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Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla)

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Abstract

Main conclusion

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.

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Abbreviations

MITEs:

Miniature inverted-repeat transposable elements

TIRs:

Terminal inverted repeats

TSDs:

Target site duplications

Mya:

Million years ago

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Authors and Affiliations

  1. The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People’s Republic of China

    Mingbing Zhou, Guiyun Tao, Peiyao Pi, Yihang Zhu, Youhuang Bai & Xianwen Meng

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  1. Mingbing Zhou
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  2. Guiyun Tao
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Correspondence to Mingbing Zhou.

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Funding

This work was supported by the grant from the National Natural Science Foundation of China (Grant nos. 31270645 and 31470615), and through Talents Program of Natural Science Foundation of Zhejiang Province (Grant no. LR12C16001).

Electronic supplementary material

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Supplementary Table S1 The sequences of primers for test PhTo25 insertion sites (DOCX 15 kb)

425_2016_2544_MOESM2_ESM.xls

Supplementary Table S2 The structural characteristics, sequences and copy number of the representative sequences of 362 MITE families (XLS 242 kb)

Supplementary Table S3 The AT content of 362 MITE family sequences (XLS 66 kb)

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Zhou, M., Tao, G., Pi, P. et al. Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla). Planta 244, 775–787 (2016). https://doi.org/10.1007/s00425-016-2544-0

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