Characterization and comparative analyses of muscle transcriptomes in Dorper and small-tailed Han sheep using RNA-Seq technique.
Characterization and comparative analyses of muscle transcriptomes in Dorper and small-tailed Han sheep using RNA-Seq technique.
复制标题
DOI：
10.1371/journal.pone.0072686
复制
发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Chen C
中科院分区：
文献类型：
--
作者：
Zhang C;Wang G;Wang J;Ji Z;Liu Z;Pi X;Chen C
羊是一种重要的家畜，也是许多医学相关研究的模型。对绵羊肌肉中基因表达的研究将大大促进我们对肌肉生长的理解。RNA-seq是最近通过高通量测序开发的转录组分析方法。尽管RNA-seq最近已广泛应用于各种生物体，但很少有RNA-seq研究在牲畜，特别是绵羊中进行。本研究分别从小尾寒羊（SH）和杜泊羊（DP）的肱二头肌中构建了两个cDNA文库。利用Illumina高通量测序技术和生物信息学技术确定转录物丰度和特征。对于SH和DP库，我们分别获得了50,264,608和52,794,216个高质量的读取。大约三分之二的读取可以映射到绵羊基因组。此外，还分别观察到40,481和38,851个潜在编码单核苷酸多态性（cSNP），其中两个样本之间共有59,139个cSNP坐标不同。共有5116个和5265个内参基因分别经历了13827次和15684次选择性剪接事件。在5′、3′或两端共扩增6,989个内参基因，发现123,678个新转录单位。在两个文库中共鉴定出1300个显著差异表达基因。这些结果表明，这两种动物的肌肉转录组存在许多差异。本研究进行了初步分析，为今后绵羊基因组研究奠定了基础。
The sheep is an important domestic animal and model for many types of medically relevant research. An investigation of gene expression in ovine muscle would significantly advance our understanding of muscle growth. RNA-seq is a recently developed analytical approach for transcriptome profiling via high-throughput sequencing. Although RNA-seq has been recently applied to a wide variety of organisms, few RNA-seq studies have been conducted in livestock, particularly in sheep. In this study, two cDNA libraries were constructed from the biceps brachii of one Small-tailed Han sheep (SH) and one Dorper sheep (DP). The Illumina high-throughput sequencing technique and bioinformatics were used to determine transcript abundances and characteristics. For the SH and DP libraries, we obtained a total of 50,264,608 and 52,794,216 high quality reads, respectively. Approximately two-thirds of the reads could be mapped to the sheep genome. In addition, 40,481 and 38,851 potential coding single nucleotide polymorphisms (cSNPs) were observed, respectively, of which a total of 59,139 cSNP coordinates were different between the two samples. Up to 5,116 and 5,265 respective reference genes had undergone 13,827 and 15,684 alternative splicing events. A total of 6,989 reference genes were extended at the 5’, 3’ or both ends, and 123,678 novel transcript units were found. A total of 1,300 significantly differentially expressed genes were identified between the two libraries. These results suggest that there are many differences in the muscle transcriptomes between these two animals. This study addresses a preliminary analysis and offers a foundation for future genomic research in the sheep.
登录
查看更多内容
通过双端 RNA 测序，对具有生长和脂肪沉积极端表型的全同胞对的三种组织中的猪转录组进行全局观察
影响因子：
4.4
作者：
Chen C;Ai H;Ren J;Li W;Li P;Qiao R;Ouyang J;Yang M;Ma J;Huang L
通讯作者：
Huang L
DOI：
10.1016/j.cbd.2010.12.002
发表时间：
2011-06-01
影响因子：
3
作者：
Faulconnier, Y.;Chilliard, Y.;Leroux, C.
通讯作者：
Leroux, C.
影响因子：
3.6
作者：
Graham, N. S.;May, S. T.;Parr, T.
通讯作者：
Parr, T.
影响因子：
4.4
作者：
Esteve-Codina A;Kofler R;Palmieri N;Bussotti G;Notredame C;Pérez-Enciso M
通讯作者：
Pérez-Enciso M
影响因子：
4.4
作者：
Byrne K;Vuocolo T;Gondro C;White JD;Cockett NE;Hadfield T;Bidwell CA;Waddell JN;Tellam RL
通讯作者：
Tellam RL