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Jamaludin NA, Jamaluddin JAF, Rahim MA, Mohammed Akib NA, Ratmuangkhwang S, Mohd Arshaad W, Mohd Nor SA. Mitochondrial marker implies fishery separate management units for spotted sardinella, Amblygaster sirm (Walbaum, 1792) populations in the South China Sea and the Andaman Sea. PeerJ 2022; 10:e13706. [PMID: 35860045 PMCID: PMC9290996 DOI: 10.7717/peerj.13706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/19/2022] [Indexed: 01/17/2023] Open
Abstract
The spotted sardinella, Amblygaster sirm (Walbaum, 1792), is a commercial sardine commonly caught in Malaysia. Lack of management of these marine species in Malaysian waters could lead to overfishing and potentially declining fish stock populations. Therefore, sustainable management of this species is of paramount importance to ensure its longevity. As such, molecular information is vital in determining the A. sirm population structure and management strategy. In the present study, mitochondrial DNA Cytochrome b was sequenced from 10 A. sirm populations: the Andaman Sea (AS) (two), South China Sea (SCS) (six), Sulu Sea (SS) (one), and Celebes Sea (CS) (one). Accordingly, the intra-population haplotype diversity (Hd) was high (0.91-1.00), and nucleotide diversity (π) was low (0.002-0.009), which suggests a population bottleneck followed by rapid population growth. Based on the phylogenetic trees, minimum spanning network (MSN), population pairwise comparison, and F ST,and supported by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA) tests, distinct genetic structures were observed (7.2% to 7.6% genetic divergence) between populations in the SCS and its neighboring waters, versus those in the AS. Furthermore, the results defined A. sirm stock boundaries and evolutionary between the west and east coast (which shares the same waters as western Borneo) of Peninsular Malaysia. In addition, genetic homogeneity was revealed throughout the SCS, SS, and CS based on the non-significant F STpairwise comparisons. Based on the molecular evidence, separate management strategies may be required for A. sirm of the AS and the SCS, including its neighboring waters.
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Affiliation(s)
- Noorul Azliana Jamaludin
- Centre for Global Sustainability Studies (CGSS), Universiti Sains Malaysia, Penang, Malaysia,Marine Capture Fisheries Division, Fisheries Research Institute, Sitiawan, Perak, Malaysia
| | | | | | - Noor Adelyna Mohammed Akib
- Centre for Global Sustainability Studies (CGSS), Universiti Sains Malaysia, Penang, Malaysia,School of Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Sahat Ratmuangkhwang
- Andaman Coastal Research Station for Development, Kasetsart University, Ranong, Thailand
| | - Wahidah Mohd Arshaad
- Southeast Asia Fisheries Development Center (SEAFDEC), Marine Fisheries Resources Development and Management Department (MFRDMD), Kuala Terengganu, Terengganu, Malaysia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
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Thaijongrak P, Chotwiwatthanakun C, Laphyai P, Prachumwat A, Kruangkum T, Sobhon P, Vanichviriyakit R. Molecular characterization and expression profiling of transformer 2 and fruitless-like homologs in the black tiger shrimp, Penaeus monodon. PeerJ 2022; 10:e12980. [PMID: 35194532 PMCID: PMC8858584 DOI: 10.7717/peerj.12980] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 01/31/2022] [Indexed: 01/11/2023] Open
Abstract
Transformer 2 (tra 2) and fruitless (fru) genes have been proven to play a key role in sex determination pathways in many Arthropods, including insects and crustaceans. In this study, a paralog of P. monodon tra 2 (Pmtra 2), P. monodon ovarian associated transformer 2 (PmOvtra 2) and 2 isoforms of P. monodon fruitless-like gene (Pmfru-1 and Pmfru-2) were identified and characterized. The full cDNA sequence of PmOvtra 2 consisted of 1,774 bp with the longest open reading frame (ORF) of 744 bp encoding for 247 amino acids. The PmOvtra 2 exhibited a predicted RNA-recognition motif (RRM) domain and two arginine-serine (RS) regions, suggesting its function in RNA splicing. The full cDNA sequence of Pmfru-1 consisted of 1,306 bp with 1,182 bp ORF encoding for 393 amino acids, whereas the full cDNA sequence of Pmfru-2 consisted of 1,858 bp with 1,437 bp ORF encoding 478 amino acids. The deduced amino acid sequences of Pmfru-1 and Pmfru-2 exhibited highly conserved domains of Fru proteins, including Broad-complex, Tramtrack and Bric-a-brac (BTB), and zinc finger (ZF) domains. In addition, Pmfru-1 and Pmfru-2 were suggestively originated from the same single genomic locus by genomic sequence analysis. Specifically, Pmfru pre-mRNA was alternatively spliced for Pmfru-1 and Pmfru-2 to include mutually exclusive exon 7 and exon 6, respectively. Temporal and spatial expression of PmOvtra 2, Pmfru-1, and Pmfru-2 were also investigated by qPCR. The results showed that all were expressed in early developmental stages with undifferentiated gonads starting from nauplius until postlarvae. The expression of PmOvtra 2 started at nauplius stage and gradually increased from mysis to postlarvae (PL) 1. However, the expression of Pmfru-1 was low at the nauplii stage and slightly increased from protozoea to PL5, whereas the expression of Pmfru-2 maintained a low level from nauplius to mysis and then gradually increased at the PL stages. Expressions of PmOvtra 2, Pmfru-1, and Pmfru-2 were detected in various tissues including nervous tissue, gill, heart, hepatopancreas, gut, and gonads. Interestingly, the sexually dimorphic expression of PmOvtra 2, Pmfru-1, and Pmfru-2 was demonstrated in fully developed gonads in which the ovary showed significantly higher expressions than the testis. The great difference in the expression pattern of PmOvtra 2, Pmfru-1, and Pmfru-2 in the ovary and testis suggested their roles in the female sex determination in P. monodon.
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Affiliation(s)
- Prawporn Thaijongrak
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand,Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand,Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Charoonroj Chotwiwatthanakun
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand,Nakhonsawan Campus, Mahidol University, Nakhonsawan, Thailand
| | - Phaivit Laphyai
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand,Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Anuphap Prachumwat
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand,National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Thanapong Kruangkum
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand,Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Prasert Sobhon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Rapeepun Vanichviriyakit
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand,Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
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Genetic diversity and population structure of wild and domesticated black tiger shrimp (Penaeus monodon) broodstocks in the Indo-Pacific regions using consolidated mtDNA and microsatellite markers. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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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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Sajeela KA, Gopalakrishnan A, Basheer VS, Mandal A, Bineesh KK, Grinson G, Gopakumar SD. New insights from nuclear and mitochondrial markers on the genetic diversity and structure of the Indian white shrimp Fenneropenaeus indicus among the marginal seas in the Indian Ocean. Mol Phylogenet Evol 2019; 136:53-64. [PMID: 30954588 DOI: 10.1016/j.ympev.2019.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 03/09/2019] [Accepted: 04/03/2019] [Indexed: 01/03/2023]
Abstract
Genetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho = 0.44 ± 0.02) and the expected heterozygosity (He = 0.73 ± 0.01) were high across loci and populations indicating high microsatellite variation. Pairwise FST and Bayesian clustering indicated the occurrence of four genetically distinct stocks out of the eight sampled populations with implications for specific management approaches. Mantel test for isolation by distance proved that genetic differentiation is not related to geographic distance between populations. Mitochondrial COI sequence analysis showed concordant differentiation pattern as well indicated the relevance of COI in population genetics of shrimps. Pairwise ɸST and phylogenetic and Bayesian analyses revealed four distinct clades, as observed with nuclear markers. Divergence time analysis revealed the origin and initial divergence of F. indicus corresponds to late Miocene and divergence to phylogroups in the Pleistocene. BSP analysis presented a long stable population size with a slight decrease in the late Pleistocene and gradually expanded to the current status. The information here will be useful in commercial shrimp breeding and selection programmes and management of natural stocks of Indian white shrimp.
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Affiliation(s)
- K A Sajeela
- Central Marine Fisheries Research Institute, Kochi 682 018, Kerala, India.
| | - A Gopalakrishnan
- Central Marine Fisheries Research Institute, Kochi 682 018, Kerala, India
| | - V S Basheer
- Peninsular and Marine Fish Genetic Resources (PMFGR) Centre-NBFGR, CMFRI, Kochi 682 018, Kerala, India
| | - A Mandal
- Rajiv Gandhi Centre for Aquaculture (RGCA), Sirkali 609 113, Nagapattinam, Tamil Nadu, India
| | - K K Bineesh
- Zoological Survey of India, Andaman and Nicobar Regional Centre, Haddo, Port Blair 744 102, India
| | - G Grinson
- Central Marine Fisheries Research Institute, Kochi 682 018, Kerala, India
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SriHari M, Abidi ZJ, Ayyathurai K. Lack of genetic differentiation in milkfish, Chanos chanos (Forsskål, 1775), revealed by mitochondrial ATPase 6/8 genes. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:511-516. [PMID: 30836041 DOI: 10.1080/24701394.2019.1568425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The milkfish, Chanos chanos, is a commercially important cultured species which is distributed throughout south and southeast Asian countries. Captive breeding and seed production techniques have been standardized recently in India and there is a need for analyzing its population structure along the Indian coast. A total of 80 samples from four different locations across the Indian coast were analyzed by using ATPase 6/8 genes. Analysis revealed the existence of 25 haplotypes across populations with the haplotype diversity in the range of 0.5684-0.8053 and the nucleotide diversity varied from 0.001838 to 0.002519. The variation within and among populations accounted for 97.43% and 2.75%, respectively. The observed FST values were found to be non-significant (p > 0.05). Results from this study indicated that there is lack of genetic divergence between the populations of milkfish along the Indian coast.
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Affiliation(s)
- Murugesan SriHari
- a Department of Fisheries Resource Management, ICAR-Central Institute of Fisheries Education , Mumbai , India
| | - Zeba Jaffer Abidi
- a Department of Fisheries Resource Management, ICAR-Central Institute of Fisheries Education , Mumbai , India
| | - Kathirvelpandian Ayyathurai
- b Peninsular and Marine Fish Genetic Resources Centre , ICAR - National Bureau of Fish Genetic Resources , Cochin , India
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Gopalakrishnan A, Vineesh N, Ismail S, Menon M, Akhilesh KV, Jeena NS, Paulton MP, Vijayagopal P. Mitochondrial signatures revealed panmixia in Lutjanus argentimaculatus (Forsskål 1775). J Genet 2018. [DOI: 10.1007/s12041-018-0899-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Rumisha C, Leermakers M, Elskens M, Mdegela RH, Gwakisa P, Kochzius M. Genetic diversity of the giant tiger prawn Penaeus monodon in relation to trace metal pollution at the Tanzanian coast. MARINE POLLUTION BULLETIN 2017; 114:759-767. [PMID: 27829502 DOI: 10.1016/j.marpolbul.2016.10.057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/21/2016] [Accepted: 10/22/2016] [Indexed: 06/06/2023]
Abstract
The genetic diversity of giant tiger prawns in relation to trace metals (TMs) pollution was analysed using 159 individuals from eight sites at the Tanzanian coast. The seven microsatellites analysed showed high degree of polymorphism (4-44 alleles). The measured genetic diversity (Ho=0.592±0.047) was comparable to that of populations in the Western Indian Ocean. Apart from that, correlation analysis revealed significant negative associations between genetic diversity and TMs pollution (p<0.05), supporting the genetic erosion hypothesis. Limited gene flow was indicated by a significant genetic differentiation (FST=0.059, p<0.05). The Mantel test rejected the isolation-by-distance hypothesis, but revealed that gene flow along the Tanzanian coast is limited by TMs pollution. This suggests that TMs affect larvae settlement and it may account for the measured deficiency of heterozygosity. This calls for strengthened pollution control measures in order to conserve this commercially important species.
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Affiliation(s)
- Cyrus Rumisha
- Vrije Universiteit Brussel (VUB), Ecology and Biodiversity, Marine Biology, Pleinlaan 2, 1050 Brussels, Belgium; Sokoine University of Agriculture, Department of Biological Sciences, 3038 Morogoro, Tanzania.
| | - Martine Leermakers
- Vrije Universiteit Brussel (VUB), Analytical, Environmental and Geo-Chemistry, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marc Elskens
- Vrije Universiteit Brussel (VUB), Analytical, Environmental and Geo-Chemistry, Pleinlaan 2, 1050 Brussels, Belgium
| | - Robinson H Mdegela
- Sokoine University of Agriculture, Department of Medicine & Public Health, 3021 Morogoro, Tanzania
| | - Paul Gwakisa
- Sokoine University of Agriculture, Department of Microbiology, Parasitology and Immunology, Genome Science Center, 3019 Morogoro, Tanzania
| | - Marc Kochzius
- Vrije Universiteit Brussel (VUB), Ecology and Biodiversity, Marine Biology, Pleinlaan 2, 1050 Brussels, Belgium
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Vineesh N, Kathirvelpandian A, Divya PR, Mohitha C, Basheer VS, Gopalakrishnan A, Jena JK. Hints for panmixia in Scomberomorus commerson in Indian waters revealed by mitochondrial ATPase 6 and 8 genes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2822-4. [PMID: 26104155 DOI: 10.3109/19401736.2015.1053084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Scomberomorus commerson is an economically important migratory fish distributed worldwide. The genetic stock structure of S. commerson distributed along the Indian waters was identified using mitochondrial ATPase 6 and 8 genes. A total of 842 bp sequence of ATPase 6/8 genes obtained in this study revealed 23 haplotypes with mean low nucleotide diversity and high haplotype diversity. Co-efficient of genetic differentiation (FST) values obtained for pair wise populations were low and non-significant with an overall value of -0.02074. The high haplotype and low nucleotide diversity values together with mismatch distribution analysis suggested a history of genetic bottleneck events or founder effect, with subsequent population expansion in S. commerson. The findings of the present study indicated the panmixia nature of the species which can be managed as a unit stock in Indian waters.
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Affiliation(s)
- N Vineesh
- a Peninsular and Marine Fish Genetic Resources Centre, NBFGR, CMFRI Campus , Cochin , Kerala , India
| | - A Kathirvelpandian
- a Peninsular and Marine Fish Genetic Resources Centre, NBFGR, CMFRI Campus , Cochin , Kerala , India
| | - P R Divya
- a Peninsular and Marine Fish Genetic Resources Centre, NBFGR, CMFRI Campus , Cochin , Kerala , India
| | - C Mohitha
- a Peninsular and Marine Fish Genetic Resources Centre, NBFGR, CMFRI Campus , Cochin , Kerala , India
| | - V S Basheer
- a Peninsular and Marine Fish Genetic Resources Centre, NBFGR, CMFRI Campus , Cochin , Kerala , India
| | - A Gopalakrishnan
- b Central Marine Fisheries Research Institute , Cochin , Kerala , India , and
| | - J K Jena
- c National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India
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Divya PR, Gopalakrishnan A, Basheer VS, Swaminathan R, Mohitha C, Joy L, Kumar R, Manoj P, Jena JK. Mitochondrial ATPase 6/8 genes to infer the population genetic structure of silver pomfret fishPampus argenteusalong the Indian waters. ACTA ACUST UNITED AC 2014; 26:189-94. [DOI: 10.3109/19401736.2013.879655] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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High levels of genetic diversity in Penaeus monodon populations from the east coast of India. SPRINGERPLUS 2013; 2:671. [PMID: 24363984 PMCID: PMC3868705 DOI: 10.1186/2193-1801-2-671] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/26/2013] [Indexed: 11/10/2022]
Abstract
Quality production of the shrimp Penaeus monodon in hatchery operations depends heavily on the evaluation of genetic diversity and population structure of brood stocks. Mitochondrial DNA (mtDNA) sequences have been widely used to study genetic variability and relationships in many crustacean groups, and these same markers may be incorporated into evaluation studies of shrimp broods and populations. For this purpose we looked at variation in mitochondrial D-loop sequences as an indicator of genetic diversity in shrimp populations from a region of India that represents the main sources of new material for brood stocks. In our study of these populations the overall mean genetic diversity was 0.191. The highest level of genetic diversity (0.357) was observed in the Kakinada population, whereas the lowest diversity (0.0171) was observed in the Nellore population. The results also indicate that overall, the populations along the Andhra Pradesh coast are genetically diverse despite the fact that there is considerable gene flow between them. From the results, it is evident that east cost of India shows high genetic diversity among P. monodon broods and no evidence of loss of diversity due to excessive inbreeding. The fact that the genetic variability of these populations has been maintained, despite ten years of dependence on these broods, shows that at the present time there is no indication of over exploitation.
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Liu T, Yu Z, Han L, Wang X, Liu C. Experimental and theoretical study on the 1:1 supramolecular complexes of formamide with adrenaline. Gene 2012; 496:136-40. [DOI: 10.1016/j.gene.2012.01.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 01/18/2012] [Indexed: 11/30/2022]
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