TY - JOUR
T1 - Characterization of pikeperch (Sander lucioperca) transcriptome and development of SSR markers
AU - Han, Xiaofei
AU - Ling, Qufei
AU - Li, Caijuan
AU - Wang, Guocheng
AU - Xu, Zhengchao
AU - Lu, Guoqing
N1 - Funding Information:
We appreciate great advice and comments from Dr. Moli Huang and Gaochuan Zhang at Soochow University, China. This work was financially supported by Scientific Fund of Jiangsu Province ( BY2015039-10 ), Scientific Fund of Changshu Science and Technology Bureau ( CN201408 ) and the Priority Academic Program Development of Jiangsu Higher Education Institutions, China.
Publisher Copyright:
© 2016 Elsevier Ltd.
PY - 2016/6/1
Y1 - 2016/6/1
N2 - 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.
AB - 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.
KW - Illumina RNA-sequencing
KW - SSR markers
KW - Sander lucioperca
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U2 - 10.1016/j.bse.2016.04.001
DO - 10.1016/j.bse.2016.04.001
M3 - Article
AN - SCOPUS:84963517831
VL - 66
SP - 188
EP - 195
JO - Biochemical Systematics and Ecology
JF - Biochemical Systematics and Ecology
SN - 0305-1978
ER -