THE SHRIMP EPIGENOME (ShrimpENCODE) PROJECT

The goal of ShrimpENCODE project is to identify economically important traits such as resistance to bacterial (AHPND) and viral diseases (WSSV, IHHNV, TSV), resilience to environmental stress, high growth and reproduction using the genome sequence assembly of the first specific pathogen-free (SPF) Penaeus (Litopenaeus) vannamei produced and domesticated by the breeding program of the U.S. Marine Shrimp Farming Program (USMSFP). The genome size of SPF shrimp is ~2.87Gb. A pilot genome sequence has been produced and has been useful to characterize 300 repetitive sequences, transposable elements expansion (like Gypsy-4_LVa), endogenous viruses (Nimav-1_LVa, WSSV-EVE, IHHNV-EVE) and chimeric TSV gene. A public, continuous, fully assembled genome sequence for the first SPF P. vannamei is urgently needed to understand genome evolution; inbreeding effects and genome rearrangements affecting shrimp production traits.

Experimental design to study generational toxicology - epigenetic changes caused by glyphosate. Alcivar-Warren et al. 2020.

A public, continuous, fully assembled genome sequence for the first SPF P. vannamei is urgently needed to understand genome evolution; inbreeding effects and genome rearrangements affecting shrimp production traits.

The ShrimpENCODE session at the 113th meeting of the National Shellfisheries Association (NSA) will address international efforts to identify economically important traits using the first draft genome sequence assembly (reference ASM378908v1; 1.6Gb) from an adult male Penaeus vannamei breed: Kehai No.1 farmed in China. The following topics will be presented: 317 transposable elements of the original SPF shrimp from the USA; non-canonical epigenetic system of bacterial origin; crustacean hyperglycemic hormone (CHH) in molting and male sexual differentiation, CHH gene in the endogenous nimavirus Nimav-1_LVa; gut microbiota of P. vannamei, differences between plant and animal-based diet; Fem-1 antisense transcript and sexual development; sex-markers for shrimp, sex-biased genes, bacterial genes in the shrimp genome, homology of NonLTR-1_LVa non-LTR retrotranspon of SPF L. vannamei to NLRS non-LTR retrotransposon associated with abdominal segment deformity disease (ASDD) of farmed shrimp; NonLTR-1_LVa expression in ovaries before and after eyestalk ablation, transcriptomics on WSSV- and AHPND-challenged P. monodon; horizontal plasmid transfer between Vibrio parahaemolyticus as a novel mechanism for genetic exchange and environmental adaptation mediated by the insertion sequence ISVal1; black gill disease syndrome, 30 metals in shrimp, transcriptome from hepatopancreas of control and cadmium-treated postlarvae stage 42 (PL42), population growth of wild Penaeids in Chesapeake Bay, and transgenerational epigenetic inheritance (TGEI) of shrimp exposed to glyphosate.