De Novo Transcriptome Assembly and Differential Gene Expression Profiling of Three Capra hircus Skin Types during Anagen of the Hair Growth Cycle
Despite that goat is one of the best nonmodel systems for villus growth studies and hair biology, limited gene resources associated with skin or hair follicles are available. In the present study, using Illumina/Solexa sequencing technology, we de novo assembled 130 million mRNA-Seq reads into a tot...
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| Format: | Article |
| Language: | English |
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Wiley
2013-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2013/269191 |
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| author | Teng Xu Xudong Guo Hui Wang Xiaoyuan Du Xiaoyu Gao Dongjun Liu |
| author_facet | Teng Xu Xudong Guo Hui Wang Xiaoyuan Du Xiaoyu Gao Dongjun Liu |
| author_sort | Teng Xu |
| collection | DOAJ |
| description | Despite that goat is one of the best nonmodel systems for villus growth studies and hair biology, limited gene resources associated with skin or hair follicles are available. In the present study, using Illumina/Solexa sequencing technology, we de novo assembled 130 million mRNA-Seq reads into a total of 49,115 contigs. Searching public databases revealed that about 45% of the total contigs can be annotated as known proteins, indicating that some of the assembled contigs may have previously uncharacterized functions. Functional classification by KOG and GO showed that activities associated with metabolism are predominant in goat skin during anagen phase. Many signaling pathways was also created based on the mapping of assembled contigs to the KEGG pathway database, some of which have been previously demonstrated to have diverse roles in hair follicle and hair shaft formation. Furthermore, gene expression profiling of three skin types identified ~6,300 transcript-derived contigs that are differentially expressed. These genes mainly enriched in the functional cluster associated with cell cycle and cell division. The large contig catalogue as well as the genes which were differentially expressed in different skin types provide valuable candidates for further characterization of gene functions. |
| format | Article |
| id | doaj-art-3a84b432dcfc40dea772e2b7ebb0a3d7 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2013-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-3a84b432dcfc40dea772e2b7ebb0a3d72025-02-03T01:20:23ZengWileyInternational Journal of Genomics2314-436X2314-43782013-01-01201310.1155/2013/269191269191De Novo Transcriptome Assembly and Differential Gene Expression Profiling of Three Capra hircus Skin Types during Anagen of the Hair Growth CycleTeng Xu0Xudong Guo1Hui Wang2Xiaoyuan Du3Xiaoyu Gao4Dongjun Liu5The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot, Inner Mongolia Autonomous Region 010021, ChinaThe Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot, Inner Mongolia Autonomous Region 010021, ChinaThe Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot, Inner Mongolia Autonomous Region 010021, ChinaThe Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot, Inner Mongolia Autonomous Region 010021, ChinaThe Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot, Inner Mongolia Autonomous Region 010021, ChinaThe Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot, Inner Mongolia Autonomous Region 010021, ChinaDespite that goat is one of the best nonmodel systems for villus growth studies and hair biology, limited gene resources associated with skin or hair follicles are available. In the present study, using Illumina/Solexa sequencing technology, we de novo assembled 130 million mRNA-Seq reads into a total of 49,115 contigs. Searching public databases revealed that about 45% of the total contigs can be annotated as known proteins, indicating that some of the assembled contigs may have previously uncharacterized functions. Functional classification by KOG and GO showed that activities associated with metabolism are predominant in goat skin during anagen phase. Many signaling pathways was also created based on the mapping of assembled contigs to the KEGG pathway database, some of which have been previously demonstrated to have diverse roles in hair follicle and hair shaft formation. Furthermore, gene expression profiling of three skin types identified ~6,300 transcript-derived contigs that are differentially expressed. These genes mainly enriched in the functional cluster associated with cell cycle and cell division. The large contig catalogue as well as the genes which were differentially expressed in different skin types provide valuable candidates for further characterization of gene functions.http://dx.doi.org/10.1155/2013/269191 |
| spellingShingle | Teng Xu Xudong Guo Hui Wang Xiaoyuan Du Xiaoyu Gao Dongjun Liu De Novo Transcriptome Assembly and Differential Gene Expression Profiling of Three Capra hircus Skin Types during Anagen of the Hair Growth Cycle International Journal of Genomics |
| title | De Novo Transcriptome Assembly and Differential Gene Expression Profiling of Three Capra hircus Skin Types during Anagen of the Hair Growth Cycle |
| title_full | De Novo Transcriptome Assembly and Differential Gene Expression Profiling of Three Capra hircus Skin Types during Anagen of the Hair Growth Cycle |
| title_fullStr | De Novo Transcriptome Assembly and Differential Gene Expression Profiling of Three Capra hircus Skin Types during Anagen of the Hair Growth Cycle |
| title_full_unstemmed | De Novo Transcriptome Assembly and Differential Gene Expression Profiling of Three Capra hircus Skin Types during Anagen of the Hair Growth Cycle |
| title_short | De Novo Transcriptome Assembly and Differential Gene Expression Profiling of Three Capra hircus Skin Types during Anagen of the Hair Growth Cycle |
| title_sort | de novo transcriptome assembly and differential gene expression profiling of three capra hircus skin types during anagen of the hair growth cycle |
| url | http://dx.doi.org/10.1155/2013/269191 |
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