Systematic identification of long non-coding RNAs in pre-ovulatory ovarian follicles of goats

We deep sequenced and analyzed lncRNA using deep RNA sequencing (RNA-seq) in pre-ovulatory follicle samples of Macheng black goats and Boer goats. A total of 41.3 Gb lncRNA clean data were obtained and mapped to the goat reference genome with TopHat2. We first carried out a series of rigorous screening work and three analytical softwares (CPC, PFAM, and CNCI), and a total of 895 lncRNAs from 99,106 assembled transcripts were identified. These lncRNAs consisted of 88.0% long intergenic non-coding RNAs (lincRNAs), 12.0% antisense lncRNAs, virtually no intronic lncRNAs were detected. Sixty-seven lncRNAs were upregulated and 21 were downregulated in the pre-ovulatory follicles of the Boer group compared to their expression in the Macheng group.