Illumina-based de novo transcriptome sequencing and analysis of Chinese forest musk deer

Abstract

The Chinese forest musk deer (Moschus berezovskii Flerov) is an endangered artiodactyl mammal. The musk secreted by sexually mature males is highly valued for alleged pharmaceutical properties and perfume manufacturing. However, the genomic and transcriptomic resources of musk deer remain deficiently represented and poorly understood. Next-generation sequencing technique is an efficient method for generating an enormous amount of sequence data that can represent a large number of genes and their expression levels. In the present study, we used Illumina HiSeq technology to perform de novo assembly of heart and musk gland transcriptomes from the Chinese forest musk deer. A total of 239,383 transcripts and 176,450 unigenes were obtained, of which 37,329 unigenes were matched to known sequences in the NCBI nonredundant protein (Nr) database; 31,039 unigenes were assigned to 61 GO terms, and 11,782 to 332 KEGG pathways. Additionally, 592 and 2282 differentially expressed genes were found to be specifically expressed in the heart and musk gland, respectively. The abundant transcriptomic data generated in the present report will provide a comprehensive sequence resource for Chinese forest musk deer as well as lay down a foundation which will help in accelerating genetic and functional genomics research in this species.

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features

“…Other studies have shown that testosterone plays an important role in the seasonal development of musk glands [92], and oxytocin may regulate the function of muskrat scented glands by the locally expressed receptors [94]. Studies based on transcriptome [42,43] and genetic analysis [35] have shown that a considerable number of genes involved in musk metabolism pathways, such as steroid biosynthesis, flavone and flavonol biosynthesis, terpenoid backbone biosynthesis, aldosterone-regulated sodium reabsorption was played a significant role in musk secretion. In this study, we identified 21 up-regulation DEGs which were closely associated with metabolism and response of steroid, terpenoid and hormone which were coincident with the previous reports [35,42,43].…”

“…Studies based on transcriptome [42,43] and genetic analysis [35] have shown that a considerable number of genes involved in musk metabolism pathways, such as steroid biosynthesis, flavone and flavonol biosynthesis, terpenoid backbone biosynthesis, aldosterone-regulated sodium reabsorption was played a significant role in musk secretion. In this study, we identified 21 up-regulation DEGs which were closely associated with metabolism and response of steroid, terpenoid and hormone which were coincident with the previous reports [35,42,43]. Although there have been several studies on the secretion of musk, the genetic mechanisms of musk secretion are still poorly understood.…”

“…Then precise alignment aware of gene structure on the target DNA sequences was performed by GeneWise (v2.4.1) [106]. Thirdly, RNA-Seq data of mixture tissues, as well as previously reported RNA-Seq data [42] of musk gland (SRR2098995, SRR2098996) and heart (SRR2142357) were mapped to the genome by Tophat2 (v2.1.1) [107] (Additional file 1: Table S9). The transcripts were assembled with Cufflinks (v2.2.1) [108] and merged with cuffmerge.…”

“…The RNA sequencing of mixture tissues was performed with the standard Illumina HiSeq protocol (2 × 150 bp). The RNA-Seq data [42] of two musk glands (SRR2098995, SRR2098996) and one heart tissue (SRR2142357) were downloaded from SRA. The raw reads were cleaned with Trimmomatic (v0.36) [120] and mapped to the assembled genome with STAR (v020201) [54] (Additional file 1: Table S12), which showed a higher mapping efficiency than Tophat2 (v2.1.1) [107].…”

“…In recent years, there has been significant progress in the studies of musk deer ecology, taxonomy, evolution history by paleontological, morphological, ecological and ethological and molecular analysis [22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40]. The musk composition and secretory mechanism of musk have been explored by various aspects, including microsatellite, mtDNA marker, and transcriptome sequencing data [41][42][43][44][45][46]. Besides, the gut microbial communities have been illustrated by metagenome sequencing [9,47,48].…”