Shrimp Transcriptome Offers Secure Future Food Source, Better Understanding of Ocean Food Chain


Litopenaeus vannamei, the whiteleg shrimp, is the number one human food source from the sea. Over a million tons are harvested annually—a huge consumption volume that may not be sustainable. Mariculture, or “sea farming,” could help secure this harvest, but can be economically risky. Because inver- tebrates like shrimp have primitive immune systems, they can’t be vaccinated against diseases that can wipe out a farm colony.

Noushin Ghaffari of Texas A&M AgriLife Genomics and Bioinformatics and colleagues in a multinational collaboration are working to determine the whiteleg shrimp’s full genetic sequence.

This knowledge can suggest ways of protecting this and related human food species of shrimp from disease. It will also help scientists understand the genetics of krill, a tiny crustacean vital to ocean food webs and forming the main diet of baleen whales. The collaboration is led by Michael F. Criscitiello at the College of Veterinary Med- icine and Biomedical Sciences, Texas A&M University, and Rogerio R. Sotelo-Mundo at the Centro de Investigación en Alimentación y Desarrollo, Mexico.

“The whiteleg shrimp has been one of the fastest growing aquaculture species. It also has very good potential for establishing food security for the U.S. and its neighbors, including Mexico.”

Noushin Gaffari, Texas A&M University



As a first step in understanding the genomic structure of the whiteleg shrimp, Ghaffari and her collaborators created a novel assembly of the “transcriptome” from several organs in a male whiteleg shrimp. The transcriptome is the sequence of only the active genes in a given tissue. A subset of the full genome, the transcriptome offered a quick way to identify the proteins and nucleic acids the shrimp needs to carry out its life functions.

But even the “smaller” task of assembling the transcriptome posed a huge computational challenge, requiring the team to assemble and match the sequences of about 400 mil- lion nucleic acid fragments. XSEDE ECSS staff at PSC helped the team leverage the Blacklight supercomputer’s very large memory to perform this task, adapting the gold-standard transcrip- tome assembly software, Trinity, to Blacklight in the process. The team also annotated the transcriptome assembly—creating essentially the equivalent of a legend in a roadmap. This identified over 87,000 candidate genes that will offer insights into invertebrate immunity. The investigators published their results in Nature Scientific Reports in November 2014.

“For the transcriptome assembly, I needed Trinity software. [Blacklight] is a great system; there are not many other supercomputers that provide that much RAM.”

—Noushin Gaffari, Texas A&M University

Pictured above (top to bottom): pieces of the carapace of a whiteleg shrimp; a healthy whiteleg shrimp as harvested; and a whiteleg shrimp killed by the Taura syndrome virus (TSV). Herman Gunawan, Bangka, Indonesia.