Decipher the transcriptome of Litopenaeus vannamei by assembling ESTs and compare gene expression in different libraries

• Main Authors: Yi-Ching Lin, 林宜靜
• Other Authors: Chung-Yen Lin
• Format: Others
• Language: zh-TW
• Published: 2012
• Online Access: http://ndltd.ncl.edu.tw/handle/62251690231092365891

碩士 === 國立臺灣大學 === 漁業科學研究所 === 100 === The Pacific white shrimp, Litopenaeus vannamei, has became a more important animal in shrimp aquaculture. Although its genome has not been fully sequenced, this economically important species has attracted researchers for building a rich source of ESTs for benefiting both the basic biology and the applied science. Expressed Sequence Tags (ESTs), are short sequences derived from a batch-wise partial sequencing result of cDNA library, which may represents the relative expression level of transcripts in the library. It is an effective approach to get numerous sequences of protein coding genes of a species without previous knowing about the genome context. In this study, we collected 161,241 ESTs of white shrimp from public database. Reference sequences from two taxonomically closed species Daphnia pulex and Drosophila melanogaster were used for selecting subset for de novo assembling. Totally, 37,401 assembled sequences, including 16,886 contigs and 20,515 singletons, were obtained. Over 40% of the assemblies could be matched to homolog sequences in non-redundant protein database and/or protein domain feature in Pfam database. Six tissues including eyestalk, gills, hemocyte, hepatopancreas, lymphoid organ and nerve cord are the major tissue source of this collection. Assemblies were annotated and the expression level of each assembled contig/ singleton in each tissue was calculated by the number of ESTs contributed to this contig/singleton. Enrichment analyses were further applied to detect Gene Ontology terms, and KEGG pathway for describing the unique function of each tissue. For example, the unique expressing subset of hepatopancreas is related to hemocyanin in KEGG pathway enrichment analysis result, while the unique subset in eyestalk represent actin and myosin genes. In summary, this study provides an alternative strategy of assembling EST and the data produced from this research can assist any studies about white shrimp in the future. Reference URL: http://ips.iis.sinica.edu.tw/lv