Abstract
Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering ~1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture.
Highlights
Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries
The L. vannamei genome size was measured to be 2.45 Gb by flow cytometry (Supplementary Fig. 1), similar to the size estimated by k-mer analysis (2.60 Gb, Supplementary Fig. 2)
We found three prominent genome characteristics from L. vannamei that might underlie the rapid evolution of penaeid shrimp, namely, abundant SSRs, a high proportion of taxon-specific genes, and extensive tandem gene duplications
Summary
The subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. While its native range is in the East Pacific Ocean, L. vannamei is widely farmed in Central and South America and in Asia, in China, Indonesia, Thailand, and Vietnam, with a number of breeding lines available These lines are mostly produced through traditional selective breeding procedures, and genomic information would be extremely useful for future genetic manipulation. As early as 1997, in an international workshop on genome mapping of aquaculture animals, the penaeid shrimp was identified as one of five target organisms for genome sequencing, together with salmon, catfish, tilapia, and oyster[5] The genomes of the latter four species have been published over the past decade[6,7,8,9], but no complete genome of the shrimp has been reported to date, despite the efforts of a number of major research groups. Our genomic analyses reveal that selective breeding has exerted a significant impact on the genome of L. vannamei broodstocks and the genetic resources acquired from this study will be useful for further genetic improvements in shrimp culture
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