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

Noushin Ghaffari, Alejandro Sanchez-Flores, Ryan Doan, Karina D. Garcia-Orozco, Patricia L. Chen, Adrian Ochoa-Leyva, Alonso A. Lopez-Zavala, J. Salvador Carrasco, Chris Hong, Luis G. Brieba, Enrique Rudiño-Piñera, Philip D. Blood, Jason E. Sawyer, Charles D. Johnson, Scott V. Dindot, Rogerio R. Sotelo-Mundo, Michael F. Criscitiello*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

82 Scopus citations

Abstract

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.

Original languageEnglish
Article number7081
JournalScientific Reports
Volume4
DOIs
StatePublished - 25 Nov 2014
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by grants from Texas A&M Agrilife and Texas Veterinary Medical Diagnostic Laboratory #124151 to CDJ, SVD, and MFC, Texas A&M and Mexican CONACyT to RRS, SVD and MFC, USDA Formula Animal Health to MFC and SVD, and Mexican National Institute of Fisheries (INAPESCA) to RRS, LGB, ERP, SVD and MFC. The generation of RNA-Seq raw data was outsourced to Ambry Genetics, Aliso Viejo CA. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number OCI-1053575, to provide compute time on the Blacklight system at the Pittsburgh Supercomputing Center (PSC).

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