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Comparative Genomic Analysis Reveals Multiple Long Terminal Repeats, Lineage-Specific Amplification, and Frequent Interelement Recombination for Cassandra Retrotransposon in Pear (Pyrus bretschneideri Rehd.)

文献类型： 外文期刊

作者： Yin, Hao 1 ; Du, Jianchang 2 ; Li, Leiting 1 ; Jin, Cong 1 ; Fan, Lian 1 ; Li, Meng 1 ; Wu, Jun 1 ; Zhang, Shaoling 1 ;

作者机构： 1.Nanjing Agr Univ, Coll Hort, State Key Lab Crop Genet & Germplasm Enhancement, Nanjing, Jiangsu, Peoples R China

2.Jiangsu Acad Agr Sci, Inst Ind Crops, Bioinformat Grp, Nanjing, Jiangsu, Peoples R China

关键词： Cassandra retrotransposon;TRIM;amplification;recombination;pear;Rosaceae

期刊名称：GENOME BIOLOGY AND EVOLUTION （ 影响因子：3.416； 五年影响因子：4.079 ）

ISSN： 1759-6653

年卷期： 2014 年 6 卷 6 期

页码：

收录情况： SCI

摘要： Cassandra transposable elements belong to a specific group of terminal-repeat retrotransposons in miniature (TRIM). Although Cassandra TRIM elements have been found in almost all vascular plants, detailed investigations on the nature, abundance, amplification timeframe, and evolution have not been performed in an individual genome. We therefore conducted a comprehensive analysis of Cassandra retrotransposons using the newly sequenced pear genome along with four other Rosaceae species, including apple, peach, mei, and woodland strawberry. Our data reveal several interesting findings for this particular retrotransposon family: 1) A large number of the intact copies contain three, four, or five long terminal repeats (LTRs) (similar to 20% in pear); 2) intact copies and solo LTRs with or without target site duplications are both common (similar to 80% vs. 20%) in each genome; 3) the elements exhibit an overall unbiased distribution among the chromosomes; 4) the elements are most successfully amplified in pear (5,032 copies); and 5) the evolutionary relationships of these elements vary among different lineages, species, and evolutionary time. These results indicate that Cassandra retrotransposons contain more complex structures (elements with multiple LTRs) than what we have known previously, and that frequent interelement unequal recombination followed by transposition may play a critical role in shaping and reshaping host genomes. Thus this study provides insights into the property, propensity, and molecular mechanisms governing the formation and amplification of Cassandra retrotransposons, and enhances our understanding of the structural variation, evolutionary history, and transposition process of LTR retrotransposons in plants.

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[1]Development of a novel and efficient strategy for practical identification of Pyrus spp (Rosaceae) cultivars using RAPD fingerprints. Lin, J.,Chang, Y. H.,Wang, X. C.,Fang, J. G.,Wang, X. C.,Fang, J. G.. 2011

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[3]Genome-wide identification of pear HD-Zip gene family and expression patterns under stress induced by drought, salinity, and pathogen. Wang, Hong,Lin, Jing,Li, Xiao Gang,Chang, Youhong.

[4]Systematic selection and validation of appropriate reference genes for gene expression studies by quantitative real-time PCR in pear. Xu, Yuanyuan,Li, Hui,Li, Xiaogang,Lin, Jing,Wang, Zhonghua,Yang, Qingsong,Chang, Youhong.

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