DNA barcoding of fishes from Zhoushan coastal waters using mitochondrial COI and 12S rRNA genes

Yehui WANG; Na SONG; Shude LIU; Zhi CHEN; Anle XU; Tianxiang GAO

Your Location：

Home >

Browse articles >

DNA barcoding of fishes from Zhoushan coastal waters using mitochondrial COI and 12S rRNA genes

Aquaculture and Fisheries | Updated：2024-10-14

- DNA barcoding of fishes from Zhoushan coastal waters using mitochondrial COI and 12S rRNA genes
- Journal of Oceanology and Limnology Vol. 41, Issue 5, Pages: 1997-2009(2023)
- Affiliations：
  
  1.Fisheries College, Ocean University of China, Qingdao 266003, China
  2.Shandong Fisheries Development and Resources Conservation Center, Yantai 264003, China
  3.College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China
  4.School of Fishery, Zhejiang Ocean University, Zhoushan 316000, China
- Author bio：
  
  ‍Corresponding authors: happyxu1234@163.‍com; gaotianxiang0611@zjou.edu.cn
- Funds：
- DOI：
  CLC：
- Received：06 May 2022，
  
  Accepted：18 July 2022，
  
  Online First：22 August 2022，
  
  Published：01 September 2023
- Accepted：
Scan QR Code
WANG Yehui,SONG Na,LIU Shude,et al.DNA barcoding of fishes from Zhoushan coastal waters using mitochondrial COI and 12S rRNA genes[J].Journal of Oceanology and Limnology,2023,41(05):1997-2009.
DOI：

WANG Yehui,SONG Na,LIU Shude,et al.DNA barcoding of fishes from Zhoushan coastal waters using mitochondrial COI and 12S rRNA genes[J].Journal of Oceanology and Limnology,2023,41(05):1997-2009. DOI：

摘要

Abstract

Accurate species identification is a key component of biodiversity research. DNA barcoding is an effective molecular method used for fish species identification. We aimed to study the DNA barcoding of fish in Zhoushan coastal waters

explore the differences and applicability of two gene fragments (12S rRNA and COI) of DNA barcoding in fish species identification

and established a comprehensive fish barcoding reference database. Two hundred and eighty-seven captured fish samples from Zhoushan coastal waters were identified using morphological characteristics and DNA barcoding. A total of 264 12S rRNA sequences (belonging to eight orders

31 families

55 genera

and 66 species) and 188 COI sequences (belonging to seven orders

30 families

48 genera

and 58 species) were obtained. The lengths of the 12S rRNA sequences ranged from 165 to 178 bp

and the guanine-cytosine (GC) content was 45.37%. The average 12S rRNA interspecific and intraspecific genetic distances (K2P) were 0.10% and 26.66%

respectively. The length of the COI sequence ranged 574‍‍‍–‍655 bp

and the content of GC was 45.97%. The average 12S rRNA interspecific and intraspecific genetic distances (K2P) were 0.16% and 27.45%

respectively. The minimum interspecific genetic distances of 12S rRNA and COI (1.23% and 1.86%) were both greater than their maximum intraspecific genetic distances (2.42% and 8.66%). Three molecular analyses (NJ tree

ABGD

and GMYC) were performed to accurately identify and delineate species. Clustering errors occurred when the 12S rRNA sequences were delimited using the NJ tree method

and the delimitation results of ABGD and GMYC are consistent with the final species identification results. Our results demonstrate that DNA barcoding based on 12S rRNA and COI can be used as an effective tool for fish species identification

and 12S rRNA has good application prospects in the environmental DNA (eDNA) metabarcoding of marine fish.

关键词

Keywords

references

Bagley J C , De Podestà Uchôa de Aquino P , Breitman M F et al . 2019 . DNA barcode and minibarcode identification of freshwater fishes from Cerrado headwater streams in Central Brazil . Journal of Fish Biology , 95 ( 4 ): 1046 - 1060 , https://doi.org/10.1111/jfb.14098 https://doi.org/10.1111/jfb.14098 .

Bouckaert R , Heled J , Kühnert D et al . 2014 . BEAST 2: a software platform for Bayesian evolutionary analysis . PLoS Computational Biology , 10 ( 4 ): e1003537 , https://doi.org/10.1371/journal.pcbi.1003537 https://doi.org/10.1371/journal.pcbi.1003537 .

Casiraghi M , Labra M , Ferri E et al . 2010 . DNA barcoding: a six-question tour to improve users' awareness about the method . Briefings in Bioinformatics , 11 ( 4 ): 440 - 453 , https://doi.org/10.1093/bib/bbq003 https://doi.org/10.1093/bib/bbq003 .

Cawthorn D M , Steinman H A , Witthuhn R C . 2012 . Evaluation of the 16S and 12S rRNA genes as universal markers for the identification of commercial fish species in South Africa . Gene , 491 ( 1 ): 40 - 48 , https://doi.‍‍org/10.1016/j.gene.2011.09.009 https://doi.‍‍org/10.1016/j.gene.2011.09.009 . https://do 10.1016/j.gene.2011.09.009 http://dx.doi.org/10.1016/j.gene.2011.09.009

Chen D G , Zhang M Z . 2015 . Marine Fishes of China . Ocean University of China Press , Qingdao , China. (in Chinese with English abstract)

Chen Z . 2019 . Establishment and Application of eDNA Method for Fish Diversity Survey around Zhejiang Coastal Area . Ocean University of China, Qingdao, China . (in Chinese)

Cheng P , Zhang A B , Wang Z S . 2012 . Mini DNA barcode utilizes in fish classification . Journal of Capital Normal University (Natural Science Edition) , 33 ( 2 ): 47 - 52 , https://doi.‍‍org/10.3969/j.‍issn.‍1004-9398.2012.02.009. https://doi.‍‍org/10.3969/j.‍issn.‍1004-9398.2012.02.009. (in Chinese with English abstract)

Clare E L , Lim B K , Fenton M B et al . 2011 . Neotropical bats: estimating species diversity with DNA barcodes . PLoS One , 6 ( 7 ): e22648 , https://doi.‍‍org/10.1371/journal.pone.0022648 https://doi.‍‍org/10.1371/journal.pone.0022648 . https://do 10.1371/journal.pone.0022648 http://dx.doi.org/10.1371/journal.pone.0022648

Collins R A , Boykin L M , Cruickshank R H et al . 2012 . Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification . Methods in Ecology and Evolution , 3 ( 3 ): 457 - 465 , https://doi.org/10.1111/j.2041-210X.2011.00176.x https://doi.org/10.1111/j.2041-210X.2011.00176.x

Darriba D , Taboada G L , Doallo R et al . 2012 . jModelTest 2: more models, new heuristics and parallel computing . Nature methods , 9 ( 8 ): 772 - 772 , https://doi.org/10.1038/nmeth.2109 https://doi.org/10.1038/nmeth.2109 .

Dubey B , Meganathan P R , Haque I . 2011 . DNA mini-barcoding: an approach for forensic identification of some endangered Indian snake species . Forensic Science International : Genetics , 5 ( 3 ): 181 - 184 , https://doi.org/10.1016/j.fsigen.2010.03.001 https://doi.org/10.1016/j.fsigen.2010.03.001 .

Ezard T , Fujisawa T , Barraclough T G . 2009 . Splits: species' limits by threshold statistics . R Package Version , 1 ( 11 ): r29 . Retrieved from http://R-Forge.R-project.‍org/projects/splits http://R-Forge.R-project.‍org/projects/splits .

Fujisawa T , Barraclough T G . 2013 . Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets . Systematic Biology , 62 ( 5 ): 707 - 724 , https://doi.org/10.1093/sysbio/syt033 https://doi.org/10.1093/sysbio/syt033 .

Gold Z , Curd E E , Goodwin K D et al . 2021 . Improving metabarcoding taxonomic assignment: a case study of fishes in a large marine ecosystem . Molecular Ecology Resources , 21 ( 7 ): 2546 - 2564 , https://doi.‍‍org/10.1111/1755-0998.13450 https://doi.‍‍org/10.1111/1755-0998.13450 . https://do 10.1111/1755-0998.13450 http://dx.doi.org/10.1111/1755-0998.13450

Hajibabaei M , Smith M A , Janzen D H et al . 2006 . A minimalist barcode can identify a specimen whose DNA is degraded . Molecular Ecology Notes , 6 ( 4 ): 959 - 964 , https://doi.org/10.1111/j.1471-8286.2006.01470.x https://doi.org/10.1111/j.1471-8286.2006.01470.x

Hebert P D N , Cywinska A , Ball S L et al . 2003a . Biological identifications through DNA barcodes. Proceedings of the Royal Society of London . Series B : Biological Sciences , 270 ( 1512 ): 313 - 321 , https://doi.‍‍org/10.1098/rspb.2002.2218 https://doi.‍‍org/10.1098/rspb.2002.2218 .

Hebert P D N , Penton E H , Burns J M et al . 2004a . Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator . Proceedings of the National Academy of Sciences of the United States of America , 101 ( 41 ): 14812 - 14817 , https://doi.org/10.1073/pnas.0406166101 https://doi.org/10.1073/pnas.0406166101 .

Hebert P D N , Ratnasingham S , De Waard J R . 2003b . Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London . Series B : Biological Sciences , 270 ( S1 ): S96 - S99 , https://doi.‍‍org/10.1098/rsbl.2003.0025 https://doi.‍‍org/10.1098/rsbl.2003.0025 .

Hebert P D N , Stoeckle M Y , Zemlak T S et al . 2004b . Identification of birds through DNA barcodes . PLoS Biology , 2 ( 10 ): e312 , https://doi.org/10.1371/journal.pbio.0020312 https://doi.org/10.1371/journal.pbio.0020312 .

Hubert N , Delrieu-Trottin E , Irisson J O et al . 2010 . Identifying coral reef fish larvae through DNA barcoding: a test case with the families Acanthuridae and Holocentridae . Molecular Phylogenetics and Evolution , 55 ( 3 ): 1195 - 1203 , https://doi.org/10.1016/j.ympev.2010.02.023 https://doi.org/10.1016/j.ympev.2010.02.023 .

Hubert N , Espiau B , Meyer C et al . 2015 . Identifying the ichthyoplankton of a coral reef using DNA barcodes . Molecular Ecology Resources , 15 ( 1 ): 57 - 67 , https://doi.org/10.1111/1755-0998.12293 https://doi.org/10.1111/1755-0998.12293 .

Humair P F , Douet V , Cadenas F M et al . 2007 . Molecular identification of bloodmeal source in Ixodes ricinus ticks using 12S rDNA as a genetic marker . Journal of Medical Entomology , 44 ( 5 ): 869 - 880 , https://doi.org/10.1093/jmedent/44.5.869 https://doi.org/10.1093/jmedent/44.5.869 .

Keskİn E , Atar H H . 2013 . DNA barcoding commercially important fish species of Turkey . Molecular Ecology Resources , 13 ( 5 ): 788 - 797 , https://doi.org/10.1111/1755-0998.12120 https://doi.org/10.1111/1755-0998.12120 .

Ko H L , Wang Y T , Chiu T S et al . 2013 . Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding . PLoS One , 8 ( 1 ): e53451 , https://doi.org/10.1371/journal.pone.0053451 https://doi.org/10.1371/journal.pone.0053451 .

Larkin M A , Blackshields G , Brown N P et al . 2007 . Clustal W and Clustal X version 2.0 . Bioinformatics , 23 ( 21 ): 2947 - 2948 , https://doi.org/10.1093/bioinformatics/btm404 https://doi.org/10.1093/bioinformatics/btm404 .

Liu S , Liu J , Zhuang Z et al . 2010 . Monophyletic origin and synonymic phenomena in the sub-family Cynoglossinae inferred from mitochondrial DNA sequences . Biodiversity Science , 18 : 275 - 282 , https://doi.org/10.3724/SP.J.1003.2010.275. https://doi.org/10.3724/SP.J.1003.2010.275. (in Chinese with English abstract)

Liu Y , Li S F , Cheng J H . 2006 . A study on seasonal changes of the fish communities in the East China Sea and the Huanghai Sea . Acta Oceanologica Sinica , 28 ( 4 ): 108 - 114 , https://doi.‍‍org/10.3321/j.issn:0253-4193.2006.04.014. https://doi.‍‍org/10.3321/j.issn:0253-4193.2006.04.014. (in Chinese with English abstract)

Lo P C , Liu S H , Nor S A M et al . 2017 . Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade . PLoS One , 12 ( 4 ): e0176623 , https://doi.org/10.1371/journal.pone.0176623 https://doi.org/10.1371/journal.pone.0176623 .

Melton T , Holland C . 2007 . Routine forensic use of the mitochondrial 12S ribosomal RNA gene for species identification . Journal of Forensic Sciences , 52 ( 6 ): 1305 - 1307 , https://doi.org/10.1111/j.1556-4029.2007.00553.x https://doi.org/10.1111/j.1556-4029.2007.00553.x .

Meusnier I , Singer G A C , Landry J F et al . 2008 . A universal DNA mini-barcode for biodiversity analysis . BMC Genomics , 9 ( 1 ): 214 , https://doi.org/10.1186/1471-2164-9-214 https://doi.org/10.1186/1471-2164-9-214 .

Miya M , Gotoh R O , Sado T . 2020 . MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples . Fisheries Science , 86 ( 6 ): 939 - 970 , https://doi.org/10.1007/s12562-020-01461-x https://doi.org/10.1007/s12562-020-01461-x .

Miya M , Sato Y , Fukunaga T et al . 2015 . MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species . Royal Society Open Science , 2 ( 7 ): 150088 , https://doi.org/10.1098/rsos.150088 https://doi.org/10.1098/rsos.150088 .

Nei M , Kumar S . 2000 . Molecular Evolution and Phylogenetics . Oxford University Press, Oxford . https://do 10.1093/oso/9780195135848.001.0001 http://dx.doi.org/10.1093/oso/9780195135848.001.0001

Nneji L M , Adeola A C , Ayoola A O et al . 2020 . DNA barcoding and species delimitation of butterflies (Lepidoptera) from Nigeria . Molecular Biology Reports , 47 ( 12 ): 9441 - 9457 , https://doi.‍‍org/10.1007/s11033-020-05984-5 https://doi.‍‍org/10.1007/s11033-020-05984-5 . https://do 10.1007/s11033-020-05984-5 http://dx.doi.org/10.1007/s11033-020-05984-5

Pegg G G , Sinclair B , Briskey L et al . 2006 . MtDNA barcode identification of fish larvae in the southern Great Barrier Reef-Australia . Scientia Marina , 70 ( S2 ): 7 - 12 , https://doi.org/10.3989/scimar.2006.70s27 https://doi.org/10.3989/scimar.2006.70s27 .

Pons J , Barraclough T G , Gomez-Zurita J et al . 2006 . Sequence-based species delimitation for the DNA taxonomy of undescribed insects . Systematic Biology , 55 ( 4 ): 595 - 609 , https://doi.org/10.1080/10635150600852011 https://doi.org/10.1080/10635150600852011 .

Puillandre N , Lambert A , Brouillet S et al . 2012 . ABGD, automatic barcode gap discovery for primary species delimitation . Molecular Ecology , 21 ( 8 ): 1864 - 1877 , https://doi.org/10.1111/j.1365-294X.2011.05239.x https://doi.org/10.1111/j.1365-294X.2011.05239.x .

Saitou N , Nei M . 1987 . The neighbor-joining method: a new method for reconstructing phylogenetic trees . Molecular Biology and Evolution , 4 ( 4 ): 406 - 425 .

Sambrook J , Russel D W . 2001 . Molecular Cloning: A Laboratory Manual. 3 rd edn . Cold Spring Harbor Laboratory Press , New York .

Shen J A , Cheng Y H . 1987 . A study on the deep sea demersal fish communities and their structures in the East China Sea . Journal of Fisheries of China , 11 ( 4 ): 293 - 306 . (in Chinese with English abstract)

Shen Y J , Guan L H , Wang D Q et al . 2016 . DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River . Ecology and Evolution , 6 ( 9 ): 2702 - 2713 , https://doi.org/10.1002/ece3.2060 https://doi.org/10.1002/ece3.2060 .

Shi R Z , Xiong X , Huang M H et al . 2020 . High resolution melting (HRM) analysis of a 12S rRNA mini barcode as a novel approach for codfish species authentication in processed fish products . European Food Research and Technology , 246 ( 5 ): 891 - 899 , https://doi.org/10.1007/s00217-020-03456-5 https://doi.org/10.1007/s00217-020-03456-5 .

Tamura K , Peterson D , Peterson N et al . 2011 . MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods . Molecular Biology and Evolution , 28 ( 10 ): 2731 - 2739 , https://doi.org/10.1093/molbev/msr121 https://doi.org/10.1093/molbev/msr121 .

Vartak V R , Narasimmalu R , Annam P K et al . 2015 . DNA barcoding detected improper labelling and supersession of crab food served by restaurants in India . Journal of the Science of Food and Agriculture , 95 ( 2 ): 359 - 366 , https://doi.org/10.1002/jsfa.6728 https://doi.org/10.1002/jsfa.6728 .

Wang L J , Wu Z H , Liu M X et al . 2018 . DNA barcoding of marine fish species from Rongcheng Bay, China . PeerJ , 6 : e5013 , https://doi.org/10.7717/peerj.5013 https://doi.org/10.7717/peerj.5013 .

Wang Y H , Duan J N , Shi H L et al . 2020 . Species identification of small fish in Xixuan Island coastal waters of Zhoushan using DNA barcoding . Journal of Applied Ichthyology , 36 ( 1 ): 75 - 84 , https://doi.org/10.1111/jai.13995 https://doi.org/10.1111/jai.13995 .

Wang Z D , Guo Y S , Chen R L et al . 2009 . CO I barcoding sequences of Teleosts in the South China Sea . Oceanologia et Limnologia Sinica , 40 ( 5 ): 608 - 614 , https://doi.org/10.3321/j.‍issn:‍0029-814X.‍2009.05.014. https://doi.org/10.3321/j.‍issn:‍0029-814X.‍2009.05.014. (in Chinese with English abstract)

Ward R D , Zemlak T S , Innes B H et al . 2005 . DNA barcoding Australia's fish species . Philosophical Transactions of the Royal Society B : Biological Sciences , 360 ( 1462 ): 1847 - 1857 , https://doi.org/10.1098/rstb.2005.1716 https://doi.org/10.1098/rstb.2005.1716 .

Wu Z J , Gao F L , Shen J G . 2010 . Bioinformatics Analysis Practice . Science Press , Beijing , China. (in Chinese)

Xing B P , Lin H S , Zhang Z L et al . 2018 . DNA barcoding for identification of fish species in the Taiwan Strait . PLoS One , 13 ( 6 ): e0198109 , https://doi.org/10.1371/journal.pone.0198109 https://doi.org/10.1371/journal.pone.0198109 .

Xu C Y , Shen C C , Cai J T et al . 2017 . Species identification of partial fish larvae and juveniles in Fujian coastal areas based on cytochrome C oxidase subunit I barcoding . Journal of Fishery Sciences of China , 24 ( 6 ): 1176 - 1183 , https://doi.‍org/10.3724/SP.‍J.‍1118.2017.17068. https://doi.‍org/10.3724/SP.‍J.‍1118.2017.17068. (in Chinese with English abstract) . https://do 10.3724/sp.j.1118.2017.17068 http://dx.doi.org/10.3724/sp.j.1118.2017.17068

Xu L , Van Damme K , Li H et al . 2019 . A molecular approach to the identification of marine fish of the Dongsha Islands (South China Sea) . Fisheries Research , 213 : 105 - 112 , https://doi.org/10.1016/j.fishres.2019.01.011 https://doi.org/10.1016/j.fishres.2019.01.011 .

Yu C G , Chen Q Z , Chen X Q et al . 2010 . Species composition and quantitative distribution of fish in the Zhoushan fishing ground and its adjacent waters . Oceanologia et Limnologia Sinica , 41 ( 3 ): 410 - 417 . (in Chinese with English abstract)

Zhang J B , Hanner R . 2011 . DNA barcoding is a useful tool for the identification of marine fishes from Japan . Biochemical Systematics and Ecology , 39 ( 1 ): 31 - 42 , https://doi.org/10.1016/j.bse.2010.12.017 https://doi.org/10.1016/j.bse.2010.12.017 .

Zhao S L , Xu H X , Zhong J S et al . 2016 . Marine Fishes in Zhejiang Province . Zhejiang Science and Technology Press, Hangzhou, China . (in Chinese)

Zhoushan Municipal Statistics Bureau , Zhoushan Investigation Team of the National Bureau of Statistics . 2010 . Zhoushan Statistical Yearbook . China Statistics Press , Beijing , China. (in Chinese with English abstract)

Views

Downloads

CSCD

Alert me when the article has been cited

Submit

Tools

Publicity Resources

DNA barcoding of the family Sparidae along the coast of China and revelation of potential cryptic diversity in the IndoWest Pacific oceans based on COI and 16S rRNA genes

Molecular phylogeography and population history of Saccostrea mordax based on mitochondrial DNA

Epiphytic zooplankton community profiles in a typical urban wetland as revealed by DNA metabarcoding

First record of abnormal body coloration in a rockfish Sebastes koreanus (Scorpaenoidei: Sebastidae) from coastal water of China based on morphological characteristics and DNA barcoding

Investigation on Interaction Mechanism Between Rim Sealing Flow and Mainstream Flow in High-Pressure Turbine

Related Author

Yehui WANG

Na SONG

Shude LIU

Zhi CHEN

Anle XU

Tianxiang GAO

Renxie WU

Haoran ZHANG

Related Institution

WANG et al.: Fish identification using DNA barcoding

College of Life Sciences, Hebei University

Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences

College of Fisheries, Guangdong Ocean University

School of Marine Science and Engineering, Qingdao Agricultural University

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