De novo assembly of Chinese forest musk deer (Moschus berezovskii) transcriptome from Next-Generation mRNA Sequencing
- Published
- Accepted
- Subject Areas
- Agricultural Science, Bioinformatics, Genetics, Genomics, Zoology
- Keywords
- Chinese forest musk deer (Moschus berezovskii), Transcriptome, mRNA-seq, De novo assembly
- Copyright
- © 2016 Xu et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. De novo assembly of Chinese forest musk deer (Moschus berezovskii) transcriptome from Next-Generation mRNA Sequencing. PeerJ Preprints 4:e2252v1 https://doi.org/10.7287/peerj.preprints.2252v1
Abstract
Musk secretion in male musk deer is regarded as a propitious mode of sexual election to attract a greater number of females. However, the genetic mechanisms of musk secretion are still poorly understood and unresolved making it necessary to elucidate the possible genetic mechanisms of musk formation. In the present study, we used heart and musk gland tissues from a male musk deer for next-generation mRNA sequencing, integrated with de novo assembly, unigenes annotation and differentially expressed genes analysis. A total of 239,383 transcripts and 208,730 unigenes were obtained from 2 pooled RNA samples. Annotated analysis indicated steroid compound metabolism (steroid biosynthesis, steroid hormone biosynthesis, aldosterone-regulated sodium reabsorption, terpenoid backbone biosynthesis) related to musk formation were annotated to many pathways; relevant genes were identified as well. In addition, 8,986 differentially expressed genes (6,068 up- and 2,198 down-regulated) between heart and musk gland were identified, among them, steroid component metabolism were abundant. Further exploration of functional enrichment analysis showed that pathways involved in musk secretion were up-regulated in musk gland compared with heart, especially steroid biosynthesis and terpenoid backbone biosynthesis whose metabolic productions were key components of musk. We identified several candidate genes such as DHCR7, DHCR24, NSDHL, CYP3A5, FDFT1, FDPS and HMGCL which were closely involved in metabolism of steroid, terpenoid and ketone bodies. Our data are expected to represent the most comprehensive sequence resource available for the forest musk deer so far, and provide a basis for further research on molecular genetics and functional genomics of musk secretion.
Author Comment
This is a preprint submission to PeerJ Preprints.
Supplemental Information
Figure 1 Length distribution of assembled transcripts of Moschus berezovskii
Figure 1 Length distribution of assembled transcripts of Moschus berezovskii
Figure 2 SNP density (panel A and B) and mutation spectrum (panel C and D) of heart and musk gland of Moschus berezovskii
Figure 2 SNP density (panel A and B) and mutation spectrum (panel C and D) of heart and musk gland of Moschus berezovskii
Figure 3 FPKM boxplot and DEGs of heart and musk gland of Moschus berezovskii. (A) Log2(FPKM) values of two different tissues
Figure 3 FPKM boxplot and DEGs of heart and musk gland of Moschus berezovskii. (A) Log2(FPKM) values of two different tissues. Tentacles express the range of maximum and minimum value of expression quantity, the boxes express 25%-75% of log2(FPKM), and the black lines in the box express the median. (B) The up- and down-regulated DEGs identified between heart and musk gland
Figure 4 DEGs of heart and musk gland of Moschus berezovskii
Figure 4 DEGs of heart and musk gland of Moschus berezovskii
Figure 5 TOP 5 pathways with the largest number of DEGs enriched for up- (blue bars) and down-regulated(red bars) of Moschus berezovskii
Figure 5 TOP 5 pathways with the largest number of DEGs enriched for up- (blue bars) and down-regulated(red bars) of Moschus berezovskii able
Figure 6 The KEGG pathways enriched for the differentiated expression genes between the heart and musk gland of Moschus berezovskii
Figure 6 The KEGG pathways enriched for the differentiated expression genes between the heart and musk gland of Moschus berezovskii
Figure S1 Statistics of unigenes annotated in different databases
Figure S1 Statistics of unigenes annotated in different databases
Table S1. Percentage of homologous hits of the Moschus berezovskii transcripts to other species
Table S1. Percentage of homologous hits of the Moschus berezovskii transcripts to other species
Table S2. The functional GO categories enriched for the differentiated expression genes between the heart and musk gland
Table S2. The functional GO categories enriched for the differentiated expression genes between the heart and musk gland