Giant Tiger Shrimp Penaeus Monodon Research Articles

Determining patterns of tissue tropism for IHHNV, GAV and YHV-7 infection in giant black tiger shrimp (Penaeus monodon) using real-time RT-qPCR

Disease management in shrimp aquaculture is heavily dependent on accurate and rapid pathogen detection and diagnosis. Understanding the presence and distribution of pathogens within various tissues of the shrimp host is critical to ensure detection efforts are targeted for optimal sensitivity and reliability. Modern advancements in molecular technologies, including nucleic acid extraction and RT-qPCR, have yielded significant improvements in pathogen detection capabilities. Despite these advancements and their widespread adoption within both research and industry applications, evidence to inform their optimised use, such as revisions to tissue-specific viral detection to support selection of appropriate target tissues, has not been established. To address these gaps, this study aimed to establish contemporary evidence of viral tissue tropism for three major shrimp pathogens. TaqMan qPCR analysis was used to determine tissue-specific loading of viral pathogens in naturally infected Penaeus monodon pleopod, gill, hepatopancreas, lymphoid organ, abdominal muscle tissue, hindgut and ventral nerve cord. The viral targets analysed included Penaeus stylirostris penstyldensovirus 1 (PstDV1), formerly named infectious hypodermal haematopoietic necrosis virus (IHHNV) and, two genotypes of the yellow head virus complex, including genotype 2 known as gill associated virus (YHV-2/ GAV), and genotype 7 (YHV-7). QPCR analyses demonstrated the highest level of genetic IHHNV detection from gill tissue, followed sequentially by hindgut, pleopod, hepatopancreas, lymphoid organ, ventral nerve cord and abdominal muscle. For the yellow head viruses (GAV and YHV-7), no significant differences in genetic viral detection were demonstrated, although a non-significant advantage was observed for lymphoid organ and hindgut tissue. Beyond establishing contemporary evidence of viral distribution to improve understanding of host-viral interactions, these findings offer supporting evidence for revisions to appropriate target tissue recommendations, within the World Organisation for Animal Health (WOAH, founded as OIE) Manual of Diagnostic Tests for Aquatic Animals, for optimised modern shrimp pathogen detection.

Characterization of the Virulency of Vibrio spp. in Giant Tiger Shrimp (Penaeus monodon) from Peninsular Malaysia

Nowadays, bacterial diseases caused by Vibrio spp. pose a significant obstacle to aquaculture growth, affecting socioeconomic development. The presence of pathogenic Vibrio spp. are gaining attention due to widespread mortality in fish and shellfish worldwide. This study investigates the distribution of virulence genes and their pathogenicity by experimentally infecting a healthy group of cultured shrimp, specifically Penaeus monodon. A total of 225 Vibrio spp. isolated from 210 cultured shrimp from various geographical regions in Peninsular Malaysia were examined, resulting in 13 Vibrio spp. being identified and characterized. According to virulence gene assessment, only eight of the 11 virulence genes were detected in the isolates, including chiA (89%), flaC (74%), tlh (72%), toxR (70%), luxR (40%), pirA (11%), pirB (11%), and hlyA (0.4%). Other virulence genes, such as tdh, trh, and ctxA, were not found in any of the isolates (0%). Then, three Vibrio isolates, including V. parahaemolyticus S12-3, V. campbellii S10-4, and V. rotiferianus S24-4, were selected for pathogenicity test based on highest number of virulence genes in each species. These species were subjected to immersion challenge test against postlarvae (PL) P. monodon approximately PL-20 with three different concentrations of 1 × 106, 1 × 107, and 1 × 108 CFU/mL. The V. parahaemolyticus S12-3 was determined to have lethal concentration 50 (LC50) 1 × 105 CFU/mL after 168 hr of exposure. The immersion challenge test resulted in a pale hepatopancreas and empty guts in P. monodon. Histopathological examination showed sloughing of epithelial cells in the hepatopancreatic tubule, hemocytic infiltration, massive vacuolation, and loss of hepatopancreatic tubule structure. Overall, the study demonstrated the virulence and pathogenicity of V. parahaemolyticus S12-3 toward P. monodon, which could be associated with its virulence properties. Furthermore, the current findings will be useful in developing microbiological risk assessments for shrimp farming and aquaculture management.

Characterization and Expression of Cytochrome b5 Gene and Protein in Ovaries of Giant Tiger Shrimp Penaeus monodon

The full-length transcript of cytochrome b5 (PmCytb5) in the giant tiger shrimp (Penaeus monodon) was characterized. It was 1539 bp with an open reading frame (ORF) of 432 bp deducing to 143 amino acids. The deduced PmCytb5 protein contained predicted cytochrome b5-like heme/steroid binding domain (Cytb5, positions 17-91) and a transmembrane domain (positions 120-139). In non-ablated wild adults, PmCytb transcript was significantly increased in mature ovaries while it was earlier upregulated in late vitellogenic stage in eyestalk-ablated shrimp (P<0.05). Progesterone injection (0.1 μg/g) induced the expression of PmCytb5 at 48 hours post injection (hpi, P<0.05) but serotonin (50 μg/g) did not alter its expression (P>0.05) in domesticated adults. The cytoplasmic PmCytb5 protein was upregulated from immature ovaries in the early vitellogenic stage and comparably expressed in subsequent stages in non-ablated wild broodstock. In eyestalk-ablated wild broodstock, a similar expression profile was observed but its expression was further increased in late vitellogenic, and mature stages. The membrane PmCytb5 protein was upregulated in late vitellogenic and mature stages in the former but expressed at a similar level in different ovarian stages in eyestalk-ablated broodstock. Results suggested the important role of PmCytb5 in ovarian development of P. monodon.

Occurrence and Characteristics of Microplastics in Wild and Farmed Shrimps Collected from Cau Hai Lagoon, Central Vietnam.

This study investigated the occurrence of microplastics (MPs) in the gastrointestinal tracts (GT) and tissues of four common shrimps (including two wild-caught shrimps and two farmed shrimps) collected from a high-diversity lagoon in central Vietnam. The numbers of MP items in greasy-back shrimp (Metapenaeus ensis), green tiger shrimp (Penaeus semisulcatus), white-leg shrimp (Litopenaeus vannamei), and giant tiger shrimp (Penaeus monodon), determined per weight and individual, were 0.7 ± 0.3, 0.6 ± 0.2, 1.1 ± 0.4, and 0.5 ± 0.3 (items/g-ww), and 2.5 ± 0.5, 2.3 ± 0.7, 8.6 ± 3.5, 7.7 ± 3.5 (items/individual), respectively. The concentration of microplastics in the GT samples was significantly higher than that in the tissue samples (p < 0.05). The number of microplastics in the farmed shrimp (white-leg shrimp and black tiger shrimp) was statistically significantly higher than the number of microplastics in the wild-caught shrimp (greasy-back and green tiger shrimps) (p <0.05). Fibers and fragments were the dominant shapes of the MPs, followed by pellets, and these accounted for 42-69%, 22-57%, and 0-27% of the total microplastics, respectively. The chemical compositions determined using FTIR confirmed six polymers, in which rayon was the most abundant polymer, accounting for 61.9% of the MPs found, followed by polyamide (10.5%), PET (6.7%), polyethylene (5.7%), polyacrylic (5.8%), and polystyrene (3.8%). As the first investigation on the MPs in shrimps from Cau Hai Lagoon, central Vietnam, this study provides useful information on the occurrences and characteristics of the microplastics in the gastrointestinal tracts and tissues of four shrimp species that live in different living conditions.

Identifying the Suitable Integrated Multi-trophic Aquaculture (IMTA) Species Combination for Penaeus monodon (Fabricius, 1798) for a Sustainable Pond Aquaculture

The environmental problem caused by aquaculture contributes to poor production of the giant tiger shrimp (Penaeus monodon) globally and locally. Integrated multi-trophic aquaculture (IMTA) lessens aquaculture environmental impacts through the addition of species in the system that could efficiently utilize inorganic and organic waste naturally. IMTA technique was designed to identify which among the species combination is suitable for Penaeus monodon IMTA pond culture. Four (4) treatment combinations from different trophic levels were evaluated for their suitability as IMTA species combinations in two areas: Mukas, Kolambugan, Lanao del Norte [with Penaeus monodon, Siganus guttatus, Ulva fasciata, and Perna viridis (M1); P. monodon, S. guttatus, Gracilaria verrucosa, and P. viridis (M2); P. monodon, C. chanos, Ulva fasciata, and Modiolus modulaides (M3); and P. monodon, C. chanos, G. verrucosa, and M. modulaides (M4)] and in Naawan, Misamis Oriental [with P. monodon, S. guttatus, U. fasciata, and P. viridis (N1); P. monodon, S. guttatus, G. verrucosa, P. viridis (N2), P. monodon, C. chanos, U. fasciata, and P. viridis (N3); and P. monodon, C. chanos, G. verrucosa, and P. viridis (N4)]. All treatments showed non-significant growth of P. monodon at 2.66–3.21% d–1 (M1, M2, M3, and M4) and 0.09–0.17% d–1 (N1, N2, N3, and N4). The survival rate of P. monodon in N1 (32.59 ± 4.73%) and N2 (30.27 ± 2.51%) showed a highly significant difference as compared to N3 (24.08 ± 4.25%) and N4 (21.95 ± 4.76%). Treatments M3, M4, N3, and N4 generated the highest economic return of USD 101.83–237.58 compared to treatments M1, M2, N1, and N2. All water parameters are within the optimum for the growth and survival of the IMTA organisms. The results revealed that a combination of C. chanos with either of the seaweeds and mussels (M3, M4, N3, and N4) is suitable for IMTA pond culture for P. monodon.

Association analysis of alpha-amylase (AMY) and cathepsin L (CTSL) SNPs with growth traits in giant tiger shrimp Penaeus monodon

Alpha-amylase (AMY) and cathepsin-L (CTSL) were selected as candidate genes for SNP discovery for growth traits of P. monodon. Six SNPs were found in AMY and three in CTSL in P. monodon. Association analyses for the candidate SNPs with important economic traits were performed in populations. That allele A at CTLS-213 SNP, AA, and GA, tended to be associated with increased body weight. Shrimps with genotype GG had significantly smaller CL, CW, and CH values than those with GT and TT genotypes (P &lt; 0.05). While CTLS-820 SNP was found to be significantly associated with CH and FSL (P &lt;0.05). These SNPs will be valid for marker-assisted selection breeding programs in P. monodon.

Development of a global SNP resource for diversity, provenance, and parentage analyses on the Indo-Pacific giant black tiger shrimp (Penaeus monodon)

The giant black tiger shrimp (Penaeus monodon) is an important aquaculture and fishery species and is the second most farmed penaeid shrimp species globally. Genomic resources available in giant black tiger shrimp research are growing rapidly. However, considering the large number of animals that would require SNP genotyping for commercial applications (i.e., selective breeding programs), there is a commercial need to identify low-density SNP panels for rapid, robust, and cost-effective use in global diversity, provenance, and pedigree determination. Using the raw (n = 131,929 SNPs) and high-quality (n = 10,593 SNPs; Vu et al., 2021) datasets, five low-density panels were identified for the standardized determination of: (1) global diversity (n = 2155 SNPs), (2) global provenance (n = 1200 SNPs), (3) Pacific Ocean (PO) pedigree (n = 217 SNPs), (4) Sri Lanka (SLK) pedigree (n = 226 SNPs), and (5) West Indian Ocean (WIO) pedigree (n = 220 SNPs). A total of 3433 unique genome-wide SNPs comprise these five low-density panels.Genetic diversity simulations demonstrated that the global diversity panel was able to estimate unbiased genetic diversity within and among all Indo-Pacific P. monodon populations as accurately as the entire high-quality dataset (n = 10,593 SNPs). Both DAPC and NetView analyses demonstrated that the global provenance panel was able to trace P. monodon collected from the same region back to their original basin and genetic cluster, while Monte-Carlo tests demonstrated that individuals could be accurately assigned back to their original basin, region, and basin-specific sampling location with 100%, 100%, and 69–100% accuracy, respectively. In silico analyses demonstrated that the PO, SLK, and WIO pedigree panels were able to accurately assign theoretical progenies back to their parent-pair with 100% accuracy using only 30–40 of the most informative SNP markers.This study provides globally effective and accurate low-density SNP panels for Indo-Pacific P. monodon, which can help aquaculture practices and fishery management strategies through improved diversity, provenance, and pedigree determination as well as facilitation of global data consistency, global database development, and global analysis standards establishment.

Effects of bioactive substances to prolong the shelf‐life and inhibit the formation of black spots in black tiger shrimp (Penaeus monodon) preserved at 0 degree C

AbstractThe objective of this study was to extend the shelf‐life and inhibit the process of black spots formation in giant black tiger shrimp (Penaeus monodon) by using 1.5 % solutions of the bioactives including: gallic acid, caffelic acid and cinnamaldehyde. Shrimp samples were dipped in the solutions for ten minutes, at 4°C and stored at 0°C for 15 days. Total viable count (TVC), melanosis evaluation method, chemical quality indexes including total volatile base nitrogen (TVB‐N), trimethylamine nitrogen (TMA‐N), pH and hypoxanthine values were used to evaluate the effectiveness of the treatments. TVC values, melanosis score of shrimp samples treated with bioactive compounds appeared more slowly, TVB‐N and TMA‐N values changed exponentially, hypoxanthine values increased linearly with storage time, and pH decreased on day 2, then increased gradually. Shelf life of treated samples were found to be longer than that of the control sample (8 days), and had a better ability to inhibit melanosis, in particular, the samples treated with a solution of cinnamaldehyde had the longest shelf life of 14 days, compared with 13 days of samples treated with caffelic acid and 12 days of the ones treated with gallic acid.

Isolation and Expression Analysis of cAMP-Dependent Protein Kinase and Adenylyl Cyclase-Associated Protein 1-like cDNAs in the Giant Tiger Shrimp Penaeus monodon

Characterization of genes exhibiting differential expression profiles during ovarian development is important for understanding reproductive maturation of the giant tiger shrimp (Penaeus monodon). Here, the partial cDNAs of P. monodon cAMP-dependent protein kinase, catalytic subunit 1 (PmPkaC1) and adenylyl cyclase-associated protein 1-like (PmCap1-l) were studied. They were more preferentially expressed in ovaries than testes of cultured juveniles and wild broodstock. PmPkaC1 mRNA in ovaries of non-ablated broodstock was significantly increased during vitellogenesis (P&lt;0.05). However, unilateral eyestalk ablation (the removal of one eyestalk) resulted in a significant reduction of its expression (P&lt;0.05). PmCap1-l was not differentially expressed during ovarian development in wild non-ablated broodstock. It was up-regulated in mature ovaries following eyestalk ablation (P&lt;0.05). The PmCap1-l transcript in each ovarian stage of the former was significantly lower than that of the latter (P&lt;0.05). The levels of ovarian PmPkaC1 and vitellogenin 1 (PmVtg1) treated in vitro with 17-20β-DHP (0.1, 1.0 and 10.0 μg/ml for 24 h) was not significantly different from the control (P&gt;0.05). Nevertheless, the expression of PmCap1-l was increased in ovaries treated with 0.1 and 10 μg/ml 17-20β-DHP at 24 hours post treatment (hpt, P&lt;0.05).

Preparation and Characterization of Giant Tiger Shrimp (Penaeus monodon) Shell-Based Chitin as Biocoagulant For Water Purification

Abstract: Giant tiger shrimp (Penaeus monodon) shells are solid waste that can be utilized for water purification by converting them into chitin-based biocoagulant. The extraction and deproteination of giant tiger shrimp shells (Penaeus monodon) resulted in 83.34% w/w, followed by a demineralization yield of 91.61% w/w product. Chitin extract was used as a biocoagulant using the Jar test method on a fixed variable of 1 L well water and the independent variables of chitin weight (mg) and stirring speed (rpm). The results showed that 15 mg/L chitin reduced the turbidity value of well water from 3.08-1.03 NTU and decreased the Total Dissolved Solids (TDS) from 555-500 mg/L, at 200 rpm and pH 8.4. In conclusion, our investigation proves that chitin derived from giant tiger shrimp shells can be used as a biocoagulant for water purification.Abstrak: Kulit udang merupakan limbah padat yang dapat digunakan untuk penjerniahan air, dengan mengonversi limbah tersebut menjadi biokoagulan berbasis chitin. Limbah kulit udang Windu (Penaeus monodon) diekstrak menjadi chitin sebagai bahan baku Biokoagulan dalam penjernihan air sumur. Proses ekstraksi kulit udang windu (Penaeus monodon) diperoleh rendemen sebesar 83,34% melalui proses deproteinasi, diperoleh rendemen sebanyak 91,61% melalui proses demineralisasi. Hasil ekstrak chitin digunakankan sebagai biokoagulan dengan metode Jar test pada variabel tetap sebesar 1 L air sumur dan variabel berubah adalah massa chitin dan waktu pengadukan. Hasil penelitian menunjukkan bahwa 15 mgram/L chitin mampu menurunkan nilai kekeruhan air sumur dari 3,08-1,03 (NTU) dan menurunkan Total Dissolved Solids TDS dari 555-500 (mgram/L), dengan kecepatan rotasi 200 rpm untuk nilai pH 8,4. Kesimpulan, penelitian ini menunjukkan bahwa chitin yang diperoleh dari kulit udang windu dapat digunakan sebagai biokoagulan pada proses penjernihan air.

Molecular detection of six viral pathogens from Australian wild sourced giant black tiger shrimp (Penaeus monodon) broodstock

Disease presents a considerable challenge to the sustainability and development of global shrimp aquaculture. The Australian black tiger shrimp (Penaeus monodon) aquaculture industry is heavily reliant on wild-sourced broodstock for seedstock production, representing a large and under evaluated biosecurity risk. Currently, there is a paucity of quantitative, large-scale data detailing the extent of pathogenic agents in wild-sourced P. monodon broodstock. This study presents a comprehensive investigation of the presence and level of detection of endemic pathogen targets in wild-sourced P. monodon broodstock collected from the two primary sources of supply for the Australian shrimp aquaculture industry using quantitative polymerase chain reaction (qPCR). Broodstock pleopod samples (N = 7472) were analysed by TaqMan qPCR for the detection of six viral pathogens. In total, 44.9% of wild-sourced broodstock were positive for the detection of at least one pathogen target. White spot syndrome virus and yellow head virus-1 were not detected in any sample. Infectious hypodermal haematopoietic necrosis virus (30%) and gill-associated virus (28.1%) were the most prevalent pathogen targets detected. Whenzhou (syn. Wenzhou) shrimp virus-2 and yellow head virus-7 were each cumulatively detected in less than 3% of broodstock samples. Geographic source, sex and year of collection of broodstock significantly influenced prevalence of detection. The current study will be valuable to the Australian shrimp aquaculture industry to improve understanding of the presence of pathogens in wild-sourced broodstock, along with informing management decisions related to wild broodstock collection and associated biosecurity practices.

Shrimp Parvovirus Circular DNA Fragments Arise From Both Endogenous Viral Elements and the Infecting Virus.

Some insects use endogenous reverse transcriptase (RT) to make variable viral copy DNA (vcDNA) fragments from viral RNA in linear (lvcDNA) and circular (cvcDNA) forms. The latter form is easy to extract selectively. The vcDNA produces small interfering RNA (siRNA) variants that inhibit viral replication via the RNA interference (RNAi) pathway. The vcDNA is also autonomously inserted into the host genome as endogenous viral elements (EVE) that can also result in RNAi. We hypothesized that similar mechanisms occurred in shrimp. We used the insect methods to extract circular viral copy DNA (cvcDNA) from the giant tiger shrimp (Penaeus monodon) infected with a virus originally named infectious hypodermal and hematopoietic necrosis virus (IHHNV). Simultaneous injection of the extracted cvcDNA plus IHHNV into whiteleg shrimp (Penaeus vannamei) resulted in a significant reduction in IHHNV replication when compared to shrimp injected with IHHNV only. Next generation sequencing (NGS) revealed that the extract contained a mixture of two general IHHNV-cvcDNA types. One showed 98 to 99% sequence identity to GenBank record AF218266 from an extant type of infectious IHHNV. The other type showed 98% sequence identity to GenBank record DQ228358, an EVE formerly called non-infectious IHHNV. The startling discovery that EVE could also give rise to cvcDNA revealed that cvcDNA provided an easy means to identify and characterize EVE in shrimp and perhaps other organisms. These studies open the way for identification, characterization and use of protective cvcDNA as a potential shrimp vaccine and as a tool to identify, characterize and select naturally protective EVE to improve shrimp tolerance to homologous viruses in breeding programs.

Population Structure, Genetic Connectivity, and Signatures of Local Adaptation of the Giant Black Tiger Shrimp (Penaeus monodon) throughout the Indo-Pacific Region.

The giant black tiger shrimp (Penaeus monodon) is native to the Indo-Pacific and is the second most farmed penaeid shrimp species globally. Understanding genetic structure, connectivity, and local adaptation among Indo-Pacific black tiger shrimp populations is important for informing sustainable fisheries management and aquaculture breeding programs. Population genetic and outlier detection analyses were undertaken using 10,593 genome-wide single nucleotide polymorphisms (SNPs) from 16 geographically disparate Indo-Pacific P. monodon populations. Levels of genetic diversity were highest for Southeast Asian populations and were lowest for Western Indian Ocean (WIO) populations. Both neutral (n = 9,930) and outlier (n = 663) loci datasets revealed a pattern of strong genetic structure of P. monodon corresponding with broad geographical regions and clear genetic breaks among samples within regions. Neutral loci revealed seven genetic clusters and the separation of Fiji and WIO clusters from all other clusters, whereas outlier loci revealed six genetic clusters and high genetic differentiation among populations. The neutral loci dataset estimated five migration events that indicated migration to Southeast Asia from the WIO, with partial connectivity to populations in both oceans. We also identified 26 putatively adaptive SNPs that exhibited significant Pearson correlation (P < 0.05) between minor allele frequency and maximum or minimum sea surface temperature. Matched transcriptome contig annotations suggest putatively adaptive SNPs involvement in cellular and metabolic processes, pigmentation, immune response, and currently unknown functions. This study provides novel genome-level insights that have direct implications for P. monodon aquaculture and fishery management practices.

Infectious myonecrosis virus (IMNV) and Decapod iridescent virus 1 (DIV1) detected in captured, wild Penaeus monodon

Infectious myonecrosis virus (IMNV) was first discovered in the Americas in 2004 as a new lethal pathogen of cultivated whiteleg shrimp Penaeus vannamei, but infections were not lethal for the giant tiger shrimp Penaeus monodon. In 2007, it was reported in diseased P. vannamei cultivated in Indonesia but, until recently, not from other countries in Asia. Decapod iridescent virus (DIV1) was first reported from China in 2016 and is lethal for the crayfish Cherax quadricarinatus and Procambarus clarkii, for the penaeid shrimp P. vannamei and for the palaemonid shrimp Macrobrachium rosenbergii and Exopalaemon carinicauda. It has not yet been reported from other Asian countries. Here we describe the occurrence of positive test results for IMNV and DIV1 using polymerase chain reaction (PCR) technology during screening of grossly normal, broodstock-size, wild P. monodon captured and held in a biosecurity facility for screening. Amplicons for each virus were obtained from two widely separated targets in the relevant viral genomes listed at GenBank, and sequencing revealed 99–100% identity to the targets for each virus. Due to the positive results, the captured specimens were immediately destroyed within the quarantine facility. The results raised the possibility that grossly normal, captured P. monodon might serve as potential vehicles for introduction of IMNV and/or DIV1 to shrimp hatcheries and farms. Thus, we recommend that appropriate precautions be taken and that surveillance programs for farmed and wild populations be undertaken to avoid this possibility.

Full genome characterization of Laem Singh virus (LSNV) in shrimp Penaeus monodon

Laem Singh virus (LSNV) was discovered in 2006 and proposed as a necessary but insufficient cause of retarded growth in the giant tiger shrimp Penaeus monodon. Its closest relatives were plant viruses including an unassigned Sobemovirus and viruses in the family Luteoviridae. During succeeding years, attempts to obtain the full LSNV genome sequence by genome walking failed. However, recent publication of the full sequence of Wenzhou shrimp virus 9 (WZSV 9) at GenBank revealed that LSNV sequences in our database shared 99% sequence identity with it. Thus, we hypothesized that LSNV and WZSV 9 were different isolates of the same virus species. Here we confirm that hypothesis by cloning and sequencing of the full genome of LSNV from P. monodon and by showing that it consists of two fragments each with 99% identity to the matching fragments of WZSV.

Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis

BackgroundRestrictions to gene flow, genetic drift, and divergent selection associated with different environments are significant drivers of genetic differentiation. The black tiger shrimp (Penaeus monodon), is widely distributed throughout the Indian and Pacific Oceans including along the western, northern and eastern coastline of Australia, where it is an important aquaculture and fishery species. Understanding the genetic structure and the influence of environmental factors leading to adaptive differences among populations of this species is important for farm genetic improvement programs and sustainable fisheries management.ResultsBased on 278 individuals obtained from seven geographically disparate Australian locations, 10,624 high-quality SNP loci were used to characterize genetic diversity, population structure, genetic connectivity, and adaptive divergence. Significant population structure and differentiation were revealed among wild populations (average FST = 0.001–0.107; p < 0.05). Eighty-nine putatively outlier SNPs were identified to be potentially associated with environmental variables by using both population differentiation (BayeScan and PCAdapt) and environmental association (redundancy analysis and latent factor mixed model) analysis methods. Clear population structure with similar spatial patterns were observed in both neutral and outlier markers with three genetically distinct groups identified (north Queensland, Northern Territory, and Western Australia). Redundancy, partial redundancy, and multiple regression on distance matrices analyses revealed that both geographical distance and environmental factors interact to generate the structure observed across Australian P. monodon populations.ConclusionThis study provides new insights on genetic population structure of Australian P. monodon in the face of environmental changes, which can be used to advance sustainable fisheries management and aquaculture breeding programs.

Isolation of Differentially Expressed Transcripts by cDNA-AFLPaba and Expression Analysis of DEAD Box ATP-Dependent RNA Helicase 48 in Ovaries of the Giant Tiger Shrimp Penaeus monodon

Genes involved in ovarian development of the giant tiger shrimp (Penaeus monodon) were isolated by cDNA-AFLP analysis. In total, 75 primer combinations were screened against cDNA of different stages of ovaries (premature ovaries of juveniles and previtellogenic, vitellogenic and mature ovaries of wild intact and eyestalk-ablated broodstock; N = 6 for each group). Eighteen cDNA-AFLP fragments were cloned and sequenced. Nucleotide sequences of ten fragments significantly matched EF-1α (7e63), DEAD box ATP-dependent RNA helicase 48 (PmDdx48; 8e-61), tyrosine phosphatase n9 (1e-42), autophagy related protein Atg4-like protein (3e-36), nuclear pore complex protein nup154 (6e-20), GK14382 gene product (1e-20), L-3-hydroxyacryl coenzyme A dehydrogenase short chain (8e-13) and three different hypothetical proteins. The remaining fragments did not match any previously deposited sequence (E-value &gt; 10-4). The full-length cDNA of PmDdx48 was successfully characterized. It was 1646 bp containing an open reading frame (ORF) of 1209 bp corresponding to 402 amino acids. PmDdx48 was up-regulated in late vitellogenic and mature ovaries of wild intact broodstock and in mature ovaries of wild eyestalk-ablated broodstock (P&lt;0.05). Unilateral eyestalk ablation resulted in down-regulation of PmDdx48 in late vitellogenic and mature ovaries compared to that of wild intact broodstock (P&lt;0.05).

Comparative Proteomics for Identification of ReproductionRelated Proteins in Testes of the Giant Tiger Shrimp Penaeus monodon

Testicular proteome of wild and domesticated 14- and 18-month-old broodstock of the giant tiger shrimp Penaeus monodon was examined. Among 344 differentially expressed proteins identified, 11 proteins (e.g. p97/VCP-binding protein p135, lipoxygenase homology domains 1 and dipeptidyl-peptidase, accounting for 4.95% of proteins with known functions) were found in wild broodstock but not in domesticated broodstock while 152 (68.47%) proteins were commonly found in all groups of samples. Reproduction-related proteins such as vasa-like protein, Wee1-like protein kinase, serine/threonine protein kinase, mitogen activated protein kinase kinase 2, GTP-binding protein alpha subunit, seven membrane helix receptor, nuclear receptor subfamily 3, were identified. To examine a possible role of the signal transduction system in development of testes of P. monodon, the expression level of testicular serine/arginine rich-protein kinase 3 (PmSrpk3) mRNA of domesticated juveniles and broodstock was examined and it was significantly lower than that of wild P. monodon broodstock (P&lt;0.05). PmSrpk3 expression was significantly induced by serotonin (P&lt;0.05) but not progesterone (P&gt;0.05) injection. The expression profiles of PmSrpk3 indicated reduced reproductive maturation of domesticated male P. monodon and exogenous administration of serotonin may be applied for promoting the testicular development of captive P. monodon

Identification of a Growth-Associated Single Nucleotide Polymorphism (SNP) in Cyclin C of the Giant Tiger Shrimp Penaeus monodon.

The full-length cDNA of cyclin C of the giant tiger shrimp Penaeus monodon (PmCyC) was isolated by RACE-PCR. It was 1443bp in length containing an open reading frame (ORF) of 804bp and 267 deduced amino acids. Tissue distribution analysis indicated that PmCyC was more abundantly expressed in ovaries and testes than other tissues of female and male juveniles (P<0.05). A pair of primers was designed, and an amplification product of 403bp containing an intron of 123bp was obtained. Polymorphism of amplified PmCyC gene segments of the 5th (3-month-old G5, N=30) and 7th (5-month-old G7, N=18) generations of domesticated juveniles was analyzed. Four conserved SNPs (T>C134, T>C188, G>A379, and T>C382) were found within the examined sequences. A TaqMan genotyping assay was developed for detection of a T>C134 SNP. Association analysis indicated that this SNP displayed significant association with body weight (P<4.2e-10) and total length (P<2e-09) of the examined G7 P. monodon (N=419) with an allele substitution effect of 5.02±0.78g and 1.41±0.19cm, respectively. Juveniles with C/C134 (22.80±2.51g and 12.97±0.53cm, N=19) and T/C134 (20.41±0.93g and 12.77±0.21cm, N=129) genotypes exhibited a significantly greater average body weight and total length than those with a T/T134 genotype (14.72±0.53g and 11.37±0.13cm, N=271) (P<0.05).

Giant tiger shrimp (Penaeus monodon, Fabricius 1798) identification: A combined morphological and molecular approach

Giant tiger shrimp (Penaeus monodon, Fabricius 1798) identification: A combined morphological and molecular approach