MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
PLoS One. 2012;7(10):e47442. doi: 10.1371/journal.pone.0047442. Epub 2012 Oct 11.
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 now available transcriptome data of L. vannamei are insufficient for research requirements, and have not been adequately assembled and annotated.
METHODOLOGY/PRINCIPAL FINDINGS: This 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/SIGNIFICANCE: The 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.
太平洋白对虾（Litopenaeus vannamei）是世界上主要的养殖虾种，已引起广泛关注，其相关研究需要越来越多的基因组背景知识。目前已有的白对虾转录组数据不能满足研究需求，且尚未进行充分的组装和注释。
方法/主要发现：本研究首次采用新一代高通量 DNA 测序技术——Solexa/Illumina GA II 法，分析了白对虾幼体的全基因组转录组。生成了超过 24 亿个原始数据，使用 SOAP denovo 软件组装了 109169 条平均长度为 396bp 的 unigenes。选择了 73505 条高质量序列的 unigenes进行注释分析，其中 37.80%可在 NCBI Nr 数据库中匹配，37.3%在 Swissprot 中匹配，44.1%在 TrEMBL 中匹配。使用 BLAST 和 BLAST2Go 软件，将 11153 个 unigenes分类到 25 个 COG 蛋白质同源群（COG）类别，将 8171 个 unigenes分配到 51 个 GO 功能组，将 18154 个 unigenes划分到 220 个 KEGG 途径。为了初步验证组装和注释结果的部分内容，选择了 12 条与许多胚胎发育相关基因同源的组装 unigenes进行 RT-PCR 电泳和 Sanger 测序分析，以及胚胎发育过程中的实时 PCR 表达谱分析。
结论/意义：使用新一代测序技术分析的白对虾转录组丰富了白对虾基因的信息，这将有助于我们了解甲壳动物的基因组背景，并促进对白对虾的研究。
