title: Isolation and characterization of putative functional long terminal repeat retrotransposons in the Pyrus genome.
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 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.
authors.affiliation: Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058 China ; Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403 China.
authors.forename: Shuang
authors.initials: S
authors.lastname: Jiang
authors.affiliation: Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021 China.
authors.forename: Danying
authors.initials: D
authors.lastname: Cai
authors.affiliation: Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058 China ; The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, The Ministry of Agriculture of China, Hangzhou, Zhejiang 310058 China ; Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, Zhejiang 310058 China.
authors.forename: Yongwang
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Department of Horticulture, Zhejiang University, Hangzhou, Zhejiang 310058 China ; The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, The Ministry of Agriculture of China, Hangzhou, Zhejiang 310058 China ; Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, Zhejiang 310058 China.
authors.forename: Yuanwen
authors.initials: Y
authors.lastname: Teng
keywords: Distribution; Genetic diversity; Insertion time; Pyrus; Retrotransposons