Analysis of the skin transcriptome in two oujiang color varieties of common carp.
Analysis of the skin transcriptome in two oujiang color varieties of common carp.
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DOI：
10.1371/journal.pone.0090074
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Lu G
中科院分区：
文献类型：
--
作者：
Wang C;Wachholtz M;Wang J;Liao X;Lu G
体色和着色模式是维持生存和繁殖活动的重要表型性状。对瓯江彩鲤品种进行了研究。在中国浙江省分布范围较窄，有1,200多年的养殖历史，一直表现出多种体色模式。这些变体中不同颜色模式的分子机制尚不清楚。在实际应用中，必须开发能够区分不同表型的分子标记，以辅助选择育种。在这项探索性研究中，我们对瓯江鲤鱼的两个合并皮肤组织样本进行了Roche 454转录组测序，这两个样本对应于不同的颜色模式，红色带大黑点（RB）和全白色（WW），总共产生了737,525个序列读数。将本研究中获得的读段与从NCBI SRA数据库下载的鲤鱼Roche 454测序读段共同组装，得到43，923个isotig和546，676个singleton。发现超过31，445个（71.6%）同源体与nr蛋白数据库具有显著的BLAST匹配（E<1 e-10），对应于12，597个注释的斑马鱼基因。共有70，947个isotig和singleton（转录本）被Gene Ontology注释，60，221个转录本被发现具有相应的EC编号。在145个斑马鱼色素基因中，有117个在瓯江彩鲤转录组中得到同源序列，其中18个仅在单基因组中发现。我们的转录组分析揭示了瓯江鲤超过52，902个SNP，并确定了63个SNP标记，无论是RB还是WW都是唯一的。本研究获得的瓯江彩鲤转录组，沿着恢复了彩鲤的色素基因，并开发了彩鲤花色特异性分子标记，为进一步研究彩鲤花色的分子机制，通过分子标记辅助选择育种促进瓯江彩鲤的养殖提供了基础。
Body color and coloration patterns are important phenotypic traits to maintain survival and reproduction activities. The Oujiang color varieties of common carp (Cyprinus carpio var. color), with a narrow distribution in Zhejiang Province of China and a history of aquaculture for over 1,200 years, consistently exhibit a variety of body color patterns. The molecular mechanism underlying diverse color patterns in these variants is unknown. To the practical end, it is essential to develop molecular markers that can distinguish different phenotypes and assist selective breeding. In this exploratory study, we conducted Roche 454 transcriptome sequencing of two pooled skin tissue samples of Oujiang common carp, which correspond to distinct color patterns, red with big black spots (RB) and whole white (WW), and a total of 737,525 sequence reads were generated. The reads obtained in this study were co-assembled jointly with common carp Roche 454 sequencing reads downloaded from NCBI SRA database, resulting in 43,923 isotigs and 546,676 singletons. Over 31 thousand (31,445; 71.6%) isotigs were found with significant BLAST matches (E<1e-10) to the nr protein database, which corresponds to 12,597 annotated zebrafish genes. A total of 70,947 isotigs and singletons (transcripts) were annotated with Gene Ontology, and 60,221 transcripts were found with corresponding EC numbers. Out of 145 zebrafish pigmentation genes, orthologs for 117 were recovered in Oujiang color carp transcriptome, including 18 found only among singletons. Our transcriptome analysis revealed over 52,902 SNPs in Oujiang common carp, and identified 63 SNP markers that are putatively unique either for RB or WW. The transcriptome of Oujiang color varieties of common carp obtained through this study, along with the pigmentation genes recovered and the color pattern-specific molecular markers developed, will facilitate future research on the molecular mechanism of color patterns and promote aquaculture of Oujiang color varieties of common carp through molecular marker assisted-selective breeding.
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