Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture

• Published in: Scientific reports Vol. 4; no. 1; p. 7081
• Main Authors: Ghaffari, Noushin, Sanchez-Flores, Alejandro, Doan, Ryan, Garcia-Orozco, Karina D., Chen, Patricia L., Ochoa-Leyva, Adrian, Lopez-Zavala, Alonso A., Carrasco, J. Salvador, Hong, Chris, Brieba, Luis G., Rudiño-Piñera, Enrique, Blood, Philip D., Sawyer, Jason E., Johnson, Charles D., Dindot, Scott V., Sotelo-Mundo, Rogerio R., Criscitiello, Michael F.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25-11-2014; Nature Publishing Group
• Subjects: 38/39; 38/90; 38/91; 631/114/2184; 631/114/2403; 631/208/212/2019; Algorithms; Animals; Aquaculture; Crustacea - genetics; Crustacea - metabolism; Crustaceans; Daphnia - metabolism; Databases, Genetic; DNA Replication - genetics; Economic importance; Gene expression; Genomics; Gills; Global economy; Hepatopancreas; Homology; Humanities and Social Sciences; Immune System - metabolism; Immunogenetics; Marine aquaculture; multidisciplinary; Penaeidae - genetics; Penaeidae - metabolism; Ribonucleic acid; RNA; Science; Seafood; Sequence Analysis, RNA; Shellfish; Species; Transcriptome; User-Computer Interface
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep07081

We present a new transcriptome assembly of the Pacific whiteleg shrimp (
Litopenaeus vannamei
), the species most farmed for human consumption. Its functional annotation, a substantial improvement over previous ones, is provided freely. RNA-Seq with Illumina HiSeq technology was used to analyze samples extracted from shrimp abdominal muscle, hepatopancreas, gills and pleopods. We used the Trinity and Trinotate software suites for transcriptome assembly and annotation, respectively. The quality of this assembly and the affiliated targeted homology searches greatly enrich the curated transcripts currently available in public databases for this species. Comparison with the model arthropod
Daphnia
allows some insights into defining characteristics of decapod crustaceans. This large-scale gene discovery gives the broadest depth yet to the annotated transcriptome of this important species and should be of value to ongoing genomics and immunogenetic resistance studies in this shrimp of paramount global economic importance.