title: Transcriptome analysis of the Capra hircus ovary.
abstract: BACKGROUND
  Capra hircus is an important economic livestock animal, and therefore, it is necessary to discover transcriptome information about their reproductive performance. In this study, we performed de novo transcriptome sequencing to produce the first transcriptome dataset for the goat ovary using high-throughput sequencing technologies. The result will contribute to research on goat reproductive performance.
  
  
  RESULTS
  RNA-seq analysis generated more than 38.8 million clean paired end (PE) reads, which were assembled into 80,069 unigenes (mean size = 619 bp). Based on sequence similarity searches, 64,824 (60.6%) genes were identified, among which 29,444 and 11,271 unigenes were assigned to Gene Ontology (GO) categories and Clusters of Orthologous Groups (COG), respectively. Searches in the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG) showed that 27,766 (63.4%) unigenes were mapped to 258 KEGG pathways. Furthermore, we investigated the transcriptome differences of goat ovaries at two different ages using a tag-based digital gene expression system. We obtained a sequencing depth of over 5.6 million and 5.8 million tags for the two ages and identified a large number of genes associated with reproductive hormones, ovulatory cycle and follicle. Moreover, many antisense transcripts and novel transcripts were found; clusters with similar differential expression patterns, enriched GO terms and metabolic pathways were revealed for the first time with regard to the differentially expressed genes.
  
  
  CONCLUSIONS
  The transcriptome provides invaluable new data for a functional genomic resource and future biological research in Capra hircus, and it is essential for the in-depth study of candidate genes in breeding programs.
authors.affiliation: Chongqing Engineering Research Center for Herbivores Resource Protection and Utilisation, Southwest University, Chongqing, China.
authors.forename: Zhong Quan
authors.initials: ZQ
authors.lastname: Zhao
authors.affiliation: Chongqing Engineering Research Center for Herbivores Resource Protection and Utilisation, Southwest University, Chongqing, China.
authors.forename: Li Juan
authors.initials: LJ
authors.lastname: Wang
authors.affiliation: Chongqing Engineering Research Center for Herbivores Resource Protection and Utilisation, Southwest University, Chongqing, China.
authors.forename: Xiao Wei
authors.initials: XW
authors.lastname: Sun
authors.affiliation: Genetic Engineering and Stem Cell Biology Laboratory, Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, South Korea.
authors.forename: Jiao Jiao
authors.initials: JJ
authors.lastname: Zhang
authors.affiliation: Chongqing Engineering Research Center for Herbivores Resource Protection and Utilisation, Southwest University, Chongqing, China.
authors.forename: Yong Ju
authors.initials: YJ
authors.lastname: Zhao
authors.affiliation: Chongqing Engineering Research Center for Herbivores Resource Protection and Utilisation, Southwest University, Chongqing, China.
authors.forename: Ri Su
authors.initials: RS
authors.lastname: Na
authors.affiliation: Chongqing Engineering Research Center for Herbivores Resource Protection and Utilisation, Southwest University, Chongqing, China.
authors.forename: Jia Hua
authors.initials: JH
authors.lastname: Zhang
mesh_terms: D000818:Animals; D005260:Female; D020869:Gene Expression Profiling / Q000662:veterinary*; D006041:Goats / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing / Q000662:veterinary; D010053:Ovary / Q000254:growth & development / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000662:veterinary; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger
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