Abstract
BackgroundPacific white shrimp (Litopenaeus vannamei), the major species of farmed shrimps in the world, has been attracting extensive studies, which require more and more genome background knowledge. The now available transcriptome data of L. vannamei are insufficient for research requirements, and have not been adequately assembled and annotated.Methodology/Principal FindingsThis is the first study that used a next-generation high-throughput DNA sequencing technique, the Solexa/Illumina GA II method, to analyze the transcriptome from whole bodies of L. vannamei larvae. More than 2.4 Gb of raw data were generated, and 109,169 unigenes with a mean length of 396 bp were assembled using the SOAP denovo software. 73,505 unigenes (>200 bp) with good quality sequences were selected and subjected to annotation analysis, among which 37.80% can be matched in NCBI Nr database, 37.3% matched in Swissprot, and 44.1% matched in TrEMBL. Using BLAST and BLAST2Go softwares, 11,153 unigenes were classified into 25 Clusters of Orthologous Groups of proteins (COG) categories, 8171 unigenes were assigned into 51 Gene ontology (GO) functional groups, and 18,154 unigenes were divided into 220 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. To primarily verify part of the results of assembly and annotations, 12 assembled unigenes that are homologous to many embryo development-related genes were chosen and subjected to RT-PCR for electrophoresis and Sanger sequencing analyses, and to real-time PCR for expression profile analyses during embryo development.Conclusions/SignificanceThe L. vannamei transcriptome analyzed using the next-generation sequencing technique enriches the information of L. vannamei genes, which will facilitate our understanding of the genome background of crustaceans, and promote the studies on L. vannamei.
Highlights
Pacific white shrimp, Litopenaeus vannamei, formerly Penaeus vannamei, belongs to the Penaeidae family of decapod crustaceans, is the major species of farmed shrimps in the world [1]
Using BLAST and BLAST2Go softwares, 11,153 unigenes were classified into 25 Clusters of Orthologous Groups of proteins (COG) categories, 8171 unigenes were assigned into 51 Gene ontology (GO) functional groups, and 18,154 unigenes were divided into 220 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways
The coding regions (CDSs) of the assembled .200 bp unigenes were determined by matching sequences against NCBI Nr, UniProtKB, KEGG, and COG databases in turn using the BLASTx algorithm of the BLAST software with a significant threshold of E value,0.00001
Summary
Litopenaeus vannamei, formerly Penaeus vannamei, belongs to the Penaeidae family of decapod crustaceans, is the major species of farmed shrimps in the world [1]. By May 2012, 162,993 ESTs from many organs and tissues have been released on Genbank These data have been used for cloning functional genes, selecting genetic molecular markers, and designing cDNA microarrays [2,9,10,11]. Because of the limitations of the traditional methods used for ESTs sequencing, the available transcriptome data of L. vannamei are still insufficient for research requirements relative to the size of its genome. Pacific white shrimp (Litopenaeus vannamei), the major species of farmed shrimps in the world, has been attracting extensive studies, which require more and more genome background knowledge. The available transcriptome data of L. vannamei are insufficient for research requirements, and have not been adequately assembled and annotated
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