DNA barcoding discriminates Pampus minor (Liu et al., 1998) from Pampus species

Enmian Guo; Yuan Liu; Jing Liu; Zhaoxia Cui

doi:10.1007/s00343-010-9917-1

Your Location：

Home >

Browse articles >

DNA barcoding discriminates Pampus minor (Liu et al., 1998) from Pampus species

Updated：2023-05-16

- DNA barcoding discriminates Pampus minor (Liu et al., 1998) from Pampus species
- Journal of Oceanology and Limnology Vol. 28, Issue 6, Pages: 1266-1274(2010)
- Affiliations：
  
  1. Qingdao Agriculture University
  2. Institute of Oceanology Chinese Academy of Sciences
- Author bio：
- Funds：
- DOI：10.1007/s00343-010-9917-1
  CLC：
- Online First：30 October 2010，
  
  Published：2010
- Accepted：
Scan QR Code
Guo, E., Liu, Y., Liu, J. et al. DNA barcoding discriminates Pampus minor (Liu et al., 1998) from Pampus species., Chin. J. Ocean. Limnol. 28, 1266–1274 (2010). https://doi.org/10.1007/s00343-010-9917-1
DOI：

Guo, E., Liu, Y., Liu, J. et al. DNA barcoding discriminates Pampus minor (Liu et al., 1998) from Pampus species., Chin. J. Ocean. Limnol. 28, 1266–1274 (2010). https://doi.org/10.1007/s00343-010-9917-1 DOI：

摘要

Abstract

Although Pampus minor has been classified as a new species

it still remains controversial. Was used a DNA barcoding technique based on homologous sequence analysis of the16S and COI genes to clarify the confusion over the identification of this species. Among 12 individuals whose genetic distance was 0.002

two haplotypes were found. According to the 16S sequences

the genetic distances ranged from 0.121 to 0.133 between P. minor and other Pampus species. Although the same the genetic distance between the two P. minor haplotypes was generated using COI sequences

the haplotype of Pm22-23

Pm28

and Pm32-33 was the same as that of Pci EF607462 and EF607466

while the haplotype of Pm24-27 and Pm29-31 was the same as that of Pci EF607461 and EF607463-65. In addition

the genetic distance ranged only from 0.002 to 0.005 between P. minor and Pa EF607460 and EF607458. Apart from this

the interspecies genetic distances varied from 0.135 to 0.143 between P. minor and other Pampus species according to the COI sequences. Phylogenetic trees

using combined 16S and COI data

strongly support the viewpoint that all the P. minor individuals form one clade that is in a sister position to Pampus sp. individuals (EU357803

FJ434342-FJ434343

and FJ652423-FJ652427).

关键词

Keywords

references

Arnaud S, Bonhomme F, Borsa P. 1999. Mitochondrial DNA analysis of the genetic relationships among populations of scad mackerel (Decapterus macarellus, D. macrosoma, D. russelli) in South-East Asia. Marine Biology, 135: 699–707.

Ballard J W O, de Whitlock M C. 2004. The incomplete natural history of mitochondria. Mol. Ecol., 13: 729–744.

Bensasson D, de Zhang D X, Hartl D L, Hewitt G M. 2001. Mitochondrial pseudogenes: Evolution’s misplaced witnesses. Trends. Ecol. Evol., 16: 314–321.

Cheng Q T. 1962. Stromateidae, the Fishes of South China Sea. Science Press, Beijing, China. p.759–763. (in Chinese)

Cui Z X, de Liu Y, Liu J, Luan W S. 2010. Molecular identification of Pampus fishes (Perciformes, Stromateidae). Ichthyological Research, 57: 32–39.

Doiuchi R, de Nakabo T. 2006. Molecular phylogeny of the stromateoid fishes (Teleostei: Perciformes) inferred from mitochondrial DNA sequences and compared with morphology-based hypotheses. Mol. Phyt. Evol., 39: 111–123.

Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39: 783–791.

Gao T X, de Li J, Wang Q Y, Liu J X. 2003. Sequence analysis on mitochondrial 16S rRNA gene in Fenneropenaeus chinensis. J. Fishery Sciences of China, 10: 59–62.

Grant W S, de Bowen B W. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lesson for conservation. J. Hered, 89: 415–426.

Hajibabaei M, Janzen DH, Burns J M, Hallwachs W, Hebert P D N. 2006. DNA barcodes distinguish species of tropical Lepidoptera. Proc. Natl. Acad. Sci., 103: 968–971.

Hajibabaei M, de Singer G A C, Hebert P D N, Hickey D A. 2007. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics, 23: 167–172.

Hebert P D N, de Cywinska A, Ball S L, Waard J R. 2003a. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. (B), 270: 313–321.

Hebert P D N, de Ratnasingham S, Dewaard J R. 2003b. Barcoding animal life: cytochrome c oxidase subunit I divergences among closely related species. Proc. R. Soc. Lond. B (Suppl.), 270: 96–99.

Huelsenbeck P, de Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17: 754–755.

Kochzius M, de Nölte M, Weber H, Silkenbeumer N, Hjörleifsdottir S, Hreggvidsson G O, Marteinsson V, Kappel K, Planes S, Tinti F, Magoulas A, Garcia Vazquez E, Turan C, Hervet C, Campo Falgueras D, Antoniou A, Landi M, Blohm D. 2008. DNA microarrays for identifying fishes. Mar. Biotechnol., 10: 207–217.

Kong X Y, Yu Z N, Liu Y J, Gao T X, Wu Y F. 2001. Comparative study of mitochondrial COI gene fragment between Chinese mitten crab (Eriocheir sinensis) and Japanese mitten crab (Eriocheir japonica). Journal of Ocean University of Qingdao, 31: 861–866. (in Chinese with English abstract)

Lakra W S, de Goswami M, Gopalakrishnan A. 2009. Molecular identification and phylogenetic relationships of seven Indian Sciaenids (Pisces: Perciformes, Sciaenidae) based on 16S rRNA and cytochrome c oxidase subunit I mitochondrial genes. Mol. Biol. Rep., 36: 831–839.

Liu J, de Li C S. 1998. A new pomfret species, Pampus minor sp. nov. (Stromateidae) from Chinese waters. Chin. J. Oceanol. Limnol., 16(4): 280–285.

Liu J, de Li C S, Li X S. 2002. Studies on Chinese pomfret fishes of the genus Pampus (Pisces: Stromateidae). Studia Marina Sinica, 44: 240–252. (in Chinese with English abstract)

Mai W J, Xie Z Y, Zhang L P, Shen Q, Hu C Q. 2009. Sequence Comparison and Phylogenetic Analysis of mtDNA 16S rRNA and COI gene Fragments in the Chinese Shrimp, Fennerpenaeus chinensis and Five Species of Shrimp. Natural Science Journal of Hainan University, 27: 15–23. (in Chinese with English abstract)

Martínez-Navarro E M, de Galián J, Serrano J. 2005. Phylogeny and molecular evolution of the tribe Harpalini (Coleoptera, Carabidae) inferred from mitochondrial cytochrome-oxidase I. Molec. Phylogen. Evol., 35: 127–146.

Neigel J, de Domingo A, Stake J. 2007. DNA barcoding as a tool for coral reef conservation. Coral Reefs, 26: 487–499.

Palumbi S R. 1996. Nucleic acids II: the polymerase chain reaction. In: Hillis D M, Moritz C, Mable B K ed. Molecular Systematics, Sinauer & Associates Inc., Sunderland, Massachusetts, p. 205–247.

Pfunder M, de Holzgang O, Frey J E. 2004. Development of microarray-based diagnostics of voles and shrews for use in biodiversity monitoring studies, and evaluation of mitochondrial cytochrome oxidase I vs. cytochrome b as genetic markers. Mol. Ecol., 13: 1 277–1 286.

Posada D, de Crandall K A. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics. 14: 817–818.

Rozas J, de Sánchez-DelBarrio J C, Messeguer X, Rozas R. 2003. DnaSP, DNA polymorphism analyses by coalescent and other methods. Bioinformatics, 19: 2 496–2 497.

Sambrook J, de Russell D W. 2001. Molecular Cloning: a Laboratory Manual. Cold Spring Harbor Laboratory Press, New York.

Sparks J S. 2004. Molecular phylogeny and biogeography of the Malagasy and South Asian cichlids (Teleostei: Perciformes: Cichlidae). Molec. Phylogen Evol., 30: 599–614.

Stoeckle M. 2003. Taxonomy, DNA, and the barcode of life. Bio-Science, 53: 2–3.

Swofford D L. 2002. PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods), Version 4.10. Sinauer Associates, Sunderland, Mass.

Tamura K, de Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol., 24: 1 596–1 599.

Thompson J D, de Gibson T J, Plewniak F, Jeanmougin F, Higgins D G. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25: 4 876–4 882.

Tjensvoll K, de Glover K A, Nylund A. 2006. Sequence variation in four mitochondrial genes of the salmon louse Lepeophtheirus salmonis. Dis. Aquat. Organ., 68: 251–259.

Ursvik A, de Breines R, Christiansen J S, Fevolden S E, Coucheron D H, Johansen S D. 2007. A mitogenomic approach to the taxonomy of pollocks: Theragra chalcogramma and T. wnnmarchica represent one single species. BMC Evol. Biol., 7: 87.

Ward R D, de Zemlak T S, Innes B H, Last P R, Hebert P D N. 2005. DNA barcoding Australia’s fish species. Phil. Trans. R. Soc. B., 360: 1 847–1 857.

Xiao J H, de Xiao H, Huang D W. 2004. DNA barcoding: new approach of biological taxonomy. Acta Zoologica Sinica, 50: 852–855. (in Chinese with English abstract)

Zhang F Y, Ma L B, Shi Z H, Ma C Y. 2008. Sequence variation and molecular phylogeny of mitochondrial COI gene segments from three pomfret species. Journal of Fishery Sciences of China, 15: 392–398. (in Chinese with English abstract)

Views

Downloads

CSCD

Alert me when the article has been cited

Submit

Tools

Publicity Resources

Genetic identification of two species of Pleuronichthys by DNA barcoding

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

Benthodytes occidentpalauta sp. nov., a new species of deep-sea holothuroid (Elasipodida: Psychropotidae) from the west of Kyushu-Palau Ridge in the Western Pacific Ocean

Benthodytes tetrapapillata sp. nov., a new elasipodid sea cucumber (Elasipodida: Psychropotidae) from a seamount in the Western Pacific Ocean

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

Related Author

Hanxiang Xu

Pengfei Li

Tianxiang Gao

Yan Zhang

Hui Zhang

Shufang LIU

Changting AN

Huan WANG

Related Institution

Marine Fisheries Research Institute of Zhejiang Province

Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences

Fisheries College Ocean University of China

Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory

Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery 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