Transcriptome Analysis of Female and Male Xiphophorus maculatus Jp 163 A

dc.contributor.authorZhang, Ziping
dc.contributor.authorWang, Yilei
dc.contributor.authorWang, Shuhong
dc.contributor.authorLiu, Jingtao
dc.contributor.authorWarren, Wesley C.
dc.contributor.authorMitreva, Makedonka
dc.contributor.authorWalter, Ronald B.
dc.description.abstractBackground: Xiphophorus models are important for melanoma, sex determination and differentiation, ovoviviparity and evolution. To gain a global view of the molecular mechanism(s) whereby gene expression may influence sexual dimorphism in Xiphophorus and to develop a database for future studies, we performed a large-scale transcriptome study. Methodology/Principal Findings: The 454-FLX massively parallel DNA sequencing platform was employed to obtain 742,771 and 721,543 reads from 2 normalized cDNA libraries generated from whole adult female and male X. maculatus Jp 163 A, respectively. The reads assembled into 45,538 contigs (here, a "contig" is a set of contiguous sequences), of which, 11,918 shared homology to existing protein sequences. These numbers estimate that the contigs may cover 53% of the total number of Xiphophorus transcriptome. Putative translations were obtained for 11,918 cDNA contigs, of which, 3,049 amino acid sequences contain Pfam domains and 11,064 contigs encode secretory proteins. A total of 3,898 contigs were associated with 2,781 InterPro (IPR) entries and 5,411 contigs with 132 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. There were 10,446 contigs annotated with 69,778 gene ontology (GO) terms and the three corresponding organizing principles. Fifty-four potential sex differentially expressed genes have been identified from these contigs. Eight and nine of these contigs were confirmed by real-time PCR as female and male predominantly expressed genes respectively. Based on annotation results, 34 contigs were predicted to be differentially expressed in male and female and 17 of them were also confirmed by real-time PCR. Conclusions/Significance: This is the first report of an annotated overview of the transcriptome of X. maculatus and identification of sex differentially expressed genes. These data will be of interest to researchers using the Xiphophorus model. This work also provides an archive for future studies in molecular mechanisms of sexual dimorphism and evolution, and can be used in comparative studies of other fish.
dc.description.departmentChemistry and Biochemistry
dc.format.extent6 pages
dc.format.medium1 file (.pdf)
dc.identifier.citationZhang, Z., Wang, Y., Wang, S., Liu, J., Warren, W., Mitreva, M., & Walter, R. B. (2011). Transcriptome analysis of female and male Xiphophorus maculatus Jp 163 A. PLoS One, 6(4), e18379.
dc.publisherPublic Library of Science
dc.rights.licenseThis work is licensed under a Creative Commons Attribution 4.0 International License.
dc.sourcePLoS One, 2011, Vol. 6, No. 4, Article e18379.
dc.subjectgene expression
dc.subjectgene ontologies
dc.subjectpolymerase chain reaction
dc.subjectgenome annotation
dc.subjecttranscriptome analysis
dc.subjectRNA sequencing
dc.subjectsex determination
dc.subjectChemistry and Biochemistry
dc.titleTranscriptome Analysis of Female and Male Xiphophorus maculatus Jp 163 A


Original bundle

Now showing 1 - 1 of 1
Thumbnail Image
107.97 KB
Adobe Portable Document Format

License bundle

Now showing 1 - 1 of 1
No Thumbnail Available
2.54 KB
Item-specific license agreed upon to submission