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Discovery of MicroRNAs from Batrachuperus yenyuanensis Using Deep Sequencing and Prediction of Their Targets

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Abstract

MicroRNAs (miRNAs), a family of ~22-nucleotide non-coding single-stranded RNA molecules, are considered as key post-transcriptional regulators of gene expression that regulate various biological processes in living organism. Many miRNAs have been identified in animals; however, few have been reported in Hynobiidae species. The present study is aimed to identify a full repertoire of miRNAs in Batrachuperus yenyuanensis (Yenyuan stream salamander), which would significantly increase our knowledge of miRNAs in amphibians. A small RNA library was constructed from B. yenyuanensis and sequenced using deep sequencing. As a result, 1,717,751 clean reads were obtained, representing 356 known and 80 novel miRNAs. Additionally, expression levels of eight randomly selected miRNAs in B. yenyuanensis were confirmed using the stem-loop quantitative real-time reverse transcription PCR. In addition, 13,972 targets were predicted for these identified miRNAs, although the physiological functions of many of these targets remain unknown. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that the predicted targets are involved in a variety of physiological regulatory functions in B. yenyuanensis. These results provide useful information for further research on the miRNAs involved in the growth and development of B. yenyuanensis, as well as adaptation of this species to its high-altitude habitats.

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Abbreviations

GO:

gene ontology (analysis)

KEGG:

Kyoto Encyclopedia of Genes and Genomes (enrichment analysis)

miRNA (miR):

microRNA

nt:

nucleotide

PC:

predicted candidate

snRNA:

small nuclear RNA

snoRNA:

small nucleolar RNA

UTR:

untranslated region

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Authors and Affiliations

  1. College of Animal Science and Technology, Henan University of Science and Technology, 471023, Luoyang, China

    Y. Huang, J. Xiong & X. Sun

  2. Department of Forestry and Natural Resources, Purdue University, West Lafayette, 47907, Indiana, USA

    P. B. Brown

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  1. Y. Huang
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  2. J. Xiong
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  3. P. B. Brown
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  4. X. Sun
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Correspondence to Y. Huang or J. Xiong.

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Published in Russian in Biokhimiya, 2019, Vol. 84, No. 4, pp. 520–531.

Originally published in Biochemistry (Moscow) On-Line Papers in Press, as Manuscript BM18–202, December 24, 2018.

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Huang, Y., Xiong, J., Brown, P.B. et al. Discovery of MicroRNAs from Batrachuperus yenyuanensis Using Deep Sequencing and Prediction of Their Targets. Biochemistry Moscow 84, 380–389 (2019). https://doi.org/10.1134/S0006297919040059

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