Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
, 2 (6), e508

A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

Affiliations
Comparative Study

A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

W John Kress et al. PLoS One.

Abstract

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.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Phylogenetic distribution across land plants of included taxa and PCR success of tested loci.
The cladogram indicates the major land plant lineages –. The lineages sampled in this study are highlighted in yellow. The success of each colored-coded primer in amplifying at least one species is indicated for each of the lineages; open white boxes indicate primer failure in all taxa tested; white boxes with an “X” indicate missing sample.
Figure 2
Figure 2. Properties of nine plant loci tested as putative barcodes.
Blue bars indicate PCR success; yellow bars indicate percent success in differentiating between species of a pair; maroon bars indicate PCR success combined with the ability to differentiate between species of a pair.
Figure 3
Figure 3. Properties of two-locus pairs tested as putative barcodes.
Only those locus pairs with PCR success greater than 90% are included. Yellow bars indicate percent success in differentiating between species of a pair only; maroon bars indicate PCR success combined with the ability to differentiate between species of a pair.

Similar articles

See all similar articles

Cited by 251 articles

See all "Cited by" articles

References

    1. Hebert PDN, Cywinska NA, Ball SL, deWaard JR. Biological identifications through DNA barcodes. Proc Roy Soc B-Biol Sci. 2003a;270:313–321. - PMC - PubMed
    1. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. Identification of birds through DNA barcodes. PLoS Biol. 2004a;2(10):e312. - PMC - PubMed
    1. Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R. Towards writing the encyclopedia of life: an introduction to DNA barcoding. Phil Trans Roy Soc Lond Ser B Biol Sci. 2005;360:1850–1811. - PMC - PubMed
    1. Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet. 2007 doi:10.1016/j.tig.2007.02.001. - PubMed
    1. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci U S A. 2004b;101:14812–14817. - PMC - PubMed

Publication types

MeSH terms

Feedback