Eat ‘em or Annotate ‘em: Why Pacific White Shrimp Are a Big Deal

Pacific white shrimp show up on plates all over the world. They’re valued by diners and cooks for their tender texture and mild flavor. They’re harvested from both the ocean and aquaculture.

From Aphids to Whales—the Sequencing Continues
The NCBI Eukaryotic Genome Annotation Pipeline is constantly releasing new annotations in RefSeq. Here are some recent annotations:

Aphis gossypii (cotton aphid)
Balaenoptera acutorostrata scammoni (minke whale)
Bombyx mandarina (wild silkworm)
Chelonia mydas (green sea turtle)
Empidonax traillii (willow flycatcher)
Eptesicus fuscus (big brown bat)
Eumetopias jubatus (Steller sea lion)
Falco cherrug (saker falcon)
Falco peregrinus (peregrine falcon)
Marmota flaviventris (yellow-bellied marmot)
Neopelma chrysocephalum (saffron-crested tyrant-manakin)
Ovis aries (sheep)
Pipra filicauda (wire-tailed manakin)
Rhopalosiphum maidis (corn leaf aphid)
Solanum pennellii (eudicots)
Tupaia chinensis (Chinese tree shrew)
Vigna unguiculata (cowpea)
Vombatus ursinus (common wombat)
Xiphophorus couchianus (Monterrey platyfish)

Visit our Eukaryotic RefSeq Genome Annotation Status page to see more annotations in progress.

At the National Center for Biotechnology Information (NCBI), Pacific white shrimp or Penaeus vannamei are valued for another reason.

NCBI recently announced the Annotation Release 100 of the Penaeus vannamei genome in RefSeq, based on the assembly submitted by the Institute of Oceanology, Chinese Academy of Sciences. It’s the first decapod to have its genome annotated by NCBI. (In case you’re wondering “decapod” means ten-footed, and although decapods can have a diverse number of appendages, they all share the defining feature of 10 “walking legs” or pereiopods).

NCBI predicted 24,987 protein coding genes from this shrimp with evidence from alignment of six billion RNA-Seq reads and homology with invertebrate proteins. This annotation will enable genomic research in this commercially important species.

Genome annotation is the process of finding and designating locations of individual genes and other features of assembled DNA sequences. The data are available for download and can be explored in the Genome Data Viewer, with BLAST, and in the Gene database.

In the 20 years since it launched, the Reference Sequence Database, better known as RefSeq, has grown from an initial public release of 3,439 human protein-coding transcript sequence records to more than 25 million DNA transcripts and 130 million protein records from more than 86,000 organisms.

If your interest in Pacific white shrimp runs more culinary, check out Spanish-style shrimp stew, a heart healthy recipe from the National Heart, Lung, and Blood Institute.