Cite this paper:
LI Caijuan, TENG Teng, SHEN Fanfan, GUO Jinqiang, CHEN Yining, ZHU Chuankun, LING Qufei. Transcriptome characterization and SSR discovery in Squaliobarbus curriculus[J]. HaiyangYuHuZhao, 2019, 37(1): 235-244

Transcriptome characterization and SSR discovery in Squaliobarbus curriculus

LI Caijuan1, TENG Teng1, SHEN Fanfan1, GUO Jinqiang1, CHEN Yining1, ZHU Chuankun2, LING Qufei1
1 School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China;
2 School of Life Science, Huaiyin Normal University, Huaian 223300, China
Squaliobarbus curriculus is a eurythermic fish found mainly in East Asia. The natural germplasm resources of this species, an organism of potential economic aquacultural importance, have recently been threatened by overfishing and habitat degradation. The objective of this study was to obtain functional genomic resources and candidate microsatellite markers for future genetic observation and germplasm protection of S. curriculus. Illumina paired-end sequencing generated over 22.20 million clean reads, which were assembled into 204 027 transcripts with an average length of 1 457 bp. A total of 112 570 protein-coding sequences (55.17%) were predicted, 111 934 of which had significant matches in the NCBI nonredundant protein database. Overall, 60 450, 34 830, and 77 755 transcripts were assigned to Gene Ontology, Clusters of Orthologous Groups, and Eukaryotic Orthologous Groups categories, respectively. In addition, 44 781 transcripts (21.95%) were mapped to 230 KEGG pathways. A total of 51 426 candidate simple sequence repeat (SSR) markers were identified and used to design 36 149 PCR primer pairs. Fifty of these primer pairs were randomly selected for PCR validation in 32 S. curriculus specimens, which resulted in 25 pairs yielding the expected products. Further analysis revealed that 40% (10) of the 25 amplified loci were polymorphic. The transcriptomic profile and SSR repertoire obtained in this study should facilitate population genetic studies and germplasm resource protection of S. curriculus.
Key words:    Squaliobarbus curriculus|transcriptome sequencing|SSR markers   
Received: 2017-11-02   Revised: 2018-01-20
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