Characterization of pikeperch (Sander lucioperca) transcriptome and development of SSR markers. (June 2016)

• Record Type: Journal Article
• Authors: Han, Xiaofei; Ling, Qufei; Li, Caijuan; Wang, Guocheng; Xu, Zhengchao; Lu, Guoqing
• Is Part Of: Biochemical systematics and ecology. Volume 66(2016)
• Page Start: 188
• Page End: 195
• Publication Date: 2016-06
• Subjects: Sander lucioperca -- Illumina RNA-sequencing -- SSR markers; Chemotaxonomy -- Periodicals; Biochemical variation -- Periodicals; Ecology -- Periodicals; Biochemistry -- Periodicals; Ecology -- Periodicals; Chimiotaxinomie -- Périodiques; Variation biochimique -- Périodiques; Écologie -- Périodiques; 578.012
• DOI: 10.1016/j.bse.2016.04.001
• Languages: English
• ISSNs: 0305-1978

Abstract

Abstract: The pikeperch ( Sander lucioperca L.) is one of the most economically important freshwater species and has been recently explored as a potential candidate for aquaculture. To facilitate pikeperch research, we sequenced its transcriptome and developed a set of microsatellite markers. We conducted Illumina RNA-sequencing and obtained over 50 million reads from a pooled cDNA library of different tissues. The clean reads were de novo assembled into 56, 746 transcripts, with an average length of 1474 bp. The annotation analysis demonstrated 37, 386 transcripts (65.9%) with homologous sequences in the NCBI Nr protein database. Of these annotated transcripts, 18, 576 sequences were successfully assigned into Gene Ontology (GO) terms, 23, 566 transcripts into the Cluster of Orthologous Groups (COG), and 12, 081 transcripts to 322 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Totally, 16, 368 SSRs (≥10 bp) were detected from 11, 921 unigenes. The validation of randomly selected 300 SSR markers demonstrated 87.0% of the markers can be successfully amplified, suggesting RNA-Seq is an efficient tool for the development of molecular markers. This study provides not only a valuable transcriptomic resource, but also a set of SSR markers for basic as well as applied research in pikeperch. Highlights: Over 50 million reads were generated from Illumina HiSeq 2000 and assembled into more than 56 thousand transcripts. 66% of total transcripts were found with homologs in public protein databases. Over 18 thousand transcripts were annotated with GO terms and more than 12 thousand transcripts to KEGG pathways. More than 16 thousand SSR markers were identified with 300 randomly selected SSRs validated. The transcriptomic resource and SSR markers will facilitate pikeperch aquaculture improvement and research.