The domestication of a wild-caught aquatic animal is an evolutionary process, which results in genetic discrimination at the genomic level in response to strong artificial selection. Although black tiger shrimp (Penaeus monodon) is one of the most commercially important aquaculture species, a systematic assessment of genetic divergence and structure of wild-caught and domesticated broodstock populations of the species is yet to be documented. In the present study, we used a combined approaches of skim sequencing (SkimSeq) based genotyping and gut metagenome analyses to investigate the genetic structure of broodstock individuals of P. monodon species, collected from five sampling sites across their distribution in Indo-Pacific regions. The wild-caught P. monodon broodstock population were collected from Malaysia (MS) and Japan (MJ), while domesticated broodstock populations were collected from Madagascar (MMD), Hawaii, HI, USA (MMO), and Thailand (MT). For the SkimSeq analysis, a total of 194,259 single nucleotide polymorphism (SNP) loci were identified, in which 4, 983 SNP loci were identified as putatively adaptive by the pcadapt approach. In both datasets, pairwise FST estimates high genetic divergence between wild and domesticated broodstock populations. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that non-synonymous mutated genes might be associated with the energy production, metabolic functions, respiration regulation and developmental rates, which likely act to promote adaptation to the strong artificial selection during the domestication process. Our metagenome results identified considerable variation in the gut microbiomes of wild and cultured shrimps, presumably reflecting differences in diet, host genetic divergence, and host-bacteria co-evolution. LEfSe analysis detected significant enrichment of beneficial/opportunistic pathogens from the gut microbiome of each host population, suggesting possible biomarkers for host health monitoring. Consistently, different spatial clustering analyses in both datasets categorized divergent genetic structure into two clusters: (1) wild-caught populations (MS and MJ), and (2) domesticated populations (MMD, MMO and MT). While wild shrimp broodstocks had higher gut microbial diversity, a pronounced divergence of core microbiota was found in both wild and cultured shrimp populations with altered community structure and predicted metabolic functions. Our results provide insights into the deterministic factors contributing to the interpopulation variation in the P. monodon microbiome, highlighting potential future research directions in areas such as host-bacteria co-evolution and holobiome, which may enable the assessment of host-species genomic divergence across environmental gradients.
SKIM-SEQUENCING BASED GENOTYPING REVEALS GENETIC DIVERGENCE OF THE WILD AND DOMESTICATED BROODSTOCK POPULATIONS OF BLACK TIGER SHRIMP Penaeus monodon IN THE INDO-PACIFIC REGION