Shrimp is the most important internationally traded fishery commodity in terms of value, with a global market valued at USD 37.6 billion in 2021. Despite its economic importance, research on penaeid shrimp genomics and epigenomics is lacking. So far, only five reference genome assemblies for Penaeid species are available in the Genome Database of NCBI (https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=133894): Penaeus chinensis, P. indicus, P. japonicus, P. monodon and P. vannamei.
The P. monodon reference genome sequence is the most complete of all, with an assembly size of ~2.39-Gb, and is the only sequence approximating the expected size of ~2.89-Gb (Jeffery & Gregory, 2019) of the specific pathogen-free (SPF) P. vannamei domesticated by the breeding program of the U.S. Marine Shrimp Farming Program (USMSFP), the most cultured species worldwide. The assembly size of P. chinensis (GCF_019202785.1) is ~1.47-Gb, P. indicus (GCA_018983055.1) is ~1.94-Gb, P. japonicus (GCF_017312705.1) is ~1.71-Gb, and P. vannamei cultured in China (GCF_003789085.1) is ~1.66-Gb.
Research is needed to fill the gaps in the whole reference genomes of Penaeids to address issues like identification of sex-determining genes, susceptibility to diseases caused by viral and bacterial pathogens, growth performance, environmental contamination, interactions of dengue virus with shrimp densoviruses like IHHNV and transposable elements and the impact of climate change, and further for application of molecular genomic assisted breeding techniques in shrimp.
Plans are being discussed for a special issue of the ‘Journal of Shellfish Research’ titled ‘Penaeid Shrimp Genomics and Epigenomics – Whole Reference Genomes for the Economically Important Penaeus Species’ and we welcome reviews or original articles covering genomic, epigenomic, or post-genomic profiling of penaeid shrimp that may provide the clues to solve the mechanisms of pathogenesis, evolution, and resilience to environmental change. For example, whole exomes, genomes and gene–environment susceptible microbiomes, metabolomes, proteomes, transcriptomes, and methylomes can individually and/or collectively inform specific molecular mechanisms, leading to the potential identification of factors or simple sequence repeats, transposable elements, and epigenetic marks to study transgenerational epigenetic inheritance of disease tolerance. This will eventually identify the most effective genomic selection approaches and precise treatments for emerging diseases.