Tissue-specific Temporal Exome Capture Revealed Muscle-specific Genes and SNPs in Indian Buffalo(Bubalus bubalis)

作     者：Subhash J.Jakhesara Viral B.Ahir Ketan B.Padiya Prakash G.Koringa Dharamshibhai N.Rank Chaitanya G.Joshi 

作者机构：Department of Animal BiotechnologyCollege of Veterinary Science&Animal HusbandryAnand Agricultural UniversityAnand 388001India Department of Animal Genetics and BreedingCollege of Veterinary Science&Animal HusbandryAnand Agricultural UniversityAnand 388001India 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2012年第10卷第2期

页      面：107-113页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 0905[农学-畜牧学] 08[工学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 0836[工学-生物工程] 090102[农学-作物遗传育种] 

主　　题：Hybridization Exome SNP, Bubalus bubalis Temporal gene expression 454 Sequencing 

摘      要：Whole genome sequencing of buffalo is yet to be completed, and in the near future it may not be possible to identify an exome （coding region of genome） through bioinformatics for designing probes to capture it. In the present study, we employed in solution hybridization to sequence tissue specific temporal exomes （TST exome） in buffalo. We utilized cDNA prepared from buffalo muscle tissue as a probe to capture TST exomes from the buffalo genome. This resulted in a prominent reduction of repeat sequences （up to 40%） and an enrichment of coding sequences （up to 60%）. Enriched targets were sequenced on a 454 pyro-sequencing platform, generating 101,244 reads contain- ing 24,127,779 high quality bases. The data revealed 40,100 variations, of which 403 were indels and 39,218 SNPs containing 195 nonsyn- onymous candidate SNPs in protein-coding regions. The study has indicated that 80% of the total genes identified from capture data were expressed in muscle tissue. The present study is the first of its kind to sequence TST exomes captured by use of cDNA molecules for SNPs found in the coding region without any prior sequence information of targeted molecules.