title: Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture.
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.
authors.affiliation: Genomics and Bioinformatic Services, Texas A&M AgriLife Research, College Station, TX 77845 USA.
authors.forename: Noushin
authors.initials: N
authors.lastname: Ghaffari
authors.affiliation: Unidad Universitaria de Apoyo Bioiformático, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Sanchez-Flores
authors.affiliation: Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA.
authors.forename: Ryan
authors.initials: R
authors.lastname: Doan
authors.affiliation: Centro de Investigación en Alimentación y Desarrollo (CIAD), Carretera a Ejido La Victoria, Km 0.6, Hermosillo, Sonora 83304 Mexico.
authors.forename: Karina D
authors.initials: KD
authors.lastname: Garcia-Orozco
authors.affiliation: Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA.
authors.forename: Patricia L
authors.initials: PL
authors.lastname: Chen
authors.affiliation: Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F., 14610, Mexico.
authors.forename: Adrian
authors.initials: A
authors.lastname: Ochoa-Leyva
authors.affiliation: Centro de Investigación en Alimentación y Desarrollo (CIAD), Carretera a Ejido La Victoria, Km 0.6, Hermosillo, Sonora 83304 Mexico.
authors.forename: Alonso A
authors.initials: AA
authors.lastname: Lopez-Zavala
authors.affiliation: Centro de Investigación en Alimentación y Desarrollo (CIAD), Carretera a Ejido La Victoria, Km 0.6, Hermosillo, Sonora 83304 Mexico.
authors.forename: J Salvador
authors.initials: JS
authors.lastname: Carrasco
authors.affiliation: Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Hong
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato Mexico.
authors.forename: Luis G
authors.initials: LG
authors.lastname: Brieba
authors.affiliation: Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnologia, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos Mexico.
authors.forename: Enrique
authors.initials: E
authors.lastname: Rudiño-Piñera
authors.affiliation: Pittsburgh Supercomputing Center, Pittsburgh, PA 15213 USA.
authors.forename: Philip D
authors.initials: PD
authors.lastname: Blood
authors.affiliation: Department of Animal Sciences, Texas Agrilife Research, Texas A&M University, College Station, TX 77843 USA.
authors.forename: Jason E
authors.initials: JE
authors.lastname: Sawyer
authors.affiliation: Genomics and Bioinformatic Services, Texas A&M AgriLife Research, College Station, TX 77845 USA.
authors.forename: Charles D
authors.initials: CD
authors.lastname: Johnson
authors.affiliation: Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA.
authors.forename: Scott V
authors.initials: SV
authors.lastname: Dindot
authors.affiliation: Centro de Investigación en Alimentación y Desarrollo (CIAD), Carretera a Ejido La Victoria, Km 0.6, Hermosillo, Sonora 83304 Mexico.
authors.forename: Rogerio R
authors.initials: RR
authors.lastname: Sotelo-Mundo
authors.affiliation: 1] Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA [2] Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA [3] Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843 USA.
authors.forename: Michael F
authors.initials: MF
authors.lastname: Criscitiello
mesh_terms: D000465:Algorithms; D000818:Animals; D017756:Aquaculture; D003445:Crustacea / Q000235:genetics / Q000378:metabolism; D004261:DNA Replication / Q000235:genetics; D003621:Daphnia / Q000378:metabolism; D030541:Databases, Genetic; D023281:Genomics; D007107:Immune System / Q000378:metabolism; D033561:Penaeidae / Q000235:genetics* / Q000378:metabolism*; D017747:Seafood; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014584:User-Computer Interface