Differential gene expression analysis between anagen and telogen of Capra hircus skin based on the de novo assembled transcriptome sequence

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• 作者：Teng Xu¹ ; ^{xutenggene@yahoo.com.cn} ; Xudong Guo¹ ; ^{xudguo@yahoo.com} ; Hui Wang ^{409479077@qq.com} ; Fei Hao ^cefw@163.com ; Xiaoyuan Du ^{1258304619@qq.com} ; Xiaoyu Gao ^{471682979@qq.com} ; Dongjun Liu ; ^{liudjimu@yahoo.cn}
• 关键词：CDS ; coding sequence ; SSR ; simple sequence repeat ; NR ; non-redundant protein database ; GO ; gene ontology ; KOG ; Eukaryotic Orthologous Groups of proteins ; KEGG ; Kyoto Encyclopedia of Gene and Genomes ; DEG ; differentially expressed gene ; RPKM ; reads per kil
• 刊名：Gene
• 出版年：2013
• 出版时间：10 May, 2013
• 年：2013
• 卷：520
• 期：1
• 页码：30-38
• 全文大小：1019 K

文摘

Capra hircus, an economically important livestock, plays an indispensable role in the world animal fiber industry. In the present study, using Illumina/Solexa high throughput sequencing technology, we sequenced and de novo assembled the goat skin transcriptome corresponding to the anagen and telogen of the hair growth cycle. Approximately 53 Mb of transcriptome sequences consisting of 57,040 high quality contigs was obtained. More than 8300 contigs were predicted to contain a full length coding sequence. Approximately 43 % of the total contigs were identified as harboring homologs of sequences from other organisms in the public database. Based on the assembled transcript-derived contigs, we identified about 7000 transcripts that were differentially expressed between the anagen and telogen libraries. These differentially expressed genes were mainly enriched in signal transduction mechanisms, extracellular structures and cytoskeleton from the KOG database and in ECM receptor interaction, focal adhesion and gap junction from the KEGG pathway database, indicating the essential roles of these genes may play in cell-to-cell and cell-to-matrix communications during the active hair growth phase. In addition, many signaling pathway associated ligands and/or receptors were also identified as up-regulated genes during the anagen phase compared with the telogen stage, suggesting that enhanced cross-talk among signaling transduction pathways may be required for anagen of the hair cycle. These differentially expressed genes, especially those that were over-represented in each of the functional clusters and biochemical pathways, provide valuable resources and opportunities for characterizing the gene functions associated with hair fiber growth as well as for breeding elite Cashmere goat species.