Characterization and analysis of the muscle transcriptome in black Tibetan sheep (Ovis aries) by hybrid sequencing of PacBio Iso-seq

Abstract

Black Tibetan sheep (Ovis aries) is a unique branch of Tibetan sheep in Qinghai province, which was used for wool and meat. The third-generation transcriptome was sequenced and compared with the sheep genome to explore the new transcriptome and genes of black Tibetan sheep. PacBio Iso-seq mixed cell sequencing was performed on longissimus dorsi muscle tissues of black Tibetan sheep at different ages. There was a total of 96596073037 bp base data of Iso-seq, with N50 2822 bp. Iso-seq sequencing depth was about 34.5. There were 36191 isoforms mapped to 8665 reference genes and there were 1846 novel isoforms and 25,680 new isoforms in black Tibetan sheep compared with sheep database. Among these transcripts, there were 25,323 new coding RNA and 1065 novel coding RNA, 357 new long non-coding RNA, and 781 novel long non-coding RNA. Using hmmscan compared isoforms to the animal transcription factor (TF) database, there were 519 and 156 isoforms respectively associated with ZF-C2H2 and TF family including TF-bZIP. The next family of transcription factors enriched in isoforms was bHLH, Homeobox, MYB, and others. All these results would provide a valuable genetic resource that could be further used for future genetics and genomics studies.