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利用 Illumina 配对末端测序技术对斑海豹 Phoca largha 转录组进行特征分析，并开发 SSR 标记。

Characterization of the spotted seal Phoca largha transcriptome using Illumina paired-end sequencing and development of SSR markers.

机构信息

Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China.

出版信息

Comp Biochem Physiol Part D Genomics Proteomics. 2012 Sep;7(3):277-84. doi: 10.1016/j.cbd.2012.05.001. Epub 2012 May 19.

DOI:10.1016/j.cbd.2012.05.001
PMID:22677091
Abstract

Next-generation sequencing provides a powerful new approach for developing functional genomic tools for non-model species. This study aims to investigate the spotted seal (Phoca largha) transcriptome by the approach of Illumina paired-end sequencing technology. We obtained a total of 52,146,394 reads for the mixed tissues of liver and spleen from spotted seal. The de novo assemblies yielded 354,014 contigs and 178,466 unigenes. In addition, bioinformatics analysis revealed a total of 4425 simple sequence repeats (SSRs). Fifty SSRs were randomly selected to validate amplification and determine the degree of polymorphism in the genomic DNA pools. Thirty-five primer pairs successfully amplified expected DNA fragments and detected significant polymorphism among 28 spotted seal individuals. These results contribute to the understanding of the genetic makeup of spotted seal transcriptome and provide useful information for functional genomic research in this species.

摘要

下一代测序为开发非模式物种的功能基因组工具提供了一种强大的新方法。本研究旨在通过 Illumina 配对末端测序技术研究斑海豹（Phoca largha）转录组。我们从斑海豹的混合肝脾组织中获得了总计 52,146,394 条读取。从头组装产生了 354,014 个 contigs 和 178,466 个 unigenes。此外，生物信息学分析揭示了总共 4425 个简单重复序列（SSRs）。随机选择了 50 个 SSR 来验证扩增并确定基因组 DNA 池的多态性程度。35 对引物成功扩增了预期的 DNA 片段，并在 28 只斑海豹个体中检测到显著的多态性。这些结果有助于了解斑海豹转录组的遗传组成，并为该物种的功能基因组研究提供有用信息。

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