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Jose A, Sukumaran S, Roul SK, Azeez PA, Kizhakudan SJ, Raj N, Nisha K, Gopalakrishnan A. Genetic analyses reveal panmixia in Indian waters and population subdivision across Indian Ocean and Indo-Malay Archipelago for Decapterus russelli. Sci Rep 2023; 13:22860. [PMID: 38129501 PMCID: PMC10739887 DOI: 10.1038/s41598-023-49805-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
The Indian Scad, Decapterus russelli is an important pelagic carangid widely distributed throughout the Indian Ocean and the Indo-West Pacific. Despite being widely distributed in the Indian Ocean, the information regarding genetic structuring and diversity has been lacking compared to its Indo Malay Archipelago counterparts. The present study was conducted to investigate the genetic stock structure of D. russelli based on mitochondrial (Cyt b) and nuclear (DrAldoB1) markers along Indian waters. The results indicated the presence of a single panmictic stock across the Indian Ocean region. High haplotype diversity associated with low nucleotide diversity suggested a population bottleneck followed by rapid population growth. Phylogenetic analysis revealed the absence of geographical clustering of lineages with the most common haplotype distributed globally. The pelagic life style, migratory capabilities, and larval dispersal may be the contributing factors to the observed spatial homogeneity of D. russelli. However, significant genetic differentiation was observed between the populations from Indian Ocean and Indo-Malay Archipelago. Hierarchical molecular variance analysis (AMOVA), pairwise FST comparisons and SAMOVA showed existence of two distinct genetic stocks of D. russelli in the Indian Ocean and IMA. The observed interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the Indo-Malay Archipelago and the Indian Ocean regions suggest the influence of historic isolation, ocean surface currents and biotic and abiotic features of the ocean. Also, there was a significant relationship between genetic distance and geographical distance between population pairs in a manner consistent with isolation-by-distance. These resulted in the evolution of a phylogeographic break for this species between these regions. The findings of these results suggest that D. russelli from the Indian Ocean shall be managed in its entire area of distribution as a single stock. Further, the Indian Ocean and Indo-Malayan stocks can be managed separately.
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Affiliation(s)
- Anjaly Jose
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India.
- Mangalore University, Mangalagangotri, Mangalore, Karnataka, 574199, India.
| | - Sandhya Sukumaran
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - Subal Kumar Roul
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - P Abdul Azeez
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - Shoba Joe Kizhakudan
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - Neenu Raj
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - K Nisha
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- Marine Biotechnology Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P O, Kochi, Kerala, 682018, India
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Sukumaran S, Sebastian W, Gopalakrishnan A, Mathew OK, Vysakh VG, Rohit P, Jena JK. The sequence and de novo assembly of the genome of the Indian oil sardine, Sardinella longiceps. Sci Data 2023; 10:565. [PMID: 37626109 PMCID: PMC10457283 DOI: 10.1038/s41597-023-02481-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The Indian oil sardine, Sardinella longiceps, is a widely distributed and commercially important small pelagic fish of the Northern Indian Ocean. The genome of the Indian oil sardine has been characterized using Illumina and Nanopore platforms. The assembly is 1.077 Gb (31.86 Mb Scaffold N50) in size with a repeat content of 23.24%. The BUSCO (Benchmarking Universal Single Copy Orthologues) completeness of the assembly is 93.5% when compared with Actinopterygii (ray finned fishes) data set. A total of 46316 protein coding genes were predicted. Sardinella longiceps is nutritionally rich with high levels of omega-3 polyunsaturated fatty acids (PUFA). The core genes for omega-3 PUFA biosynthesis, such as Elovl 1a and 1b,Elovl 2, Elovl 4a and 4b,Elovl 8a and 8b,and Fads 2, were observed in Sardinella longiceps. The presence of these genes may indicate the PUFA biosynthetic capability of Indian oil sardine, which needs to be confirmed functionally.
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Affiliation(s)
- Sandhya Sukumaran
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India.
| | - Wilson Sebastian
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - Oommen K Mathew
- Agrigenome Labs Pvt. Ltd., Kakkanad, Kochi, Kerala, 682042, India
| | - V G Vysakh
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - Prathibha Rohit
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - J K Jena
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
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Mitochondrial DNA based diversity studies reveal distinct and sub-structured populations of pearlspot, Etroplus suratensis (Bloch, 1790) in Indian waters. J Genet 2022. [DOI: 10.1007/s12041-021-01341-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Sebastian W, Sukumaran S, Abdul Azeez S, Muraleedharan KR, Dinesh Kumar PK, Zacharia PU, Gopalakrishnan A. Genomic investigations provide insights into the mechanisms of resilience to heterogeneous habitats of the Indian Ocean in a pelagic fish. Sci Rep 2021; 11:20690. [PMID: 34667208 PMCID: PMC8526693 DOI: 10.1038/s41598-021-00129-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/05/2021] [Indexed: 11/08/2022] Open
Abstract
The adaptive genetic variation in response to heterogeneous habitats of the Indian Ocean was investigated in the Indian oil sardine using ddRAD sequencing to understand the subpopulation structure, stock complexity, mechanisms of resilience, and vulnerability in the face of climate change. Samples were collected from different ecoregions of the Indian ocean and ddRAD sequencing was carried out. Population genetic analyses revealed that samples from the Gulf of Oman significantly diverged from other Indian Ocean samples. SNP allele-environment correlation revealed the presence of candidate loci correlated with the environmental variables like annual sea surface temperature, chlorophyll-a, and dissolved oxygen concentration which might represent genomic regions allegedly diverging as a result of local adaptation. Larval dispersal modelling along the southwest coast of India indicated a high dispersal rate. The two major subpopulations (Gulf of Oman and Indian) need to be managed regionally to ensure the preservation of genetic diversity, which is crucial for climatic resilience.
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Affiliation(s)
- Wilson Sebastian
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India.
| | - Sandhya Sukumaran
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - S Abdul Azeez
- CSIR-National Institute of Oceanography, Regional Centre Kochi, Dr Salim Ali Road, Post Box No. 1913, Kochi, Kerala, India
| | - K R Muraleedharan
- CSIR-National Institute of Oceanography, Regional Centre Kochi, Dr Salim Ali Road, Post Box No. 1913, Kochi, Kerala, India
| | - P K Dinesh Kumar
- CSIR-National Institute of Oceanography, Regional Centre Kochi, Dr Salim Ali Road, Post Box No. 1913, Kochi, Kerala, India
| | - P U Zacharia
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
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Supmee V, Songrak A, Suppapan J, Sangthong P. Population Genetic Structure of Ornate Threadfin Bream ( Nemipterus hexodon) in Thailand. Trop Life Sci Res 2021; 32:63-82. [PMID: 33936551 PMCID: PMC8054670 DOI: 10.21315/tlsr2021.32.1.4] [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] [Indexed: 10/27/2022] Open
Abstract
Ornate threadfin bream (Nemipterus hexodon) is an economically important fishery species in Southeast Asia. In Thailand, N. hexodon decreased dramatically due to overexploitation for commercial purposes. To construct an effective sustainable management plan, genetic information is necessary. Thus, in our study, the population genetic structure and demographic history of N. hexodon were investigated using 419 bp of the mitochondrial DNA sequence in cytochrome oxidase subunit I gene (mtDNA COI). A total of 142 samples was collected from nine localities in the Gulf of Thailand (Chonburi, Samut Songkhram, Surat Thani, Nakhon Si Thammarat, Songkhla), and the Andaman Sea (Satun, Trang, Krabi, Phang Nga). Fourteen polymorphic sites defined 18 haplotypes, revealing a high haplotype diversity and low nucleotide diversity among nine localities. The analysis of molecular variance (AMOVA) analysis, pairwise F ST , and minimum spanning network result revealed that the genetic structure of N. hexodon was separated into two populations: the Gulf of Thailand and the Andaman Sea population. The genetic structure of N. hexodon can be explained by a disruption of gene flow from the geographic barrier and the Pleistocene isolation of the marine basin hypothesis. Neutrality tests, Bayesian skyline analysis, mismatch distribution, and the estimated values of population growth suggested that N. hexodon had experienced a population expansion. The genetic information would certainly help us gain insight into the population genetic structure of N. hexodon living on the coast of Thailand.
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Affiliation(s)
- Verakiat Supmee
- Department of Science, Faculty of Science and Technology, Rajamangala University of Technology Srivijaya, Nakhon Si Thammarat Campus, Nakhon Si Thammarat 80110, Thailand
| | - Apirak Songrak
- Department of Fishery Technology, Faculty of Science and Fisheries Technology, Rajamangala University of Technology Srivijaya, Trang Campus, Trang 92150, Thailand
| | - Juthamas Suppapan
- Faculty of Education, Nakhon Si Thammarat Rajabhat University, Nakhon Si Thammarat 80280, Thailand
| | - Pradit Sangthong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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Signals of selection in the mitogenome provide insights into adaptation mechanisms in heterogeneous habitats in a widely distributed pelagic fish. Sci Rep 2020; 10:9081. [PMID: 32493917 PMCID: PMC7270097 DOI: 10.1038/s41598-020-65905-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/04/2020] [Indexed: 11/08/2022] Open
Abstract
Oceans are vast, dynamic, and complex ecosystems characterized by fluctuations in environmental parameters like sea surface temperature (SST), salinity, oxygen availability, and productivity. Environmental variability acts as the driver of organismal evolution and speciation as organisms strive to cope with the challenges. We investigated the evolutionary consequences of heterogeneous environmental conditions on the mitogenome of a widely distributed small pelagic fish of Indian ocean, Indian oil sardine, Sardinella longiceps. Sardines were collected from different eco-regions of the Indian Ocean and selection patterns analyzed in coding and non-coding regions. Signals of diversifying selection were observed in key functional regions involved in OXPHOS indicating OXPHOS gene regulation as the critical factor to meet enhanced energetic demands. A characteristic control region with 38–40 bp tandem repeat units under strong selective pressure as evidenced by sequence conservation and low free energy values was also observed. These changes were prevalent in fishes from the South Eastern Arabian Sea (SEAS) followed by the Northern Arabian Sea (NAS) and rare in Bay of Bengal (BoB) populations. Fishes belonging to SEAS exhibited accelerated substitution rate mainly due to the selective pressures to survive in a highly variable oceanic environment characterized by seasonal hypoxia, variable SST, and food availability.
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Sukumaran S, Sebastian W, Francis KX, Gopalakrishnan A. Contemporary and historic patterns of intraspecific diversity in Indian anchovy, Stolephorus indicus, from Indian peninsular waters. Genetica 2019; 147:259-267. [PMID: 31144087 DOI: 10.1007/s10709-019-00068-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 05/25/2019] [Indexed: 10/26/2022]
Abstract
We analyzed intraspecific diversity of Indian anchovy, Stolephorus indicus, a commercially and ecologically important species, using mitochondrial DNA markers so as to derive insights into population structuring and historical demography. Analyses were carried out on 128 and 138 individuals collected from 5 locations along the range of distribution using mitochondrial ATPase (843 bp) and COI (663 bp) sequences respectively. Significant connectivity and gene flow was detected among fishes collected from all the geographic locations as indicated by lack of structuring in Bayesian clustering analysis along with insignificant ΦST values. Oceanographic features of the Bay of Bengal, Arabian Sea and Andaman Sea may be favorable for the dispersal of anchovy larvae and subsequent gene flow. Historical demographic analyses indicated a demographic and spatial expansion taken place approximately during 125,000 years before present, the Pleistocene epoch. Indian Ocean witnessed emergence of upwelling events and consequent increase in productivity during the Pleistocene epoch causing a demographic and spatial expansion of anchovies. Management measures for this species should be devised considering it as a single stock along its entire range of distribution.
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Affiliation(s)
- Sandhya Sukumaran
- ICAR-Central Marine Fisheries Research Institute, Post Box No 1603, Ernakulam North P.O., Kochi, Kerala, 682018, India.
| | - Wilson Sebastian
- ICAR-Central Marine Fisheries Research Institute, Post Box No 1603, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - K X Francis
- ICAR-Central Marine Fisheries Research Institute, Post Box No 1603, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- ICAR-Central Marine Fisheries Research Institute, Post Box No 1603, Ernakulam North P.O., Kochi, Kerala, 682018, 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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The complete mitochondrial genome and phylogeny of Indian oil sardine, Sardinella longiceps and Goldstripe Sardinella, Sardinella gibbosa from the Indian Ocean. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0918-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Genetic population structure of Indian oil sardine, Sardinella longiceps assessed using microsatellite markers. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0946-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Population Structure of Blue Marlin, Makaira nigricans, in the Pacific and Eastern Indian Oceans. Zool Stud 2016; 55:e33. [PMID: 31966178 DOI: 10.6620/zs.2016.55-33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 04/20/2016] [Indexed: 11/18/2022]
Abstract
Hui Chen, Chia-Hao Chang, Chi-Lu Sun, Kwang-Tsao Shao, Su-Zan Yeh, and Gerard DiNardo (2016) Blue marlin Makaira nigricans is economically important for fisheries worldwide. However, overfishing has substantially reduced the stock size. Better knowledge of blue marlin population genetics will help improve management and conservation. Previous genetic studies concluded that the Pacific blue marlin should be considered a single stock. This study investigated the population genetic structure of blue marlin inhabiting the Pacific and eastern Indian oceans based on mtDNA cytochrome b (cyt b) and control region (CR) sequence variation. We collected tissue samples (n = 183) from three Pacific and one Indian Ocean, and determined the sequences of 1140 bp of cyt b and 905 bp of CR. Phylogenetic analysis revealed that blue marlin contain two clades, the Atlantic clade and the ubiquitous clade, and that all the eastern Indian and Pacific individuals collected for this study belonged to the ubiquitous clade. All eastern Indian and Pacific blue marlin possess extremely high haplotype diversity (h) and low nucleotide diversity (π). The results of pairwise ΦST, hierarchical analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA) all support that there is no population differentiation among eastern Indian and Pacific blue marlin. Neutrality tests and pairwise mismatch distribution analysis both indicated that eastern Indian and Pacific blue marlin have undergone a rapid population expansion on the order of 0.30 to 0.65 million years ago (mya). This study demonstrates that blue marlin in the Pacific and eastern Indian oceans constitute a single stock. International cooperation will be required to preserve blue marlin as a resource; moreover, the high genetic variation of blue marlin in this region suggests that unique haplotypes in the population are sensitive to high harvesting levels and could disappear.
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