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A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region
Open accessAbstract
BACKGROUND: A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. METHODOLOGY/PRINCIPAL FINDINGS: Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. CONCLUSIONS/SIGNIFICANCE: A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
DNA barcoding: error rates based on comprehensive sampling
Meyer, C. P., & Paulay, G. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030422 · Cited by 1,957
Cited by
The application of biotechnology to orchids
Hossain, M. M., Kant, R., Van, P. T., Winarto, B., Zeng, S., & Teixeira da Silva, J. A. (2013) · Critical Reviews in Plant Sciences · doi:10.1080/07352689.2012.715984 · Cited by 152
Jogam, P., Sandhya, D., Shekhawat, M. S., Alok, A., M, M., Abbagani, S., & Allini, V. R. (2020) · Industrial Crops and Products · doi:10.1016/j.indcrop.2020.112476 · Cited by 66
Metadata
- Authors
- Kress, W. J., & Erickson, D. L.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2007-06-06
- Volume
- 2
- Issue
- 6
- Pages
- e508
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2111536597
- Cited by
- 1,527
- References
- 2
- FWCI
- 29.57
- Type
- journal article
- Language
- en
- Open access
- gold
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