plant Growth Dev & Qual Improvement, Hangzhou 310058, Zhejiang, Peoples R China

5.Zhejiang Prov Key Lab Hort Plant Integrat Biol, Hangzhou 310058, Zhejiang, Peoples R China

关键词： Retrotransposons;Insertion time;Distribution;Genetic diversity;Pyrus

期刊名称：MOBILE DNA （ 影响因子：4.06； 五年影响因子：5.82 ）

ISSN： 1759-8753

年卷期： 2016 年 7 卷

页码：

收录情况： SCI

摘要： 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 in Pyrus evolution. Therefore, further analysis of retrotransposons will enhance our understanding of the evolutionary history of Pyrus. 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 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. 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 between Pyrus species suggests that the transposition of retrotransposons is an important evolutionary force driving the genetic divergence of species within the genus.

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