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Jeena NS, Rahuman S, Sebastian W, Kumar R, Sajeela KA, Kizhakudan JK, Menon KK, Roul SK, Gopalakrishnan A, Radhakrishnan EV. Mitogenomic recognition of incognito lineages in the mud spiny lobster Panulirus polyphagus (Herbst, 1793): A tale of unique genetic structuring and diversification. Int J Biol Macromol 2024; 277:134327. [PMID: 39098694 DOI: 10.1016/j.ijbiomac.2024.134327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
This study provides the first documentation of three deep conspecific lineages within Panulirus polyphagus in the Indian Ocean, bridging the gap in genetic research. Comparative mitogenomics between lineages (L) at both species and family levels, evolutionary relationships and heterogeneity of sequence divergence within Decapoda, and divergence time estimation were performed. The characterized mitogenomes ranged from 15,685-15,705 bp in size and exhibited a typical pancrustacean pattern. Among the three lineages, L1 predominated the Bay of Bengal, L2 the Arabian Sea, and L2.a, a less common lineage genetically closer to L2, was restricted to the latter region. A minor lineage L1.a, was observed in the Coral Triangle area. All PCGs displayed evidence of purifying selection across species and family levels. The largest genetic distance (K2P) between lineages was 9 %, notably between L1.a and L2.a. The phylogenetic tree subdivided the Achelates into Palinuridae and Scyllaridae, and the topology demonstrated a distinct pattern of lineage diversification within P. polyphagus. AliGROOVE analysis revealed no discernible divergence in Decapoda. The diversification of P. polyphagus appears to have occurred during Miocene, with further diversification in Pliocene. Furthermore, genetic stocks and population connectivity recognized here will provide valuable insight for spatial management planning of this dwindling resource.
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Affiliation(s)
- N S Jeena
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India.
| | - Summaya Rahuman
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India
| | - Wilson Sebastian
- Centre for Marine Living Resources and Ecology (CMLRE), Kochi, Kerala, India
| | - Rajan Kumar
- Shellfish Fisheries Division, Regional Station of CMFRI, Veraval, Gujarat, India
| | - K A Sajeela
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, Kerala, India
| | - Joe K Kizhakudan
- Mariculture Division, Regional Centre of CMFRI, Visakhapatnam, Andhra Pradesh, India
| | | | - Subal Kumar Roul
- Finfish Fisheries Division, Regional Station of CMFRI, Digha, West Bengal, India
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Farhadi A, Jeffs AG, Lavery SD. Genome-wide SNPs in the spiny lobster Panulirus homarus reveal a hybrid origin for its subspecies. BMC Genomics 2022; 23:750. [DOI: 10.1186/s12864-022-08984-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Evolutionary divergence and speciation often occur at a slower rate in the marine realm due to the higher potential for long-distance reproductive interaction through larval dispersal. One common evolutionary pattern in the Indo-Pacific, is divergence of populations and species at the peripheries of widely-distributed organisms. However, the evolutionary and demographic histories of such divergence are yet to be well understood. Here we address these issues by coupling genome-wide SNP data with mitochondrial DNA sequences to test the patterns of genetic divergence and possible secondary contact among geographically distant populations of the highly valuable spiny lobster Panulirus homarus species complex, distributed widely through the Indo-Pacific, from South Africa to the Marquesas Islands.
Result
After stringent filtering, 2020 SNPs were used for population genetic and demographic analyses, revealing strong regional structure (FST = 0.148, P < 0001), superficially in accordance with previous analyses. However, detailed demographic analyses supported a much more complex evolutionary history of these populations, including a hybrid origin of a North-West Indian Ocean (NWIO) population, which has previously been discriminated morphologically, but not genetically. The best-supported demographic models suggested that the current genetic relationships among populations were due to a complex series of past divergences followed by asymmetric migration in more recent times.
Conclusion
Overall, this study suggests that alternating periods of marine divergence and gene flow have driven the current genetic patterns observed in this lobster and may help explain the observed wider patterns of marine species diversity in the Indo-Pacific.
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Hettiarachchi SA, Hyeon JY, Mahardini A, Kim HS, Byun JH, Kim HJ, Jeong JG, Yeo JK, Kim SK, Kim SJ, Heo YS, Sathyadith J, Kang DH, Hur SP. DNA barcoding and morphological identification of spiny lobsters in South Korean waters: a new record of Panulirus longipes and Panulirus homarus homarus. PeerJ 2022; 10:e12744. [PMID: 35047236 PMCID: PMC8757375 DOI: 10.7717/peerj.12744] [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: 07/17/2021] [Accepted: 12/14/2021] [Indexed: 01/07/2023] Open
Abstract
To date, 19 species of spiny lobsters from the genus Panulirus have been discovered, of which only P. japonicus, P. penicilatus, P. stimpsoni, and P. versicolor have been documented in South Korean waters. In this study, we aimed to identify and update the current list of spiny lobster species that inhabit South Korean waters based on the morphological features and the phylogenetic profile of cytochrome oxidase I (COI) of mitochondrial DNA (mtDNA). Spiny lobsters were collected from the southern and eastern coasts of Jeju Island, South Korea. Phylogenetic analyses were performed using neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference (BI) methods. The ML tree was used to determine the spiny lobster lineages, thereby clustering the 17 specimens collected in this study into clades A, B, C, and D, which were reciprocally monophyletic with P. japonicus, P. homarus homarus, P. longipes, and P. stimpsoni, respectively. These clades were also supported by morphological examinations. Interestingly, morphological variations, including the connected pleural and transverse groove at the third abdominal somite, were observed in four specimens that were genetically confirmed as P. japonicus. This finding is novel within the P. japonicus taxonomical reports. Additionally, this study updates the documentation of spiny lobsters inhabiting South Korean waters as P. longipes and P. homarus homarus were recorded for the first time in this region.
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Affiliation(s)
- Sachithra Amarin Hettiarachchi
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Fisheries and Aquaculture, Faculty of Fisheries and Marine Sciences & Technology, University of Ruhuna, Matara, Sri Lanka,Department of Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
| | - Ji-Yeon Hyeon
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Biology, Jeju National University, Jeju, Republic of Korea
| | - Angka Mahardini
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea
| | - Hyung-Suk Kim
- Department of Kinesiology, Jeju National University, Jeju, Republic of Korea
| | - Jun-Hwan Byun
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea
| | - Han-Jun Kim
- Marine Ecosystem Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Jong-Gyun Jeong
- LED-Marine Biology Convergence Technology Research Center, Pukyong National University, Busan, Republic of Korea
| | - Jung-Kyu Yeo
- LED-Marine Biology Convergence Technology Research Center, Pukyong National University, Busan, Republic of Korea
| | - Shin-Kwon Kim
- Aquaculture Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Se-Jae Kim
- Department of Biology, Jeju National University, Jeju, Republic of Korea
| | - Youn-Seong Heo
- LED-Marine Biology Convergence Technology Research Center, Pukyong National University, Busan, Republic of Korea
| | - Jonathan Sathyadith
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
| | - Do-Hyung Kang
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
| | - Sung-Pyo Hur
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju, Republic of Korea,Department of Ocean Science, University of Science and Technology, Daejeon, Republic of Korea
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Simon CA, Muthumbi AWN, Kihia CM, Smith KMS, Cedras RB, Mahatante PT, Wangondu VW, Katikiro R. A review of marine invertebrates used as fishing baits and the implications for national and regional management in the Western Indian Ocean. AFRICAN ZOOLOGY 2021. [DOI: 10.1080/15627020.2021.2001370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Carol A Simon
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | | | - Charles M Kihia
- Department of Biological Sciences, Egerton University, Njoro, Kenya
| | - Kyle MS Smith
- Rondevlei Scientific Services, South African National Parks, Sedgefield, South Africa
| | - Riaan B Cedras
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville, South Africa
| | - Paubert T Mahatante
- Department of Marine Sciences, Centre Universitaire Régional Androy, University of Toliara, Maninday, Madagascar
| | | | - Robert Katikiro
- Department of Agricultural Economics and Business, University of Dar es Salaam, Dar es Salaam, Tanzania
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Singh SP, Groeneveld JC, Willows‐Munro S. Genetic structure and life history are key factors in species distribution models of spiny lobsters. Ecol Evol 2020; 10:14394-14410. [PMID: 33391723 PMCID: PMC7771135 DOI: 10.1002/ece3.7043] [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: 07/30/2020] [Revised: 10/08/2020] [Accepted: 10/23/2020] [Indexed: 11/06/2022] Open
Abstract
AIM We incorporated genetic structure and life history phase in species distribution models (SDMs) constructed for a widespread spiny lobster, to reveal local adaptations specific to individual subspecies and predict future range shifts under the RCP 8.5 climate change scenario. LOCATION Indo-West Pacific. METHODS MaxEnt was used to construct present-day SDMs for the spiny lobster Panulirus homarus and individually for the three genetically distinct subspecies of which it comprises. SDMs incorporated both sea surface and benthic (seafloor) climate layers to recreate discrete influences of these habitats during the drifting larval and benthic juvenile and adult life history phases. Principle component analysis (PCA) was used to infer environmental variables to which individual subspecies were adapted. SDM projections of present-day habitat suitability were compared with predictions for the year 2,100, under the RCP 8.5 climate change scenario. RESULTS In the PCA, salinity best explained P. h. megasculptus habitat suitability, compared with current velocity in P. h. rubellus and sea surface temperature in P. h. homarus. Drifting and benthic life history phases were adapted to different combinations of sea surface and benthic environmental variables considered. Highly suitable habitats for benthic phases were spatially enveloped within more extensive sea surface habitats suitable for drifting larvae. SDMs predicted that present-day highly suitable habitats for P. homarus will decrease by the year 2,100. MAIN CONCLUSIONS Incorporating genetic structure in SDMs showed that individual spiny lobster subspecies had unique adaptations, which could not be resolved in species-level models. The use of sea surface and benthic climate layers revealed the relative importance of environmental variables during drifting and benthic life history phases. SDMs that included genetic structure and life history were more informative in predictive models of climate change effects.
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Affiliation(s)
| | - Johan C. Groeneveld
- Oceanographic Research InstituteDurbanSouth Africa
- School of Life SciencesUniversity of KwaZulu‐NatalPietermaritzburgSouth Africa
| | - Sandi Willows‐Munro
- School of Life SciencesUniversity of KwaZulu‐NatalPietermaritzburgSouth Africa
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Zehady AK, Fordham BG, Ogg JG. Integrated species-phenon trees: visualizing infraspecific diversity within lineages. Sci Rep 2019; 9:18968. [PMID: 31831804 PMCID: PMC6908663 DOI: 10.1038/s41598-019-55435-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/25/2019] [Indexed: 12/03/2022] Open
Abstract
The unprecedented detail with which contemporary molecular phylogenetics are visualizing infraspecific relationships within living species and species complexes cannot as yet be reliably extended into deep time. Yet paleontological systematics has routinely dealt in (mainly) morphotaxa envisaged in various ways to have been components of past species lineages. Bridging these perspectives can only enrich both. We present a visualization tool that digitally depicts infraspecific diversity within species through deep time. Our integrated species-phenon tree merges ancestor-descendant trees for fossil morphotaxa (phena) into reconstructed phylogenies of lineages (species) by expanding the latter into "species boxes" and placing the phenon trees inside. A key programming strategy to overcome the lack of a simple overall parent-child hierarchy in the integrated tree has been the progressive population of a species-phenon relationship map which then provides the graphical footprint for the overarching species boxes. Our initial case has been limited to planktonic foraminfera via Aze & others' important macroevolutionary dataset. The tool could potentially be appropriated for other organisms, to detail other kinds of infraspecific granularity within lineages, or more generally to visualize two nested but loosely coupled trees.
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Affiliation(s)
- Abdullah Khan Zehady
- Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, West Lafayette, IN, USA
| | - Barry G Fordham
- Research School of Earth Sciences, Australian National University, Canberra, ACT, Australia.
| | - James G Ogg
- Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, West Lafayette, IN, USA
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Chengdu University of Technology, Chengdu, Sichuan, China
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Singh SP, Groeneveld JC, Hart‐Davis MG, Backeberg BC, Willows‐Munro S. Seascape genetics of the spiny lobster Panulirus homarus in the Western Indian Ocean: Understanding how oceanographic features shape the genetic structure of species with high larval dispersal potential. Ecol Evol 2018; 8:12221-12237. [PMID: 30598813 PMCID: PMC6303728 DOI: 10.1002/ece3.4684] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 01/03/2023] Open
Abstract
This study examines the fine-scale population genetic structure and phylogeography of the spiny lobster Panulirus homarus in the Western Indian Ocean. A seascape genetics approach was used to relate the observed genetic structure based on 21 microsatellite loci to ocean circulation patterns, and to determine the influence of latitude, sea surface temperature (SST), and ocean turbidity (KD490) on population-level processes. At a geospatial level, the genetic clusters recovered corresponded to three putative subspecies, P. h. rubellus from the SW Indian Ocean, P. h. megasculptus from the NW Indian Ocean, and P. h. homarus from the tropical region in-between. Virtual passive Lagrangian particles advected using satellite-derived ocean surface currents were used to simulate larval dispersal. In the SW Indian Ocean, the dispersion of particles tracked over a 4-month period provided insight into a steep genetic gradient observed at the Delagoa Bight, which separates P. h. rubellus and P. h. homarus. South of the contact zone, particles were advected southwestwards by prevailing boundary currents or were retained in nearshore eddies close to release locations. Some particles released in southeast Madagascar dispersed across the Mozambique Channel and reached the African shelf. Dispersal was characterized by high seasonal and inter-annual variability, and a large proportion of particles were dispersed far offshore and presumably lost. In the NW Indian Ocean, particles were retained within the Arabian Sea. Larval retention and self-recruitment in the Arabian Sea could explain the recent genetic divergence between P. h. megasculptus and P. h. homarus. Geographic distance and minimum SST were significantly associated with genetic differentiation in multivariate analysis, suggesting that larval tolerance to SST plays a role in shaping the population structure of P. homarus.
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Affiliation(s)
- Sohana P. Singh
- Oceanographic Research InstituteMarine ParadeSouth Africa
- School of Life SciencesUniversity of KwaZulu‐NatalPietermaritzburgSouth Africa
| | - Johan C. Groeneveld
- Oceanographic Research InstituteMarine ParadeSouth Africa
- School of Life SciencesUniversity of KwaZulu‐NatalPietermaritzburgSouth Africa
| | - Michael G. Hart‐Davis
- Institute for Coastal and Marine ResearchNelson Mandela UniversityPort ElizabethSouth Africa
- Department of Oceanography, Nansen‐Tutu Centre for Marine Environmental ResearchUniversity of Cape TownSouth Africa
- Egagasini NodeSouth African Environmental Observation NetworkCape TownSouth Africa
| | - Björn C. Backeberg
- Department of Oceanography, Nansen‐Tutu Centre for Marine Environmental ResearchUniversity of Cape TownSouth Africa
- Council for Scientific and Industrial Research, Natural Resources and the EnvironmentCoastal Systems Research GroupStellenboschSouth Africa
- Nansen Environmental and Remote Sensing CenterBergenNorway
| | - Sandi Willows‐Munro
- School of Life SciencesUniversity of KwaZulu‐NatalPietermaritzburgSouth Africa
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Al-Breiki RD, Kjeldsen SR, Afzal H, Al Hinai MS, Zenger KR, Jerry DR, Al-Abri MA, Delghandi M. Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline. BMC Genomics 2018; 19:690. [PMID: 30231936 PMCID: PMC6146514 DOI: 10.1186/s12864-018-5044-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species. RESULTS After stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise FST estimates revealed low differentiation among populations (pairwise FST range = - 0.0008 - 0.0021). Analysis of genetic variation using putatively directional FST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range = 0.0288-0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus. CONCLUSIONS Findings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes.
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Affiliation(s)
- Rufaida Dhuhai Al-Breiki
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
- College of Agriculture and Marine Sciences, Department of Marine Sciences and Fisheries, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Shannon R. Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Hasifa Afzal
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Manal Saif Al Hinai
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Mohammed Ali Al-Abri
- College of Agriculture and Marine Sciences, Department of Animal and Veterinary Sciences and Technology, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Madjid Delghandi
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
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