title: Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla).
abstract: Moso bamboo MITEs were genome-wide identified first time, and data shows that MITEs contribute to the genomic diversity and differentiation of bamboo. Miniature inverted-repeat transposable elements (MITEs) are widespread in animals and plants. There are a large number of transposable elements in moso bamboo (Phyllostachys heterocycla var. pubescens) genome, but the genome-wide information of moso bamboo MITEs is not known yet. Here we identified 362 MITE families with a total of 489,592 MITE-related sequences, accounting for 4.74 % of the moso bamboo genome. The 362 MITE families are clustered into six known and one unknown super-families. Our analysis indicated that moso bamboo MITEs preferred to reside in or near the genes that might be involved in regulation of host gene expression. Of the seven super-families, three might undergo major expansion event twice, respectively, during 8-11 million years ago (mya) ago and 22-28 mya ago; two might experience a long expansion period from 6 to 13 mya. Almost 1/3 small RNAs might be derived from the MITE sequences. Some MITE families generate small RNAs mainly from the terminals, while others predominantly from the central region. Given the high copy number of MITEs, many siRNAs and miRNAs derived from MITE sequences and the preferential insertion of MITE into gene regions, MITEs may contribute to the genomic diversity and differentiation of bamboo.
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China. zhoumingbing@zafu.edu.cn.
authors.forename: Mingbing
authors.initials: M
authors.lastname: Zhou
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China.
authors.forename: Guiyun
authors.initials: G
authors.lastname: Tao
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China.
authors.forename: Peiyao
authors.initials: P
authors.lastname: Pi
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China.
authors.forename: Yihang
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China.
authors.forename: Youhuang
authors.initials: Y
authors.lastname: Bai
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China.
authors.forename: Xianwen
authors.initials: X
authors.lastname: Meng
mesh_terms: D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018745:Genome, Plant / Q000235:genetics*; D055029:Inverted Repeat Sequences / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics; D016254:Mutagenesis, Insertional; D006109:Poaceae / Q000235:genetics*; D011110:Polymorphism, Genetic; D034741:RNA, Small Interfering / Q000235:genetics; D013997:Time Factors
chemical_list: D004251:DNA Transposable Elements; D035683:MicroRNAs; D034741:RNA, Small Interfering
keywords: Amplification; Bamboo; Gene expression; Insertion date; Miniature inverted-repeat transposable elements (MITEs); Small RNA