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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. Therefore, we used skim sequencing (SkimSeq) based genotyping approach to investigate the genetic structure of 50 broodstock individuals of P. monodon species, collected from five sampling sites (n = 10 in each site) 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). After various filtering process, a total of 194,259 single nucleotide polymorphism (SNP) loci were identified, in which 4983 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. 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). Among 4983 putatively adaptive SNP loci, only 50 loci were observed to be in the coding region. 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. This study has demonstrated the applicability of SkimSeq in a highly duplicated genome of P. monodon specifically, across a range of genetic backgrounds and geographical distributions, and would be useful for future genetic improvement program of this species in aquaculture.

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Biofloc technology is being applied increasingly in shrimp aquaculture. Many countries have adopted this technology to increase shrimp aquaculture production. Owing to its major importance, this study was conducted to identify the bacterial population from biofloc aquaculture shrimp pond water of Singkir Laut, Kedah, Malaysia. Samples of mature biofloc were collected from the biofloc pond water at different shrimp ages (day of culture [DOC]): DOC30, DOC60 and DOC90. Overall, 43 sequences of bacterial species were blasted, which were identified as Exiguobacterium spp., Bacillus spp., Vibrio spp., Acinetobacter junii, Cobetia marina, Rheinheimera aquimaris and Pseudoalteromonas spp. These bacterial species were identified mostly from heterotrophic plate count agar. The bacterial species of Exiguobacterium aestuarii, Exiguobacterium profundum and Exiguobacterium aurantiacum were identified with 16S rRNA gene sequence similarities of 98.45–99.44%. Bacterial species of Bacillus pumilus, Bacillus velezensis, Bacillus cereus, Bacillus safensis and Bacillus subtilis were identified with 16S rRNA gene sequence similarities of 98.81–99.21%. Bacterial species of Vibrio diazotrophicus, Vibrio diabolicus, Vibrio natriegens and Vibrio harveyi were identified with 16S rRNA gene sequence similarities of 98.03–99.19%. Bacteria from Rheinheimera aquimaris were also identified with 16S rRNA gene sequence similarities of 98.69–99.26%; this bacterium is a novel bacterium identified from biofloc samples of the present study and has not been reported from biofloc samples in any previous study. Exiguobacterium spp. from the novel strains of E. aestuarii and E. profundum were identified as dominant, with 23 of 43 samples isolated from a shrimp pond at time points DOC30, DOC60 and DOC90; these bacteria are Gram‐variable rod‐shaped organisms that are capable of producing extracellular enzyme activity to break down chemical structures, thereby helping to remove organic compounds from aquaculture waste. Exiguobacterium spp. are usually identified in tidal flat sediments and on muddy sea coasts. This discovery is consistent with the site of the shrimp pond near to a muddy beach area, which might be the source of seawater leading to the predominance of this type of bacteria in the biofloc samples in the studied pond.