Skip to main content
Log in

Are mini DNA-barcodes sufficiently informative to resolve species identities? An in silico analysis using Phyllanthus

  • RESEARCH NOTE
  • Published:
Journal of Genetics Aims and scope Submit manuscript

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Figure 1
Figure 2
Figure 3

References

  • Adams K. L. and Palmer J. D. 2003 Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol. Phylogenet. Evol. 29, 380–395.

  • Baumstegier J. and Kerby J. L. 2009 Effectiveness of salmon carcass tissue for use in DNA extraction and amplificaton in conservation genetic studies. N. Am. J. Fish Manag. 29, 40–49.

  • CBOL Plant Working Group 2009 A DNA barcode for land plants. Proc. Natl. Acad. Sci. USA 106, 12794–12797.

  • Cho Y., Mower J. P., Qiu Y.-L. and Palmer J. D. 2004 Mitochondrial substitution rates are extraordinarily elevated and variable within a genus of flowering plants. Proc. Natl. Acad. Sci. USA 101, 17741–17746.

  • Dean M. D. and Ballard J. W. 2001 Factors affecting mitochondrial DNA quality from museum preserved Drosophila simulans. Entomol. Exp. Appl. 98, 279–283.

  • Dubey B., Meganathan P. R. and Haque I. 2010 DNA mini-barcoding: an approach for forensic identification of some endangered snake species. Forensic Sci. Int. Genet. 5, 181–184.

  • Ficetola G. F., Coissac E., Zundel S., Riaz T., Shehzad W., Bessiere J. et al. 2010 An in silico approach for the evaluation of DNA barcodes. BMC Genomics 11, 434.

  • Gonzalez M. A., Baraloto C., Engel J., Mori S. A., Pétronelli P. et al. 2009 Identification of Amazonian trees with DNA barcodes. PLoS One 4, e7483.

  • Gu J., Su J.-X., Lin R.-Z., Li R.-Q. and Xiao P.-G. 2011 Testing four proposed barcoding markers for the identification of species within Ligustrum L. (Oleaceae). J. Syst. Evol. 49, 213–224.

  • Hajibabaei M. and McKenna C. 2012 DNA mini-barcodes. In DNA barcodes: methods and protocols, methods in molecular biology (ed. W. J. Kress and D. L. Erickson) vol. 858, pp. 339–353. University of Hertfordshire, Hertfordshire, UK.

  • Hajibabaei M., deWaard J. R. and Ivanova N. V. et al. 2005 Critical factors for assembling a high volume of DNA barcodes. Philos. Trans. R. Soc. London [B. Biol. Sci.] 360, 1959–1967.

  • Hajibabaei M., Shokralla S., Zhou X., Singer G. A. C. and Baird D. J. 2011 Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river Benthos. PLoS One 6, e17497.

  • Hajibabaei M., Smith M. A., Janzen D. H., Rodriguez J. J., Whitfield J. B. and Hebert P. D. N. 2006 A minimalist barcode can identify a specimen whose DNA is degraded. Mol. Ecol. Notes 6, 959–964.

  • Herbert P. D. N., Cywinska A., Ball S. L. and deWaard J. R. 2003 Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B. Biol. Sci. 270, 313–321.

  • Houdt J. K. J., Breman F. C., Virgilio M. and Meyer M. D. 2009 Recovering full DNA barcodes from natural history collections of Tephritid fruit flies (Tephritidae, Diptera) using mini-barcodes. Mol. Ecol. Resour. 10, 459–465.

  • Kress W. J. and Erickson D. L. 2007 A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS One 2, e508.

  • Kress W. J., Erickson D. L., Jones F. A., Swenson N. G., Perez R., Bermingham E. and Sanjur O. 2009 Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proc. Natl. Acad. Sci. USA 106, 18621–18626.

  • Kress W. J., Erickson D. L., Swenson N. G., Thompson J., Uriarte M. and Zimmerman J. K. 2010 Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot. PLoS One 5, e15409.

  • Lee P. L. M. and Prysjones R. P. 2008 Extracting DNA from museum bird eggs, and whole genome amplification of archive DNA. Mol. Ecol. Resour. 8, 551–560.

  • Meusnier I., Singer G. A. C., Landry J. F., Hickey D. A., Hebert P. D. N. and Hajibabaei M. 2008 A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 9, 214.

  • Patel S., Waugh J., Millar C. D. and Lambert D. M. 2009 Conserved primers for DNA barcoding historical and modern samples from New Zealand and Antarctic birds. Mol. Ecol. Resour. 10, 431–438.

  • Rougerie R., Smith A. M. and Fernandez-Triana J. 2010 Molecular analysis of parasitoid linkages (MAPL): gut contents of adult parasitoid wasps reveal larval hosts. Mol. Ecol. 20, 179–186.

  • Saitoh K., Uehara S. and Tega T. 2008 Genetic identification of fish eggs collected in Sendai Bay and off Johban, Japan. Icthyol. Res. 56, 200–203.

  • Shaw J., Lickey E. B., Schilling E. E. and Small R. L. 2007 Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am. J. Bot. 94, 275–288.

  • Smith M. A. and Fisher B. L. 2009 Invasions, DNA barcodes and rapid biodiversity assessment using ants of Mauritius. Front. Zool. 6, 31.

  • Sonstebo J. H., Gielly K., Brysting A. K., Elven R., Edwards M., Haile J. et al. 2010 Using next-generation sequencing for molecular reconstruction of past arctic vegetation and climate. Mol. Ecol. Resour. 10, 1009–1018.

  • Srirama R., Senthilkumar U., Sreejayan N., Ravikanth G., Gurumurthy B. R., Shivanna M. B. et al. 2010 Assessing species admixtures in raw drug trade of Phyllanthus, a hepato-protective plant using molecular tools. J. Ethnopharmacol. 130, 208–215.

  • Tamura K., Peterson D., Peterson N., Stecher G., Nei M. and Kumar S. 2011 MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731–2739.

  • Whitfield J. B. 1999 Destructive sampling and information management in molecular systematic research: an entomological perspective. In Managing the modern herbarium: an interdisciplinary approach (ed. S. Byers and D. Metsger), pp. 384. Society for Preservation of Natural History Collections and Royal Ontario Museum, Toronto, Canada.

  • Zimmermann J., Hajibabaei M., Blackburn D. C., Hanken J., Cantin E., Posfai J. et al. 2008 DNA damage in preserved specimens and tissue samples: a molecular assessment. Front. Zool. 5, 18.

Download references

Acknowledgements

The work was supported by grants from the Department of Biotechnology, Government of India to G. Ravikanth and R. Uma Shaanker.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to G. RAVIKANTH.

Additional information

[Srirama R., Gurumurthy B. R., Senthilkumar U., Ravikanth G., Uma Shaanker R. and Shivanna M. B. 2014 Are mini DNA-barcodes sufficiently informative to resolve species identities? An in silico analysis using Phyllanthus. J. Genet. 93, xx–xx]

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

SRIRAMA, R., GURUMURTHY, B.R., SENTHILKUMAR, U. et al. Are mini DNA-barcodes sufficiently informative to resolve species identities? An in silico analysis using Phyllanthus . J Genet 93, 823–829 (2014). https://doi.org/10.1007/s12041-014-0432-6

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12041-014-0432-6

Keywords

Navigation