OpenLB
Open Library of Bioscience
Advanced Search
International journal of molecular sciences
Feb 06, 2025;26 (3):

Genetic Diversity and Environmental Adaptation Signatures of the Great Seahorse () in the Coastal Regions of the Indo-Pacific as Revealed by Whole-Genome Re-Sequencing.

Wen-Xin Hao, Ying-Yi Zhang, Xin Wang, Meng Qu, Shi-Ming Wan, Qiang Lin
Author Information
  1. Wen-Xin Hao: College of Fisheries, Hubei Hongshan Laboratory/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
  2. Ying-Yi Zhang: CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
  3. Xin Wang: CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
  4. Meng Qu: CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
  5. Shi-Ming Wan: College of Fisheries, Hubei Hongshan Laboratory/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
  6. Qiang Lin: CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China. ORCID
PMID: 39941154 DOI: 10.3390/ijms26031387

Abstract

The great seahorse () is one of the larger species within the seahorse group and is widely distributed in coastal areas of the Indo-Pacific. However, the natural resources of this species continue to decrease, rendering it a vulnerable species that faces a high risk of extinction. Therefore, there is an urgent need to conduct research on the genetic diversity of this species to protect its genetic resources. In this study, we conducted whole-genome re-sequencing (WGRS) on three populations from the Red Sea (RS, n = 30), the Andaman Sea (AS, n = 13), and the South China Sea (SCS, n = 13), and a total of 1,398,936 high-quality single-nucleotide polymorphisms (SNPs) were identified. The results indicate that the average observed heterozygosity () and the average expected heterozygosity () for the RS, AS, and SCS populations are 0.2031 and 0.1987, 0.1914 and 0.1822, and 0.2083 and 0.2001, respectively. The three geographic populations exhibit a high degree of genetic differentiation with only a minimal gene flow between them. Consistently, in a population structure analysis, the three groups are also clearly distinguished, which is consistent with the results of the population differentiation coefficient. Demographic analyses revealed that the effective population size () of the SCS population underwent a dramatic bottleneck during the Last Glacial Maximum (LGM), followed by a substantial recovery, whereas the RS and AS populations maintained stable values throughout this period. To investigate adaptive responses to climate change in the SCS population, we employed selective elimination analysis, which identified 21 candidate genes potentially involved in environmental adaptation. Of particular significance were , , , , and , which likely play crucial roles in the adaptive mechanisms of . This comprehensive study not only illuminates the genetic diversity patterns of but also provides a valuable foundation for future investigations into the species' evolutionary adaptations.

Keywords

Hippocampus kelloggi Indo-Pacific environmental adaptation genetic diversity whole-genome re-sequencing

References

  1. Nat Rev Genet. 2009 Mar;10(3):195-205 [PMID: 19204717]
  2. Cell. 2007 Aug 24;130(4):624-37 [PMID: 17719541]
  3. Nat Genet. 2014 Aug;46(8):919-25 [PMID: 24952747]
  4. Conserv Physiol. 2015 Mar 17;3(1):cov009 [PMID: 27293694]
  5. Bioinformatics. 2006 Nov 1;22(21):2688-90 [PMID: 16928733]
  6. Genome Res. 2009 Sep;19(9):1655-64 [PMID: 19648217]
  7. Curr Zool. 2016 Dec;62(6):581-601 [PMID: 29491947]
  8. J Biol Chem. 2019 Apr 26;294(17):6912-6922 [PMID: 30837268]
  9. J Evol Biol. 2023 Dec;36(12):1811-1821 [PMID: 37916691]
  10. Bioinformatics. 2009 Jul 15;25(14):1754-60 [PMID: 19451168]
  11. Front Genet. 2022 Oct 03;13:898522 [PMID: 36263427]
  12. Mol Ther. 2023 Jun 7;31(6):1661-1674 [PMID: 37177784]
  13. Animals (Basel). 2022 May 27;12(11): [PMID: 35681841]
  14. Nat Commun. 2021 Feb 17;12(1):1094 [PMID: 33597547]
  15. Evol Appl. 2011 Mar;4(2):326-37 [PMID: 25567976]
  16. Int J Mol Sci. 2023 Sep 04;24(17): [PMID: 37686445]
  17. Mol Ecol Resour. 2020 Jan;20(1):154-169 [PMID: 31550072]
  18. PLoS Genet. 2019 Nov 25;15(11):e1008480 [PMID: 31765389]
  19. FEBS Lett. 2003 Nov 20;554(3):264-70 [PMID: 14623077]
  20. Nature. 2017 Sep 7;549(7670):82-85 [PMID: 28854164]
  21. BMC Genomics. 2023 Sep 15;24(1):547 [PMID: 37715145]
  22. Nature. 2016 Dec 14;540(7633):395-399 [PMID: 27974754]
  23. Nat Biotechnol. 2008 Jan;26(1):65-6 [PMID: 18183021]
  24. Mol Ecol. 2005 Apr;14(4):1073-94 [PMID: 15773937]
  25. Oncogene. 2015 Nov 5;34(45):5662-76 [PMID: 25772235]
  26. FEBS Lett. 2004 Oct 8;576(1-2):14-20 [PMID: 15474002]
  27. Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3883-8 [PMID: 17360447]
  28. Nucleic Acids Res. 2010 Sep;38(16):e164 [PMID: 20601685]
  29. Glob Chang Biol. 2014 Nov;20(11):3344-50 [PMID: 24700793]
  30. Natl Sci Rev. 2020 Jun;7(6):964-977 [PMID: 34692118]
  31. Science. 1998 Jan 23;279(5350):527-33 [PMID: 9438839]
  32. Mar Biotechnol (NY). 2022 Aug;24(4):671-680 [PMID: 35701688]
  33. PLoS One. 2015 Sep 16;10(9):e0138824 [PMID: 26376440]
  34. Mol Phylogenet Evol. 2004 Feb;30(2):261-72 [PMID: 14715219]
  35. Front Genet. 2022 Nov 10;13:1071303 [PMID: 36437943]
  36. Mitochondrial DNA A DNA Mapp Seq Anal. 2017 Mar;28(2):227-228 [PMID: 26711171]
  37. BMC Genomics. 2021 Jul 26;22(1):573 [PMID: 34311701]
  38. Proc Biol Sci. 2003 Jul 7;270(1522):1399-406 [PMID: 12965032]
  39. Mol Phylogenet Evol. 2004 Feb;30(2):273-86 [PMID: 14715220]

Grants

  1. 42425004/the National Natural Science Foundation of China
  2. 42106120/the National Natural Science Foundation of China
  3. 2023A1515012165/the Guangdong Basic and Applied Basic Research Foundation

MeSH Term

Animals
Smegmamorpha
Polymorphism, Single Nucleotide
Whole Genome Sequencing
Genetic Variation
Adaptation, Physiological
Genetics, Population
Gene Flow
Indian Ocean
Phylogeny
Pacific Ocean
Journal Article

Word Cloud

Created with Highcharts 10.0.00geneticpopulationspeciespopulationsSCSIndo-PacificdiversitythreeSeaRSn=ASseahorseresourceshighstudywhole-genomere-sequencing13identifiedresultsaverageheterozygositydifferentiationanalysisalsoadaptiveenvironmentaladaptationgreatonelargerwithingroupwidelydistributedcoastalareasHowevernaturalcontinuedecreaserenderingvulnerablefacesriskextinctionThereforeurgentneedconductresearchprotectconductedWGRSRed30AndamanSouthChinatotal1398936high-qualitysingle-nucleotidepolymorphismsSNPsindicateobservedexpected203119871914182220832001respectivelygeographicexhibitdegreeminimalgeneflowConsistentlystructuregroupsclearlydistinguishedconsistentcoefficientDemographicanalysesrevealedeffectivesizeunderwentdramaticbottleneckLastGlacialMaximumLGMfollowedsubstantialrecoverywhereasmaintainedstablevaluesthroughoutperiodinvestigateresponsesclimatechangeemployedselectiveelimination21candidategenespotentiallyinvolvedparticularsignificancelikelyplaycrucialrolesmechanismscomprehensiveilluminatespatternsprovidesvaluablefoundationfutureinvestigationsspecies'evolutionaryadaptationsGeneticDiversityEnvironmentalAdaptationSignaturesGreatSeahorseCoastalRegionsRevealedWhole-GenomeRe-SequencingHippocampuskelloggi

Similar Articles

Cited By