De novo assembly and characterization of skin transcriptome using RNAseq in sheep (Ovis aries)

Abstract

ABSTRACT. Wool is produced via synthetic processes of wool follicles, which are embedded in the skin of sheep. The development of new-generation sequencing and RNA sequencing provides new approaches that may elucidate the molecular regulation mechanism of wool follicle development and facilitate enhanced selection for wool traits through gene-assisted selection or targeted gene manipulation. We performed de novo transcriptome sequencing of skin using the Illumina Hiseq 2000 sequencing system in sheep (Ovis aries). Transcriptome de novo assembly was carried out via short-read assembly programs, including SOAPdenovo and ESTScan. The protein function, clusters of orthologous group function, gene ontology function, metabolic pathway analysis, and protein coding region prediction of unigenes were annotated by BLASTx, BLAST2GO, and ESTScan. More than 26,266,670 clean reads were collected and assembled into 79,741 unigene sequences, with a final assembly length of 35,447,962 nucleotides. A total of 22,164 unigenes were annotated, accounting for Y.J. Yue et al. 1372©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (1): 1371-1384 (2015) 36.27% of the total number of unigenes, which were divided into 25 classes belonging to 218 signaling pathways. Among them, there were 17 signal paths related to hair follicle development. Based on mass sequencing data of sheepskin obtained by RNA-Seq, many unigenes were identified and annotated, which provides an excellent platform for future sheep genetic and functional genomic research. The data could be used for improving wool quality and as a model for human hair follicle development or disease prevention.

Recent advances in understanding genetic variants associated with economically important traits in sheep (Ovis aries) revealed by high-throughput screening technologies

“…For example, several miRNAs (e.g., oar-miR-103-3p, oar-miR-148b-3p, oar-miR-320-3p, oar-miR-31-5p, oar-novel-1-5p, oar-novel-2-3p, miR-let-7, miR-199 and miR-200 families) were found to affect wool follicle development, and a large number of genes (e.g., KRTs, KRTAPs families, CST3, CSTB, S100A11, PPARD, CSTA, SIVA1, CCDC85B, FOXE1, VAX2, BAK1, ADRA1B, PKIA and HNF4A) were shown to be related to hair/ fleece development. In addition, earlier investigations indicated that several genes (e.g., DCT, MATP, TYR and TYRP1) played a central roles in coat color regulation and a few signaling pathways (Wnt, Jak-STAT, MAPK, Notch, TGF-β, Toll-like receptor and VEGF) were involved in the regulation of wool follicle bulb regression and regeneration [38][39][40][41] . Using Solexa sequencing (Illumina Genome Analyzer), Li et al identified 1910 known and 2261 novel mature miRNAs, and these miRNAs could have essential roles in telogen hair follicle development and growth, which are important for improving wool quality [77] .…”

Transcriptome Analysis of Three Sheep Intestinal Regions reveals Key Pathways and Hub Regulatory Genes of Large Intestinal Lipid Metabolism

“…Recently, several studies have reported the successful transcriptome sequencing of multiple tissues in sheep brain 15 , uterus 16 , skeletal muscle 17–19 , mammary gland 20 , milk 21 , rumen 22 , and skin 23 tissues. To the best of our knowledge, only two transcriptomic studies on sheep have recently been conducted on large intestine metabolism.…”

Transcriptome Analysis Reveals Skin Lipid Metabolism Related to Wool Diameter in Sheep

“…Yue et al . [7,8] performed de novo transcriptome sequencing of sheep skin and found fiber diameter was related to a few lipoic acid differentially expressed genes and antisense transcripts. However, no other studies have examined global gene expression in relation to wool fiber diameter.…”