title: Functional marker detection and analysis on a comprehensive transcriptome of large yellow croaker by next generation sequencing.
abstract: Large yellow croaker (Larimichthys crocea) is an important economic fish in China and Eastern Asia. Because of the exhaustive fishing and overdense aquaculture, the wild population and the mariculture of the species are facing serious challenges on germplasm degeneration and susceptibility to infectious disease agents. However, a comprehensive transcriptome from multi-tissues of the species has not been reported and functional molecular markers have not yet been detected and analyzed. In this work, we applied RNA-seq with the Illumina Hiseq2000 platform for a multi-tissue sample of large yellow croaker and assembled the transcriptome into 88,103 transcripts. Of them, 52,782 transcripts have been successfully annotated by nt/nr, InterPro, GO and KEGG database. Comparing with public fish proteins, we have found that 34,576 protein coding transcripts are shared in large yellow croaker with zebrafish, medaka, pufferfish, and stickleback. For functional markers, we have discovered 1,276 polymorphic SSRs and 261, 000 SNPs. The functional impact analysis of SNPs showed that the majority (~75%) of small variants cause synonymous mutations in proteins, followed by variations in 3' UTR region. The functional enrichment analysis illuminated that transcripts involved in DNA bindings, enzyme activities, and signal pathways prominently exhibit less single-nucleotide variants but genes for the constituent of the muscular tissue, the cytoskeleton, and the immunity system contain more frequent SNP mutations, which may reflect the structural and functional selections of the translated proteins. This is the first work for the high-throughput detection and analysis of functional polymorphic SSR and SNP markers in a comprehensive transcriptome of large yellow croaker. Our study provides valuable transcript sequence and functional marker resources for the quantitative trait locus (QTL) identification and molecular selection of the species in the research community.
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China.
authors.forename: Shijun
authors.initials: S
authors.lastname: Xiao
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China.
authors.forename: Zhaofang
authors.initials: Z
authors.lastname: Han
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China.
authors.forename: Panpan
authors.initials: P
authors.lastname: Wang
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China.
authors.forename: Fang
authors.initials: F
authors.lastname: Han
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Jiongtang
authors.initials: J
authors.lastname: Li
authors.affiliation: Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China.
authors.forename: Zhi Yong
authors.initials: ZY
authors.lastname: Wang
mesh_terms: D000818:Animals; D029941:Fish Proteins / Q000235:genetics; D005399:Fishes / Q000235:genetics; D020869:Gene Expression Profiling; D063990:Gene Ontology; D005819:Genetic Markers; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D010473:Perciformes / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D059467:Transcriptome
chemical_list: D029941:Fish Proteins; D005819:Genetic Markers