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Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture
Ghaffari, N.; Sanchez-Flores, A.; Daan, R.; Garcia-Orozco, K.D.; Chen, P.L.; Ochoa-Leyva, A.; Lopez-Zavala, A.A.; Carrasco, J. S.; Hong, C.; Brieba, L.G.; Rudinõ-Piñera, E.; Blood, P.D.; Sawyer, J.E.; Johnson, C.D.; Dindot, S.V.; Sotelo-Mundo, R.R.; Criscitiello, M.F. (2014). Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture. NPG Scientific Reports 7(7081): 10 pp. http://dx.doi.org/10.1038/srep07081
In: Scientific Reports (Nature Publishing Group). Nature Publishing Group: London. ISSN 2045-2322; e-ISSN 2045-2322, more
Peer reviewed article  
Available in  Authors 
Keywords
    Litopenaeus vannamei (Boone, 1931) [WoRMS]
    Marine/Coastal
Authors  Top 
  • Ghaffari, N.
  • Sanchez-Flores, A.
  • Daan, R.
  • Garcia-Orozco, K.D.
  • Chen, P.L.
  • Ochoa-Leyva, A.
  • Lopez-Zavala, A.A.
  • Carrasco, J. S.
  • Hong, C.
  • Brieba, L.G.
  • Rudinõ-Piñera, E.
  • Blood, P.D.
  • Sawyer, J.E.
  • Johnson, C.D.
  • Dindot, S.V.
  • Sotelo-Mundo, R.R.
  • Criscitiello, M.F.
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.
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