期刊
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS
卷 8, 期 2, 页码 103-110出版社
ELSEVIER SCIENCE INC
DOI: 10.1016/j.cbd.2012.12.005
关键词
Spotted seal (Phoca largha); Illumina paired-end sequencing; Expressed sequence tag (EST); Simple sequence repeat (SSR); Pinniped
资金
- National Natural Science Foundation of China [30972246]
- Public Science and Technology Research Funds Projects of Ocean [201105011]
- Liaoning Scientific Research Program of Ocean and Fisheries Department [200920]
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. (C) 2013 Elsevier Inc. All rights reserved.
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