Identification of novel and differentially expressed microRNAs in ovine ovary and testis tissues using solexa sequencing and bioinformatics

doi:10.1016/S2095-3119(14)60900-X

Journal of Integrative Agriculture ›› 2015, Vol. 14 ›› Issue (8): 1604-1616.DOI: 10.1016/S2095-3119(14)60900-X

Identification of novel and differentially expressed microRNAs in ovine ovary and testis tissues using solexa sequencing and bioinformatics

CHANG Wei-hua, ZHANG Yong, CHENG Zhang-rui, ZHAO Xing-xu, WANG Juan-hong, MA You-ji, HU Jun-jie, ZHANG Quan-wei

1、College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, P.R.China
2、College of Animal Science, Tarim University, Alar 843300, P.R.China
3、Royal Veterinary College, London University, Hatfield AL9 7TA, U K
4、College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, P.R.China

收稿日期:2014-06-30 出版日期:2015-08-05 发布日期:2015-08-06
通讯作者: ZHANG Yong, Mobile: +86-13893126652,Fax: +86-931-7631026, E-mail: zhangyong@gsau.edu.cn
作者简介:CHANG Wei-hua, E-mail: changweihua112@163.com;
基金资助:
The research was supported by the Department of Agriculture and Animal Husbandry of Gansu, China (2011zx08008-003), the Ministry of Agriculture of China (2009ZX08008008-002) and the Scientific Research Basic Business Expenses of Colleges and Universities, China (2011zx08008-003).

Identification of novel and differentially expressed microRNAs in ovine ovary and testis tissues using solexa sequencing and bioinformatics

CHANG Wei-hua, ZHANG Yong, CHENG Zhang-rui, ZHAO Xing-xu, WANG Juan-hong, MA You-ji, HU Jun-jie, ZHANG Quan-wei

1、College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, P.R.China
2、College of Animal Science, Tarim University, Alar 843300, P.R.China
3、Royal Veterinary College, London University, Hatfield AL9 7TA, U K
4、College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, P.R.China

Received:2014-06-30 Online:2015-08-05 Published:2015-08-06
Contact: ZHANG Yong, Mobile: +86-13893126652,Fax: +86-931-7631026, E-mail: zhangyong@gsau.edu.cn
About author:CHANG Wei-hua, E-mail: changweihua112@163.com;
Supported by:
The research was supported by the Department of Agriculture and Animal Husbandry of Gansu, China (2011zx08008-003), the Ministry of Agriculture of China (2009ZX08008008-002) and the Scientific Research Basic Business Expenses of Colleges and Universities, China (2011zx08008-003).

摘要/Abstract

摘要： MicroRNAs (miRNAs) are small, single stranded, non-coding RNA molecules, about 19–25 nucleotides in length, which regulate the development and functions of reproductive system of mammal. To discover novel miRNAs and identify the differential expression of them in ovine ovary and testis tissues, the study constructed two libraries by using next-generation sequencing technologies (Solexa high-throughput sequencing technique). As a result, 9 321 775 and 9 511 538 clean reads were obtained from the ovary and testis separately, which included 130 562 (90 genes of ovary) and 56 272 (85 genes of testis) of known miRNAs and 486 potential novel miRNAs reads. In this study, a total of 65 conserved miRNAs were significantly differentially expressed (P<0.01) between the two samples. Among them, 28 miRNAs were up-regulated and 3 miRNAs were down-regulated on ovary compared with testis. In addition, the known miRNAs with the highest expression level (5 miRNAs) and 30 novel miRNAs with the functions related to reproduction were validated using the real-time quantitative RT-PCR. Moreover, the gene ontology (GO) annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that differentially expressed miRNAs were involved in ovary and testis physiology, including signal transduction, gonad development, sex differentiation, gematogenesis, fertilization and embryo development. The results will be helpful to facilitate studies on the regulation of miRNAs during ruminant reproduction.

关键词: microRNA , ovary , testis , solexa sequencing , qRT-PCR

Abstract: MicroRNAs (miRNAs) are small, single stranded, non-coding RNA molecules, about 19–25 nucleotides in length, which regulate the development and functions of reproductive system of mammal. To discover novel miRNAs and identify the differential expression of them in ovine ovary and testis tissues, the study constructed two libraries by using next-generation sequencing technologies (Solexa high-throughput sequencing technique). As a result, 9 321 775 and 9 511 538 clean reads were obtained from the ovary and testis separately, which included 130 562 (90 genes of ovary) and 56 272 (85 genes of testis) of known miRNAs and 486 potential novel miRNAs reads. In this study, a total of 65 conserved miRNAs were significantly differentially expressed (P<0.01) between the two samples. Among them, 28 miRNAs were up-regulated and 3 miRNAs were down-regulated on ovary compared with testis. In addition, the known miRNAs with the highest expression level (5 miRNAs) and 30 novel miRNAs with the functions related to reproduction were validated using the real-time quantitative RT-PCR. Moreover, the gene ontology (GO) annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that differentially expressed miRNAs were involved in ovary and testis physiology, including signal transduction, gonad development, sex differentiation, gematogenesis, fertilization and embryo development. The results will be helpful to facilitate studies on the regulation of miRNAs during ruminant reproduction.

Key words: microRNA , ovary , testis , solexa sequencing , qRT-PCR

CHANG Wei-hua, ZHANG Yong, CHENG Zhang-rui, ZHAO Xing-xu, WANG Juan-hong, MA You-ji, HU Jun-jie, ZHANG Quan-wei. Identification of novel and differentially expressed microRNAs in ovine ovary and testis tissues using solexa sequencing and bioinformatics[J]. Journal of Integrative Agriculture, 2015, 14(8): 1604-1616.

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Identification of novel and differentially expressed microRNAs in ovine ovary and testis tissues using solexa sequencing and bioinformatics

Identification of novel and differentially expressed microRNAs in ovine ovary and testis tissues using solexa sequencing and bioinformatics

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