Non-coding transcriptome maps across twenty tissues of Korean black chicken, Yeonsan Ogye

Abstract

The Yeonsan Ogye (Ogye) is the rare chicken breed populated in Korean peninsula, which has a unique black-color appearance of entire body including feather, skin, comb, eyes, shank, and claws. Although some protein-coding genes related to the unique feature have been examined, none of non-coding elements were globally investigated. In this study, high-throughput RNA sequencing (RNA-seq) and reduced representation bisulfite sequencing (RRBS) were performed to construct whole non-coding transcriptome maps across twenty different tissues of Ogye. The resulting maps included 6900 long non-coding RNA (lncRNA) genes (9529 transcripts) comprising 1290 known and 5610 novel lncRNA genes. Comparing to lncRNAs previously annotated in galllus gallus red junglefowl, the considerable number were either fragments of protein-coding genes or not expressed in Ogye tissues. Newly annotated Ogye lncRNA genes showed a tissue-specific expression and a simple gene structures constituting with 2 or 3 exons, as previously reported. Systematic analyses of sequencing data and other genomic data demonstrated that about 39% tissue-specific lncRNAs displayed functional evidences. Particularly, HSF2-associated lncRNAs were discovered as ones functionally linked to protein-coding genes specifically expressed in black skins (skin, shank, and comb), tended to be more syntenically conserved in mammals, and were differentially expressed in black tissues against white tissues. Our findings and resulting maps provide not only a comprehensive catalogue of lncRNAs but also a set of functional lncRNAs that will facilitate understanding non-coding genome regulating unique phenotypes and future use of genomic-breeding of chicken.