title: Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.).
abstract: 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) (∼20% in pear); 2) intact copies and solo LTRs with or without target site duplications are both common (∼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.
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Yin
authors.affiliation: Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
authors.forename: Jianchang
authors.initials: J
authors.lastname: Du
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China.
authors.forename: Leiting
authors.initials: L
authors.lastname: Li
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China.
authors.forename: Cong
authors.initials: C
authors.lastname: Jin
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China.
authors.forename: Lian
authors.initials: L
authors.lastname: Fan
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China.
authors.forename: Meng
authors.initials: M
authors.lastname: Li
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, China slzhang@njau.edu.cn.
authors.forename: Shaoling
authors.initials: S
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D019143:Evolution, Molecular; D018745:Genome, Plant; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D031989:Pyrus / Q000235:genetics*; D011995:Recombination, Genetic; D018626:Retroelements; D027824:Rosaceae / Q000235:genetics; D020079:Terminal Repeat Sequences
chemical_list: D018626:Retroelements
keywords: Cassandra retrotransposon; Rosaceae; TRIM; amplification; pear; recombination