De novo sequencing of the Antarctic krill (Euphausia superba) transcriptome to identify functional genes and molecular markers

Journal of genetics

CHUNYAN MA^1¹  HONGYU MA^1,2² 

[1] East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, People’s Republic of China^1;Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou 515063, People’s Republic of China^2

关键词: transcriptome resource;    de novo assembly;    gene annotation;    molecular markers;    Euphausia superba.;   

DOI  :  

学科分类：生物科学（综合）

来源: Indian Academy of Sciences

【 摘 要 】

To provide massive genetic resources for the Antarctic krill (Euphausia superba), we sequenced and analysed thetranscriptome by using high-throughput Illumina paired-end sequencing technology. A total of 77.1 million clean reads representing ∼11.0Gb data were generated. The average length of these reads was 142 bp. De novo assembly yielded 125,211 transcripts with a N50of 690 bp. Further analysis produced 106,250 unigenes, of which 31,683 were annotated based on protein homology searches againstprotein databases. Gene ontology analysis showed that ion binding, organic substance, metabolic process, and cell part were the mostabundantly used terms in molecular function, biological process and cellular component categories, respectively. In addition, 3067 unigenes were mapped onto 311 signal pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Finally, 15,224 simple sequence repeats were identified from 13,535 transcripts, and 103,593 single-nucleotide polymorphisms werefound from 21.6% of total transcripts. These genetic resources obtained in this study forms a good foundation for investigating genefunction, and evaluating population genetic diversity for this important Southern Ocean fisheries resource, E. superba.

【 授权许可】

CC BY