Genetic diversity and population structure of the Fujian oyster <italic style="font-style: italic">Crassostrea angulata</italic> revealed by mitochondrial COⅠ gene and nuclear gene ITS2 sequences

Shiqi YU; Ziqiang HAN; Huayong QUE

doi:10.1007/s00343-025-4308-9

Your Location：

Home >

Browse articles >

Genetic diversity and population structure of the Fujian oyster Crassostrea angulata revealed by mitochondrial COⅠ gene and nuclear gene ITS2 sequences

Aquaculture and Fisheries | Updated：2026-03-26

- Genetic diversity and population structure of the Fujian oyster Crassostrea angulata revealed by mitochondrial COⅠ gene and nuclear gene ITS2 sequences
- Journal of Oceanology and Limnology Vol. 44, Issue 1, Pages: 419-432(2026)
- Affiliations：
  
  1.State Key Laboratory of Mariculture Breeding, Fisheries College, Jimei University, Xiamen 361021, China
  2.Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China
- Author bio：
  
  hanzq@jmu.edu.cn
  hque@jmu.edu.cn
- Funds：
- DOI：10.1007/s00343-025-4308-9
  CLC：
- Received：17 November 2024，
  
  Accepted：25 February 2025，
  
  Online First：22 April 2025，
  
  Published：01 January 2026
- Accepted：
Scan QR Code
YU Shiqi,HAN Ziqiang,QUE Huayong.Genetic diversity and population structure of the Fujian oyster Crassostrea angulata revealed by mitochondrial COⅠ gene and nuclear gene ITS2 sequences[J].Journal of Oceanology and Limnology,2026,44(01):419-432.
DOI：

YU Shiqi,HAN Ziqiang,QUE Huayong.Genetic diversity and population structure of the Fujian oyster Crassostrea angulata revealed by mitochondrial COⅠ gene and nuclear gene ITS2 sequences[J].Journal of Oceanology and Limnology,2026,44(01):419-432. DOI： 10.1007/s00343-025-4308-9.

摘要

Abstract

The Fujian oyster (

Crassostrea

angulata

) is an economically significant shellfish species distributed mainly along the Fujian coast

Southeast China. However

its genetic diversity and structure remain unclear. The main distribution area of the

angulata

is located in Fujian

South China. In total

420

angulata

were collected from 14 natural habitats (populations) along the Fujian coast

and their genetic diversity and structure were analyzed in the mitochondrial COⅠ and nuclear gene ITS2 sequences. Results reveal that all the 14 populations of

angulata

exhibited high levels of genetic diversity

with a total of 57 (haplotype diversity: 0.811±0.016) and 124 (haplotype diversity: 0.912±0.007) haplotypes revealed by COⅠ and ITS2

respectively. Notably

significant intermediate level of genetic differentiations between the Ningde Zhujiang (ZJ) population (

by COI: 0.035–0.142

0.05;

by ITS2: 0.078–0.123

0.05) with other populations were observed for the first time

which is also supported by the results of molecular variance analysis (

by COⅠ: 0.105

0.05;

by ITS2: 0.086

0.05) and the clustering of the ZJ population into distinct branches in the interpopulation genetic differentiation tree. Furthermore

the evolutionary tree and haplotype network analyses do not support the formation of a clear geographical genealogical structure among these 14 populations. In addition

the population dynamics analysis suggests that the

angulata

may have undergone expansion during the third ice age of the Pleistocene. These results provide a reference for the preservation and further genetic

improvement of

angulata

关键词

Keywords

references

Batista F M , López-Sanmartín M , Grade A et al . 2015 . Sequence variation in ostreid herpesvirus 1 microvar isolates detected in dying and asymptomatic Crassostrea angulata adults in the Iberian Peninsula: insights into viral origin and spread . Aquaculture , 435 : 43 - 51 , https://doi.org/10.1016/j.aquaculture.2014.09.016 https://doi.org/10.1016/j.aquaculture.2014.09.016 .

Bouckaert R , Heled J , Kühnert D et al . 2014 . BEAST 2: a software platform for Bayesian evolutionary analysis . PLoS Computational Biology , 10 ( 4 ): e 1003537 , https://doi.org/10.1371/journal.pcbi.1003537 https://doi.org/10.1371/journal.pcbi.1003537 .

Boudry P , Heurtebise S , Collet B et al . 1998 . Differentiation between populations of the Portuguese oyster, Crassostrea angulata (Lamark) and the Pacific oyster, Crassostrea gigas (Thunberg), revealed by mtDNA RFLP analysis . Journal of Experimental Marine Biology and Ecology , 226 ( 2 ): 279 - 291 , https://doi.org/10.1016/S0022-0981(97)00250-5 https://doi.org/10.1016/S0022-0981(97)00250-5 .

Cheang C C , Tsang L M , Ng W C et al . 2012 . Phylogeography of the cold‐water barnacle Chthamalus challengeri in the north-western pacific: effect of past population expansion and contemporary gene flow . Journal of Biogeography , 39 ( 10 ): 1819 - 1835 , https://doi.org/10.1111/j.1365-2699.2012.02742.x https://doi.org/10.1111/j.1365-2699.2012.02742.x .

Chiesa S , Lucentini L , Chainho P et al . 2021 . One in a million: genetic diversity and conservation of the reference Crassostrea angulata population in Europe from the Sado estuary (Portugal) . Life , 11 ( 11 ): 1173 , https://doi.org/10.3390/life11111173 https://doi.org/10.3390/life11111173 .

Clement M , Posada D , Crandall K A . 2000 . TCS: a computer program to estimate gene genealogies . Molecular Ecology , 9 ( 10 ): 1657 - 1659 , https://doi.org/10.1046/j.1365-294x.2000.01020.x https://doi.org/10.1046/j.1365-294x.2000.01020.x .

Drummond A J , Rambaut A . 2007 . BEAST: Bayesian evolutionary analysis by sampling trees . BMC Evolutionary Biology , 7 ( 1 ): 214 , https://doi.org/10.1186/1471-2148-7-214 https://doi.org/10.1186/1471-2148-7-214 .

Excoffier L , Laval G , Schneider S . 2005 . Arlequin (version 3.0): an integrated software package for population genetics data analysis . Evolutionary Bioinformatics , 1 : 47 - 50 , https://doi.org/10.1177/117693430500100003 https://doi.org/10.1177/117693430500100003 .

FAO . 2024 . The State of world Fisheries and Aquaculture. Food and Agriculture Organization of the United Nations, Rome, Italy .

Foighil D Ó , Gaffney P M , Wilbur A F et al . 1998 . Mitochondrial cytochrome oxidase Ⅰ gene sequences support an Asian origin for the Portuguese oyster Crassostrea angulata . Marine Biology , 131 ( 3 ): 497 - 503 , https://doi.org/10.1007/s002270050341 https://doi.org/10.1007/s002270050341 .

Folmer O , Black M , Hoeh W et al . 1994 . DNA primers for amplification of mitochondrial cytochrome C oxidase subunit Ⅰ from diverse metazoan invertebrates . Molecular Marine Biology and Biotechnology , 3 ( 5 ): 294 - 299 .

Fu Y X , Li W H . 1993 . Statistical tests of neutrality of mutations . Genetics , 133 ( 3 ): 693 - 709 , https://doi.org/10.1093/genetics/133.3.693 https://doi.org/10.1093/genetics/133.3.693 .

Grade A , Chairi H , Lallias D et al . 2016 . New insights about the introduction of the Portuguese oyster, Crassostrea angulata , into the North East Atlantic from Asia based on a highly polymorphic mitochondrial region . Aquatic Living Resources , 29 ( 4 ): 404 , https://doi.org/10.1051/alr/2016035 https://doi.org/10.1051/alr/2016035 .

Grant W A S , Bowen B W . 1998 . Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation . Journal of Heredity , 89 ( 5 ): 415 - 426 , https://doi.org/10.1093/jhered/89.5.415 https://doi.org/10.1093/jhered/89.5.415 .

Harrison R G . 1989 . Animal mitochondrial DNA as a genetic marker in population and evolutionary biology . Trends in Ecology & Evolution , 4 ( 1 ): 6 - 11 , https://doi.org/10.1016/0169-5347(89)90006-2 https://doi.org/10.1016/0169-5347(89)90006-2 .

Hewitt G . 2000 . The genetic legacy of the quaternary ice ages . Nature , 405 ( 6789 ): 907 - 913 , https://doi.org/10.1038/35016000 https://doi.org/10.1038/35016000 .

Ho S Y W , Saarma U , Barnett R et al . 2008 . The effect of inappropriate calibration: three case studies in molecular ecology . PLoS One , 3 ( 2 ): e 1615 , https://doi.org/10.1371/journal.pone.0001615 https://doi.org/10.1371/journal.pone.0001615 .

Hsiao S T , Chuang S C , Chen K S et al . 2016 . DNA barcoding reveals that the common cupped oyster in Taiwan is the Portuguese oyster Crassostrea angulata (Ostreoida; Ostreidae), not C . gigas . Scientific Reports , 6 ( 1 ): 34057 , https://doi.org/10.1038/srep34057 https://doi.org/10.1038/srep34057 .

Hu L S . 2020 . Taxonomy of Gryphaeidae and Related Oysters Along the Coast of China and Phylogeography of Crassostrea talonat . University of Chinese Academy of Sciences and Institute of Oceanography, Chinese Academy of Sciences, Qingdao .

Hu Y M , Li Q , Xu C X et al . 2022 . Genetic variability of mass-selected and wild populations of Iwagaki oyster ( Crassostrea nippona ) revealed by microsatellites and mitochondrial COI sequences. Aquaculture , 561 : 738737 , https://doi.org/10.1016/j.aquaculture.2022.738737 https://doi.org/10.1016/j.aquaculture.2022.738737 .

Huvet A , Lapègue S , Magoulas A et al . 2000 . Mitoch ondrial and nuclear DNA phylogeography of Crassostrea angulata , the Portuguese oyster endangered in Europe . Conservation Genetics , 1 ( 3 ): 251 - 262 , https://doi.org/10.1023/A:1011505805923 https://doi.org/10.1023/A:1011505805923 .

Kim W J , Dammannagoda S T , Jung H et al . 2014 . Mitochondrial DNA sequence analysis from multiple gene fragments reveals genetic heterogeneity of Crassostrea ariakensis in East Asia . Genes & Genomics , 36 ( 5 ): 611 - 624 , https://doi.org/10.1007/s13258-014-0198-5 https://doi.org/10.1007/s13258-014-0198-5 .

Leigh J W , Bryant D . 2015 . POPART: full-feature software for haplotype network construction . Methods in Ecology and Evolution , 6 ( 9 ): 1110 - 1116 , https://doi.org/10.1111/2041-210X.12410 https://doi.org/10.1111/2041-210X.12410 .

Li L , Wu X Y , Yu Z N . 2013 . Genetic diversity and substantial population differentiation in Crassostrea hongkongensis revealed by mitochondrial DNA . Marine Genomics , 11 : 31 - 37 , https://doi.org/10.1016/j.margen.2013.06.001 https://doi.org/10.1016/j.margen.2013.06.001 .

Li S , Li Q , Yu H et al . 2015 . Genetic structure and population history of Crassostrea angulata from the coast of Zhejiang and Fujian Provinces . Journal of Fishery Sciences of China , 22 ( 6 ): 1260 - 1269 , https://doi.org/10.3724/SP.J.1118.2015.14503. https://doi.org/10.3724/SP.J.1118.2015.14503. (in Chinese with English abstract)

Librado P , Rozas J . 2009 . DnaSP v5: a software for comprehensive analysis of DNA polymorphism data . Bioinformatics , 25 ( 11 ): 1451 - 1452 , https://doi.org/10.1093/bioinformatics/btp187 https://doi.org/10.1093/bioinformatics/btp187 .

Lin H Y , Chen Z Z , Hu J Y et al . 2017 . Numerical simulation of the hydrodynamics and water exchange in Sansha Bay . Ocean Engineering , 139 : 85 - 94 , https://doi.org/10.1016/j.oceaneng.2017.04.031 https://doi.org/10.1016/j.oceaneng.2017.04.031 .

Ma H T , Li L , Xiao S et al . 2021 . Microsatellite-based study of population genetics of Crassostrea hongkongensis in Southern China. Aquaculture Reports , 19 : 100591 , https://doi.org/10.1016/j.aqrep.2021.100591 https://doi.org/10.1016/j.aqrep.2021.100591 .

Marko P B , Hoffma J M , Emme S A et al . 2010 . The 'Expansion-Contraction' model of Pleistocene biogeography: rocky shores suffer a sea change? Molecular Ecology , 19 ( 1 ): 146 - 169 , https://doi.org/10.1111/j.1365-294X.2009.04417.x https://doi.org/10.1111/j.1365-294X.2009.04417.x .

Marko P B . 2002 . Fossil calibration of molecular clocks and the divergence times of geminate species pairs separated by the Isthmus of Panama . Molecular Biology and Evolution , 19 ( 11 ): 2005 - 2021 , https://doi.org/10.1093/oxfordjournals.molbev.a004024 https://doi.org/10.1093/oxfordjournals.molbev.a004024 .

Ni G , Li Q , Kong L F et al . 2015 . Mitochondrial phylogeography of a surf clam Mactra veneriformis in the East China Sea: genetic homogeneity across two biogeographic boundaries . Biochemical Systematics and Ecology , 61 : 493 - 500 , https://doi.org/10.1016/j.bse.2015.07.026 https://doi.org/10.1016/j.bse.2015.07.026 .

Ni L H , Li Q , Kong L F . 2011 . Microsatellites reveal fine-scale genetic structure of the Chinese surf clam Mactra chinensis (Mollusca, Bivalvia, Mactridae) in Northern China . Marine Ecology , 32 ( 4 ): 488 - 497 , https://doi.org/10.1111/j.1439-0485.2011.00436.x https://doi.org/10.1111/j.1439-0485.2011.00436.x .

Nowland S J , Silva C N S , Southgate P C et al . 2019 . Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster ( Saccostrea echinata ) reveals population subdivision and informs sustainable aquaculture development . BMC Genomics , 20 ( 1 ): 711 , https://doi.org/10.1186/s12864-019-6052-z https://doi.org/10.1186/s12864-019-6052-z .

Okonechnikov K , Golosova O , Fursov M et al . 2012 . Unipro UGENE: a unified bioinformatics toolkit . Bioinformatics , 28 ( 8 ): 1166 - 1167 , https://doi.org/10.1093/bioinformatics/bts091 https://doi.org/10.1093/bioinformatics/bts091 .

Palumbi S R . 1994 . Genetic divergence, reproductive isolation, and marine speciation . Annual Review of Ecology, Evolution, and Systematics , 25 : 547 - 572 , https://doi.org/10.1146/annurev.es.25.110194.002555 https://doi.org/10.1146/annurev.es.25.110194.002555 .

Provan J , Bennett K D . 2008 . Phylogeographic insights into cryptic glacial refugia . Trends in Ecology & Evolution , 23 ( 10 ): 564 - 571 , https://doi.org/10.1016/j.tree.2008.06.010 https://doi.org/10.1016/j.tree.2008.06.010

Rambaut A , Drummond A J , Xie D et al . 2018 . Posterior summarization in Bayesian phylogenetics using Tracer 1. 7 . Systematic Biology , 67 ( 5 ): 901 - 904 , https://doi.org/10.1093/sysbio/syy032 https://doi.org/10.1093/sysbio/syy032 .

Sekino M , Ishikawa H , Fujiwara A et al . 2016 . Occurrence of the Portuguese oyster Crassostrea angulata (Lamarck, 1819) along the coast of Shikoku Island, Japan . Plankton and Benthos Research , 11 ( 2 ): 71 - 74 , https://doi.org/10.3800/pbr.11.71 https://doi.org/10.3800/pbr.11.71 .

Stajich J E , Hahn M W . 2005 . Disentangling the effects of demography and selection in human history . Molecular Biology and Evolution , 22 ( 1 ): 63 - 73 , https://doi.org/10.1093/molbev/msh252 https://doi.org/10.1093/molbev/msh252 .

Swindell S R , Plasterer T N J . 1997 . SEQMAN: Contig Assembly . Sequence Data Analysis Guidebook , p. 75 - 89 . https://do 10.1385/0-89603-358-9:75 http://dx.doi.org/10.1385/0-89603-358-9:75

Tajima F . 1989 . Statistical method for testing the neutral mutation hypothesis by DNA polymorphism . Genetics , 123 ( 3 ): 585 - 595 , https://doi.org/10.1093/genetics/123.3.585 https://doi.org/10.1093/genetics/123.3.585 .

Tamura K , Stecher G , Kumar S . 2021 . MEGA11: molecular evolutionary genetics analysis version 11 . Molecular Biology and Evolution , 38 ( 7 ): 3022 - 3027 , https://doi.org/10.1093/molbev/msab120 https://doi.org/10.1093/molbev/msab120 .

Wang H Y , Qian L M , Liu X et al . 2010 . Classification of a common cupped oyster from southern China . Journal of Shellfish Research , 29 ( 4 ): 857 - 866 , https://doi.org/10.2983/035.029.0420 https://doi.org/10.2983/035.029.0420 .

Wang Y P , Guo X M . 2008 . ITS length polymorphism in oysters and its use in species identification . Journal of Shellfish Research , 27 ( 3 ): 489 - 493 , https://doi.org/10.2983/0730-8000(2008)27 https://doi.org/10.2983/0730-8000(2008)27 [489:ILPIOA ] 2.0.CO; 2 .

Wang Y , Song Z , Jiang C et al . 2009 . Numerical and Environmental Studies of Bays in Fujian Province: the Sansha Bay . Ocean Press , Beijing .

Weng Z H , Xie Y J , Xiao Z Q et al . 2016 . Analysis of genetic diversity in several wild and hatchery populations of Crassostrea angulata from south Fujian and south Guangdong . Journal of Tropical Oceanography , 35 ( 3 ): 94 - 98 , https://doi.org/10.11978/2015065 https://doi.org/10.11978/2015065 .

Wright S . 1965 . The interpretation of population structure by F-statistics with special regard to systems of mating . Evolution , 19 ( 3 ): 395 - 420 , https://doi.org/10.2307/2406450 https://doi.org/10.2307/2406450 .

Xu J M , Yang F , Sun S C . 2012 . Population genetic structure and phylogeography of the mud-flat crabs Helice tientsinensis and Helice latimera along the coast of China seas based on mitochondrial DNA . African Journal of Biotechnology , 11 ( 16 ): 3738 - 3750 , https://doi.org/10.5897/AJB10.1643 https://doi.org/10.5897/AJB10.1643 .

Yu S Q , Han Z Q , Chen Y T et al . 2023 . The species and distribution of Crassostrea oyster in Fujian coast . Oceanologia et Limnologia Sinica , 54 ( 6 ): 1682 - 1692 , https://doi.org/10.11693/hyhz20230400088. https://doi.org/10.11693/hyhz20230400088. (in Chinese with English abstract)

Zhan A B , Hu J J , Hu X L et al . 2009 . Fine-scale population genetic structure of Zhikong scallop ( Chlamys farreri ): do local marine currents drive geographical differentiation? Marine Biotechnology , 11 ( 2 ): 223 - 235 , https://doi.org/10.1007/s10126-008-9138-1 https://doi.org/10.1007/s10126-008-9138-1 .

Views

Downloads

CSCD

Alert me when the article has been cited

Submit

Tools

Publicity Resources

Genetic diversity and population structure of Eleutheronema rhadinum in the East and South China Seas revealed in mitochondrial COI sequences

A preliminary review on population parameters and genetic diversity in Oreochromis mossambicus: meta-regression and haplotype diversity

Genome-wide SNP markers provided insights into the reproductive strategy and genetic diversity of the green tide causative species Ulva prolifera in China

Genetic diversity and population structure of the sea star Asterias amurensis in the northern coast of China

Related Author

Ziqiang HAN

Huayong QUE

Xinxu Sun

Dongdong Xu

Bao Lou

Tao Zhang

Jian Xin

Yaoshi Guo

Related Institution

Key and Open Laboratory of Marine and Estuarine Fisheries Resource and Ecology Ministry of Agriculture East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences

Key Lab of Mariculture and Enhancement of Zhejiang Province Marine Fishery Institute of Zhejiang Province

College of Marine Science Zhejiang Ocean University

Aquaculture Research Unit, School of Agricultural and Environmental Sciences, University of Limpopo (Turfloop Campus), Private Bag X1106, Sovenga 0727, South Africa

University of Chinese Academy of Sciences

Address：Editorial Office of JOL, 88 Haijun Rd. Qingdao, 266000, China
Tel：+86-532-82898754 Email：jol@qdio.ac.cn
Technical support is provided by Beijing Founder electronics co., LTD 京ICP备09064830号-19 京公网安备11010802024621
It is recommended to read the content of this site in Chrome&IE9+. Please switch to extreme mode in browser 360.
Cookies We use cookies to help provide and enhance our service and tailor content. By continuing, you agree to the use of cookies.

⁰

Genetic diversity and population structure of the Fujian oyster Crassostrea angulata revealed by mitochondrial COⅠ gene and nuclear gene ITS2 sequences

DOI：10.1007/s00343-025-4308-9

摘要

Abstract

关键词

Keywords

references