Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, China.
Comp Biochem Physiol Part D Genomics Proteomics. 2013 Jun;8(2):103-10. doi: 10.1016/j.cbd.2012.12.005. Epub 2013 Jan 19.
Spotted seal (Phoca largha) is categorized as a critically endangered species in China. The aim of this study was to investigate spotted seal 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 the spotted seal. The de novo assemblies yielded 354,014 contigs and 178,466 unigenes. In the transcriptome, 193 unigenes were assigned to defense mechanisms. Three unigenes encoded MHC class I and 17 unigenes encoded MHC class II. 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 the expected DNA fragments and detected significant polymorphism among 28 spotted seal individuals. These results would contribute to the understanding of the genetic makeup of spotted seal transcriptome and provide useful information for functional genomic research in this species.
斑海豹（Phoca largha）在中国被列为极度濒危物种。本研究旨在通过 Illumina 配对末端测序技术研究斑海豹的转录组。我们从斑海豹的混合肝脾组织中获得了总计 52,146,394 条读段。从头组装生成了 354,014 个 contigs 和 178,466 个 unigenes。在转录组中，193 个 unigenes被分配到防御机制。三个 unigenes编码 MHC Ⅰ类，17 个 unigenes编码 MHC Ⅱ类。此外，生物信息学分析显示共有 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构成，并为该物种的功能基因组研究提供有用信息。
