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Mondal D, Mandal N. Ecological perspective of disease‐resistance prevalence in
Penaeus monodon. Transbound Emerg Dis 2020; 67:3049-3055. [DOI: 10.1111/tbed.13715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/26/2020] [Accepted: 06/30/2020] [Indexed: 11/30/2022]
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Mondal D, Dutta S, Chakrabarty U, Mallik A, Mandal N. Development and characterization of white spot disease linked microsatellite DNA markers in Penaeus monodon, and their application to determine the population diversity, cluster and structure. J Invertebr Pathol 2019; 168:107275. [PMID: 31715182 DOI: 10.1016/j.jip.2019.107275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 11/03/2019] [Accepted: 11/07/2019] [Indexed: 11/15/2022]
Abstract
Pathogens that are introduced suddenly to natural populations can potentially cause quick changes to the genetics and diversity of the host. In the past three decades, white spot syndrome virus (WSSV) has caused damaging epizootics in Penaeus monodon populations. In this study, we developed WSSV resistance- or susceptibility-linked microsatellite DNA markers, and their effectiveness was validated experimentally. WSSV-resistant marker linked retroelements and genes that may have an important role in WSSV-resistance phenomena were partially identified. Allelic data of 1,694 samples from nine distinct geographic locations in India were revealed that populations from Digha and Kochi were highly dispersed, and also showed higher genetic diversity, higher population diversity, and lower prevalence of disease resistance. A very high level of gene flow was observed within all populations and a very high level of genetic variation was present within populations. Two genetically admixture population clusters were estimated in nature. WSSV-resistance has a significant link with genetic diversity, population cluster and population diversity. Microsatellite marker analysis characterized genetic divergence, diversity and structure among wild populations.
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Affiliation(s)
- Debabrata Mondal
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata 700054, West Bengal, India
| | - Sourav Dutta
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata 700054, West Bengal, India
| | - Usri Chakrabarty
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata 700054, West Bengal, India
| | - Ajoy Mallik
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata 700054, West Bengal, India; Department of Zoology, Dinabandhu Mahavidyalaya, Bongaon, North 24 Parganas, West Bengal, India
| | - Nripendranath Mandal
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata 700054, West Bengal, India.
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XU W, CHEN S. Genomics and genetic breeding in aquatic animals: progress and prospects. FRONTIERS OF AGRICULTURAL SCIENCE AND ENGINEERING 2017; 4:305. [DOI: 10.15302/j-fase-2017154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Chen X, Li J, Xiao S, Liu X. De novo assembly and characterization of foot transcriptome and microsatellite marker development for Paphia textile. Gene 2015; 576:537-43. [PMID: 26546834 DOI: 10.1016/j.gene.2015.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/18/2015] [Accepted: 11/01/2015] [Indexed: 11/27/2022]
Abstract
Paphia textile is an important, aquaculture bivalve clam species distributed mainly in China, Philippines, and Malaysia. Recent studies of P. textile have focused mainly on artificial breeding and nutrition analysis, and the transcriptome and genome of P. textile have rarely been reported. In this work, the transcriptome of P. textile foot tissue was sequenced on an Illumina HiSeq™ 2000 platform. A total of 20,219,795 reads were generated, resulting in 4.08 Gb of raw data. The raw reads were cleaned and assembled into 54,852 unigenes with an N50 length of 829 bp. Of these unigenes, 38.92% were successfully annotated based on their matches to sequences in seven public databases. Among the annotated unigenes, 14,571 were assigned Gene Ontology terms, 5448 were classified to Clusters of Orthologous Groups categories, and 6738 were mapped to 228 pathways in the Kyoto Encyclopedia of Genes and Genomes database. For functional marker development, 5605 candidate simple sequence repeats were identified in the transcriptome and 80 primer pairs were selected randomly and amplified in a wild population of P. textile. A total of 36 loci that exhibited obvious repeat length polymorphisms were detected. The transcriptomic data and microsatellite markers will provide valuable resources for future functional gene analyses, genetic map construction, and quantitative trait loci mapping in P. textile.
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Affiliation(s)
- Xiaoming Chen
- Key Laboratory of Mariculture in the East China Sea, Ministry of Agriculture of China, Fisheries College, Jimei University, Xiamen 361021, China
| | - Jiakai Li
- Key Laboratory of Mariculture in the East China Sea, Ministry of Agriculture of China, Fisheries College, Jimei University, Xiamen 361021, China
| | - Shijun Xiao
- Key Laboratory of Mariculture in the East China Sea, Ministry of Agriculture of China, Fisheries College, Jimei University, Xiamen 361021, China
| | - Xiande Liu
- Key Laboratory of Mariculture in the East China Sea, Ministry of Agriculture of China, Fisheries College, Jimei University, Xiamen 361021, China.
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Chakrabarty U, Dutta S, Mallik A, Mondal D, Mandal N. Identification and characterisation of microsatellite DNA markers in order to recognise the WSSV susceptible populations of marine giant black tiger shrimp, Penaeus monodon. Vet Res 2015; 46:110. [PMID: 26407974 PMCID: PMC4582847 DOI: 10.1186/s13567-015-0248-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/21/2015] [Indexed: 11/10/2022] Open
Abstract
White spot disease (WSD) which is caused by white spot syndrome virus (WSSV) creates severe epizootics in captured and cultured black tiger shrimp, resulting a huge loss in the economic output of the aquaculture industry worldwide. Performing selective breeding using DNA markers would prove to be a potential cost effective strategy for long term disease control in shrimps. In the present investigation, microsatellite DNA fingerprints were compared between naturally occurring WSSV resistant and susceptible populations of Penaeus monodon. After PCR with a set of shrimp specific primers three reproducible DNA fragments of varying sizes were found, among which 442 bp and 236 bp fragments were present in considerably higher frequencies in the WSSV susceptible shrimp population (p ≤ 0.0001). After WSSV challenge experiment the copy no. of WSSV was determined using real-time PCR, where it was found to be almost 4 × 10(3) fold higher in WSSV susceptible shrimps than in the resistant ones. Thus, these microsatellite DNA markers will be useful to distinguish between WSSV susceptible and resistant brood stocks of P. monodon. Sequencing studies revealed that these DNA markers were novel in P. monodon. Highest WSSV resistance using these DNA markers, was observed in the shrimp populations of Andaman Island and Chennai among the different coastal areas of India, suggesting these places as safe for specific pathogen resistant brood stock shrimp collection. This study will be a very effective platform towards understanding the molecular pathogenesis of WSD for generation of disease free shrimp aquaculture industry.
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Affiliation(s)
- Usri Chakrabarty
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata, 700054, India.
| | - Sourav Dutta
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata, 700054, India.
| | - Ajoy Mallik
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata, 700054, India.
| | - Debabrata Mondal
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata, 700054, India.
| | - Nripendranath Mandal
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII-M, Kolkata, 700054, India.
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Lafferty KD, Harvell CD, Conrad JM, Friedman CS, Kent ML, Kuris AM, Powell EN, Rondeau D, Saksida SM. Infectious diseases affect marine fisheries and aquaculture economics. ANNUAL REVIEW OF MARINE SCIENCE 2015; 7:471-96. [PMID: 25251276 DOI: 10.1146/annurev-marine-010814-015646] [Citation(s) in RCA: 269] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Seafood is a growing part of the economy, but its economic value is diminished by marine diseases. Infectious diseases are common in the ocean, and here we tabulate 67 examples that can reduce commercial species' growth and survivorship or decrease seafood quality. These impacts seem most problematic in the stressful and crowded conditions of aquaculture, which increasingly dominates seafood production as wild fishery production plateaus. For instance, marine diseases of farmed oysters, shrimp, abalone, and various fishes, particularly Atlantic salmon, cost billions of dollars each year. In comparison, it is often difficult to accurately estimate disease impacts on wild populations, especially those of pelagic and subtidal species. Farmed species often receive infectious diseases from wild species and can, in turn, export infectious agents to wild species. However, the impact of disease export on wild fisheries is controversial because there are few quantitative data demonstrating that wild species near farms suffer more from infectious diseases than those in other areas. The movement of exotic infectious agents to new areas continues to be the greatest concern.
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Affiliation(s)
- Kevin D Lafferty
- Western Ecological Research Center, US Geological Survey, c/o Marine Science Institute, University of California, Santa Barbara, California 93106; *
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Blaylock RB, Bullard SA. Counter-Insurgents of the Blue Revolution? Parasites and Diseases Affecting Aquaculture and Science. J Parasitol 2014; 100:743-55. [DOI: 10.1645/14-605.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Chakrabarty U, Mallik A, Mondal D, Dutta S, Mandal N. Assessment of WSSV prevalence and distribution of disease-resistant shrimp among the wild population of Penaeus monodon along the west coast of India. J Invertebr Pathol 2014; 119:12-8. [DOI: 10.1016/j.jip.2014.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/19/2014] [Accepted: 03/22/2014] [Indexed: 10/25/2022]
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Dutta S, Biswas S, Mukherjee K, Chakrabarty U, Mallik A, Mandal N. Identification of RAPD-SCAR marker linked to white spot syndrome virus resistance in populations of giant black tiger shrimp, Penaeus monodon Fabricius. JOURNAL OF FISH DISEASES 2014; 37:471-480. [PMID: 23952572 DOI: 10.1111/jfd.12128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 04/15/2013] [Accepted: 04/18/2013] [Indexed: 06/02/2023]
Abstract
White spot disease (WSD) caused by white spot syndrome virus (WSSV) creates severe epizootics in shrimp aquaculture industry worldwide. Despite several efforts, no such permanent remedy was yet developed. Selective breeding using DNA markers would be a cost-effective strategy for long-term solution of this problem. In the present investigation, out of 30 random primers, only one primer produced a statistically significant (P < 0.01) randomly amplified polymorphic DNA (RAPD) marker of 502 bp, which provided a good discrimination between disease resistant and disease susceptible populations of Penaeus monodon from three geographical locations along the East coast of India. Because RAPD markers are dominant, a sequence characterized amplified region (SCAR) marker was developed by cloning and sequencing of 502 bp RAPD fragment, which generates a single 457 bp DNA fragment after PCR amplification only in the disease resistant shrimps. Challenge experiment was also conducted to validate this 457 bp SCAR marker, and the results suggested that the WSSV loads were 2.25 × 10(3) fold higher in disease susceptible than that in disease resistant shrimps using real-time PCR. Therefore, this 457 bp DNA SCAR marker will be very valuable towards the development of disease-free shrimp aquaculture industry.
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Affiliation(s)
- S Dutta
- Division of Molecular Medicine, Bose Institute, Kolkata, India
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Mallik A, Chakrabarty U, Dutta S, Mondal D, Mandal N. Study on the Distribution of Disease-Resistant Shrimp Identified by DNA Markers in Respect to WSSV Infection in Different Seasons Along the Entire East Coast of India Aiming to Prevent White Spot Disease inPenaeus monodon. Transbound Emerg Dis 2014; 63:e48-57. [DOI: 10.1111/tbed.12230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Indexed: 11/30/2022]
Affiliation(s)
- A. Mallik
- Division of Molecular Medicine; Bose Institute; Kolkata India
| | - U. Chakrabarty
- Division of Molecular Medicine; Bose Institute; Kolkata India
| | - S. Dutta
- Division of Molecular Medicine; Bose Institute; Kolkata India
| | - D. Mondal
- Division of Molecular Medicine; Bose Institute; Kolkata India
| | - N. Mandal
- Division of Molecular Medicine; Bose Institute; Kolkata India
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