Immune and bacterial toxin genes expression in different giant tiger prawn, Penaeus monodon post-larvae stages following AHPND-causing strain of Vibrio parahaemolyticus challenge

Acute Hepatopancreatic Necrosis Disease (AHPND), a disease caused by Vibrio parahaemolyticus (V-PAHPND), kills Penaeid shrimps worldwide, resulting in severe economic losses during aquaculture. To further understand how Penaeus monodon post-larvae (PL) respond towards infection of this pathogenic bacterium, the expression of several important immune and bacterial toxin genes in three stages of P. monodon PL (PL15, PL30 and PL45) upon V-PAHPND challenge, were determined. A 20-hrs challenge test with 2.7 x 10(7) cfu ml(-1) of V-PADPND resulted 81, 65 and 1.7% mortality respectively for PL30, PL15 and PL45, indicating that PL30 was most vulnerable to V-PADPNEP The immune response of shrimp PL at this stage was robust, with Toll-like receptor (TLR), prophenoloxidase (proPO), lysozyme (lyso) and penaeidin (PEN) augmented approximately 10.7, 4.7, 6.5 and 3.2-fold, respectively. The expression initiated at one hour post-infection (h.p.i), peaked at 16 h.p.i and 20 h.p.i, and decreased at 18 h.p.i, indicating the crucial involvement of these immune related genes in the defence and recovery of the first-line defence mechanisms during V-PADPND infection. This work also revealed that toxR gene represents a good indicator gene for Vibrio detection whereas PIR A, for V-PADPND pathogenicity determination of P. monodon. Overall, these findings provided novel insights into the immune response and V-PADPND No susceptibility of different P. monodon PL stages during infection, with outcomes potentially useful in enhancing the application of health therapy and biosecured aquaculture practices to minimize the damaging risk of AHPND towards sustainable production of P. monodon

Skim-sequencing based genotyping reveals genetic divergence of the wild and domesticated population of black tiger shrimp (<i>Penaeus monodon</i>) in the Indo-Pacific region

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

Image_4_Understanding the effects of salinity and Vibrio harveyi on the gut microbiota profiles of Litopenaeus vannamei.png

Increasing evidence have revealed a positive correlation between gut microbiota and shrimp health, in which a healthy shrimp gut consists of a complex and stable microbial community. Given that both abiotic and biotic factors constantly regulate shrimp gut microbiota, any changes affecting the levels of these factors could cause modification to the gut microbiota assemblage. The goal of this study was to explore the effects of salinity levels and pathogenic Vibrio harveyi infection on the diversity, structure, composition, interspecies interaction, and functional pathways of Litopenaeus vannamei gut microbiota. Juvenile shrimp were cultured at 5 ppt, 20 ppt, and 30 ppt for two months prior to Vibrio harveyi infection. After pathogenic V. harveyi challenge test, genomic DNA was isolated from the shrimp gut, and subjected to the 16S rRNA metagenomic sequencing analysis. We observed that gut microbiota diversity of shrimp cultured at 5 ppt and 30 ppt were lower than those cultured at 20 ppt after exposure to V. harveyi infection, suggesting that shrimp cultured at the two former salinity levels were more susceptible to V. harveyi infection. Network analysis also showed that shrimp cultured at 20 ppt exhibit a more stable bacterial network with complex interspecies interaction, even after induced by V. harveyi. Moreover, the presence of a high number of beneficial bacteria such as Pseudoruegeria, Rhodovulum, Ruegeria, Shimia and Lactobacillus in shrimp cultured at 20 ppt might have played a role in inhibiting the growth of V. harveyi and other potentially pathogenic bacteria. Besides, bacterial functional pathway prediction has also shown that metabolic pathways such as phenylalanine metabolism, glycine, serine and threonine metabolism, starch and sucrose metabolism, glyoxylate and dicarboxylate metabolism, carbon metabolism and biofilm formation process were significantly higher in shrimp cultured at 20 ppt. Collectively, our results suggested that 20 ppt is an optimal salinity that suppresses the growth of V. harveyi and potential pathogenic bacteria in the shrimp gut, which could possibly minimize the risk of pathogenic infection for sustainable production of healthy shrimp.</p

Image_1_Understanding the effects of salinity and Vibrio harveyi on the gut microbiota profiles of Litopenaeus vannamei.png

Increasing evidence have revealed a positive correlation between gut microbiota and shrimp health, in which a healthy shrimp gut consists of a complex and stable microbial community. Given that both abiotic and biotic factors constantly regulate shrimp gut microbiota, any changes affecting the levels of these factors could cause modification to the gut microbiota assemblage. The goal of this study was to explore the effects of salinity levels and pathogenic Vibrio harveyi infection on the diversity, structure, composition, interspecies interaction, and functional pathways of Litopenaeus vannamei gut microbiota. Juvenile shrimp were cultured at 5 ppt, 20 ppt, and 30 ppt for two months prior to Vibrio harveyi infection. After pathogenic V. harveyi challenge test, genomic DNA was isolated from the shrimp gut, and subjected to the 16S rRNA metagenomic sequencing analysis. We observed that gut microbiota diversity of shrimp cultured at 5 ppt and 30 ppt were lower than those cultured at 20 ppt after exposure to V. harveyi infection, suggesting that shrimp cultured at the two former salinity levels were more susceptible to V. harveyi infection. Network analysis also showed that shrimp cultured at 20 ppt exhibit a more stable bacterial network with complex interspecies interaction, even after induced by V. harveyi. Moreover, the presence of a high number of beneficial bacteria such as Pseudoruegeria, Rhodovulum, Ruegeria, Shimia and Lactobacillus in shrimp cultured at 20 ppt might have played a role in inhibiting the growth of V. harveyi and other potentially pathogenic bacteria. Besides, bacterial functional pathway prediction has also shown that metabolic pathways such as phenylalanine metabolism, glycine, serine and threonine metabolism, starch and sucrose metabolism, glyoxylate and dicarboxylate metabolism, carbon metabolism and biofilm formation process were significantly higher in shrimp cultured at 20 ppt. Collectively, our results suggested that 20 ppt is an optimal salinity that suppresses the growth of V. harveyi and potential pathogenic bacteria in the shrimp gut, which could possibly minimize the risk of pathogenic infection for sustainable production of healthy shrimp.</p

Image_5_Understanding the effects of salinity and Vibrio harveyi on the gut microbiota profiles of Litopenaeus vannamei.png

Increasing evidence have revealed a positive correlation between gut microbiota and shrimp health, in which a healthy shrimp gut consists of a complex and stable microbial community. Given that both abiotic and biotic factors constantly regulate shrimp gut microbiota, any changes affecting the levels of these factors could cause modification to the gut microbiota assemblage. The goal of this study was to explore the effects of salinity levels and pathogenic Vibrio harveyi infection on the diversity, structure, composition, interspecies interaction, and functional pathways of Litopenaeus vannamei gut microbiota. Juvenile shrimp were cultured at 5 ppt, 20 ppt, and 30 ppt for two months prior to Vibrio harveyi infection. After pathogenic V. harveyi challenge test, genomic DNA was isolated from the shrimp gut, and subjected to the 16S rRNA metagenomic sequencing analysis. We observed that gut microbiota diversity of shrimp cultured at 5 ppt and 30 ppt were lower than those cultured at 20 ppt after exposure to V. harveyi infection, suggesting that shrimp cultured at the two former salinity levels were more susceptible to V. harveyi infection. Network analysis also showed that shrimp cultured at 20 ppt exhibit a more stable bacterial network with complex interspecies interaction, even after induced by V. harveyi. Moreover, the presence of a high number of beneficial bacteria such as Pseudoruegeria, Rhodovulum, Ruegeria, Shimia and Lactobacillus in shrimp cultured at 20 ppt might have played a role in inhibiting the growth of V. harveyi and other potentially pathogenic bacteria. Besides, bacterial functional pathway prediction has also shown that metabolic pathways such as phenylalanine metabolism, glycine, serine and threonine metabolism, starch and sucrose metabolism, glyoxylate and dicarboxylate metabolism, carbon metabolism and biofilm formation process were significantly higher in shrimp cultured at 20 ppt. Collectively, our results suggested that 20 ppt is an optimal salinity that suppresses the growth of V. harveyi and potential pathogenic bacteria in the shrimp gut, which could possibly minimize the risk of pathogenic infection for sustainable production of healthy shrimp.</p

Application of second-generation sequencing (SGS) and third generation sequencing (TGS) in aquaculture breeding program

High-throughput sequencing technologies have expanded gene-based to genome-wide research in aquaculture species. Several techniques adopting the Second Generation Sequencing (SGS), Third Generation Sequencing (TGS) platforms and/or hybrid genome assemblies have been widely employed in various aquaculture research areas including general breeding program, disease and health management, sex determination and reproduction biology, environmental stress response, nutrigenomics, morphological appearance, and meat quality/texture. Notably, the application of these novel sequencing technologies has generated Quantitative Trait Loci (QTL) and novel genes associated with commercially important production traits, which are useful for essential processes in selective breeding programs such as population genomics evaluation, Marker-Assisted Selection (MAS) and Genomic Selection (GS). These genomic approaches are also used as genetic traceability tools for seafood fraud assessment and tracking of farm escapees for wild stock conservation. Genomic data generated by these platforms could aid in establishing proper breeding strategies for more profitable and sustainable aquaculture