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

doi:10.1038/srep07081

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 journal › Article › peer-review

86 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 language	English
Article number	7081
Journal	Scientific Reports
Volume	4
DOIs	https://doi.org/10.1038/srep07081
State	Published - 25 Nov 2014
Externally published	Yes

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).

Access to Document

10.1038/srep07081

Cite this

Ghaffari, N., Sanchez-Flores, A., Doan, R., Garcia-Orozco, K. D., Chen, P. L., Ochoa-Leyva, A., Lopez-Zavala, A. A., Carrasco, J. S., Hong, C., Brieba, L. G., Rudiño-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. Scientific Reports, 4, Article 7081. https://doi.org/10.1038/srep07081

@article{5bed2327eaf34042b1e5d3eee83a562a,

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.",

author = "Noushin Ghaffari and Alejandro Sanchez-Flores and Ryan Doan and Garcia-Orozco, {Karina D.} and Chen, {Patricia L.} and Adrian Ochoa-Leyva and Lopez-Zavala, {Alonso A.} and Carrasco, {J. Salvador} and Chris Hong and Brieba, {Luis G.} and Enrique Rudi{\~n}o-Pi{\~n}era and Blood, {Philip D.} and Sawyer, {Jason E.} and Johnson, {Charles D.} and Dindot, {Scott V.} and Sotelo-Mundo, {Rogerio R.} and Criscitiello, {Michael F.}",

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).",

year = "2014",

month = nov,

day = "25",

doi = "10.1038/srep07081",

language = "Ingl{\'e}s",

volume = "4",

journal = "Scientific Reports",

issn = "2045-2322",

publisher = "Nature Publishing Group",

}

Ghaffari, N, Sanchez-Flores, A, Doan, R, Garcia-Orozco, KD, Chen, PL, Ochoa-Leyva, A, Lopez-Zavala, AA, Carrasco, JS, Hong, C, Brieba, LG, Rudiño-Piñera, E, Blood, PD, Sawyer, JE, Johnson, CD, Dindot, SV, Sotelo-Mundo, RR & Criscitiello, MF 2014, 'Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture', Scientific Reports, vol. 4, 7081. https://doi.org/10.1038/srep07081

TY - JOUR

T1 - Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture

AU - Ghaffari, Noushin

AU - Sanchez-Flores, Alejandro

AU - Doan, Ryan

AU - Garcia-Orozco, Karina D.

AU - Chen, Patricia L.

AU - Ochoa-Leyva, Adrian

AU - Lopez-Zavala, Alonso A.

AU - Carrasco, J. Salvador

AU - Hong, Chris

AU - Brieba, Luis G.

AU - Rudiño-Piñera, Enrique

AU - Blood, Philip D.

AU - Sawyer, Jason E.

AU - Johnson, Charles D.

AU - Dindot, Scott V.

AU - Sotelo-Mundo, Rogerio R.

AU - Criscitiello, Michael F.

N1 - 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).

PY - 2014/11/25

Y1 - 2014/11/25

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84937531455&partnerID=8YFLogxK

U2 - 10.1038/srep07081

DO - 10.1038/srep07081

M3 - Artículo

C2 - 25420880

SN - 2045-2322

VL - 4

JO - Scientific Reports

JF - Scientific Reports

M1 - 7081

ER -

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

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this