Exploring the gonad transcriptome of two extreme male pigs with RNA-seq.
Exploring the gonad transcriptome of two extreme male pigs with RNA-seq.
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DOI：
10.1186/1471-2164-12-552
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发表时间：
2011-11-08
期刊：
影响因子：
4.4
通讯作者：
Pérez-Enciso M
中科院分区：
文献类型：
--
作者：
Esteve-Codina A;Kofler R;Palmieri N;Bussotti G;Notredame C;Pérez-Enciso M
尽管RNA-seq极大地推进了我们对复杂转录组景观的理解，例如在哺乳动物中发现的那些，但仍然缺乏对牲畜，特别是猪的完整RNA-seq研究。在这里，我们使用高通量RNA测序来深入了解猪雄性性腺中表达的poly-A RNA组分的特征。表达分析比较不同的定位方法和等位基因特异性表达的检测也在这项研究中进行了讨论。通过对两个表型极端的猪，一个伊比利亚猪和一个大白色猪的睾丸mRNA进行测序，我们在基因间区域发现了数百个未注释的蛋白质编码基因（PcG），其中一些基因与密切相关的物种存在同源性。有趣的是，我们还检测到2047个推定的长非编码RNA（lncRNA），其中包括469个与人类同源物。两种方法DEGseq和Cufflinks用于分析表达。DEGseq鉴定的表达基因比Cufflinks少15%，因为DEGseq仅利用明确映射的读段。此外，转录组的很大一部分是由转座因子（遇到14500个元件），如以前的研究报告。微阵列和RNA-seq技术之间的基因表达结果相对良好地相关（个体间r = 0.71）。大白色和伊比利亚之间的差异表达的基因表现出显着的配子生产和脂质代谢基因本体论类别的过度。最后，在~ 4%的杂合位点中检测到等位基因不平衡。RNA-seq是深入了解复杂转录组的强大工具。除了发现许多未纳米化的基因外，我们的研究还使我们能够确定相当一部分是由长的非编码转录本和转座因子组成的。它们的生物学作用仍有待在未来的研究中确定。就大白色猪和伊比利亚猪之间的表达差异而言，这些差异最大的是涉及精子发生和脂质代谢的基因，这与这两个品种之间的多产性和脂肪沉积的表型极端差异一致。
Although RNA-seq greatly advances our understanding of complex transcriptome landscapes, such as those found in mammals, complete RNA-seq studies in livestock and in particular in the pig are still lacking. Here, we used high-throughput RNA sequencing to gain insight into the characterization of the poly-A RNA fraction expressed in pig male gonads. An expression analysis comparing different mapping approaches and detection of allele specific expression is also discussed in this study. By sequencing testicle mRNA of two phenotypically extreme pigs, one Iberian and one Large White, we identified hundreds of unannotated protein-coding genes (PcGs) in intergenic regions, some of them presenting orthology with closely related species. Interestingly, we also detected 2047 putative long non-coding RNA (lncRNA), including 469 with human homologues. Two methods, DEGseq and Cufflinks, were used for analyzing expression. DEGseq identified 15% less expressed genes than Cufflinks, because DEGseq utilizes only unambiguously mapped reads. Moreover, a large fraction of the transcriptome is made up of transposable elements (14500 elements encountered), as has been reported in previous studies. Gene expression results between microarray and RNA-seq technologies were relatively well correlated (r = 0.71 across individuals). Differentially expressed genes between Large White and Iberian showed a significant overrepresentation of gamete production and lipid metabolism gene ontology categories. Finally, allelic imbalance was detected in ~ 4% of heterozygous sites. RNA-seq is a powerful tool to gain insight into complex transcriptomes. In addition to uncovering many unnanotated genes, our study allowed us to determine that a considerable fraction is made up of long non-coding transcripts and transposable elements. Their biological roles remain to be determined in future studies. In terms of differences in expression between Large White and Iberian pigs, these were largest for genes involved in spermatogenesis and lipid metabolism, which is consistent with phenotypic extreme differences in prolificacy and fat deposition between these two breeds.
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