The Barcode Blog

A mostly scientific blog about short DNA sequences for species identification and discovery. I encourage your commentary. -- Mark Stoeckle

Subscribe to this blog

Sign up for email notifications

Mapping routes for DNA barcoding land plants

Progressive GardensLand plants challenge standardized DNA-based identification. Different groups of land plants are deeply divergent at the DNA level, yet there are relatively few sequence differences among closely-related species. Deep divergences make it difficult to design broad-range primers that amplify DNA from the many kinds of plants, and small differences among closely-related species mean longer sequences are needed to distinguish them. Plant mitochondrial genes including COI evolve too slowly to be useful. The best strategy appears likely to be a combination of 2 or 3 gene regions from the chloroplast genome. Chloroplasts are organelles which house the plants’ photosynthetic machinery and have their own genome, like mitochondria.

In May 2007 Taxon, 19 researchers from 12 institutions in 7 countries (Brazil, Colombia, Denmark, Mexico, South Africa, U.K. and U.S.A.) report on tests of candidate barcode regions. Chase and co-investigators outline the rationale and results for selecting and testing potential land plant barcode regions. The finalists were winnowed down from more than 100 coding and non-coding regions in chloroplast DNA by testing 96 pairs of closely-related plant species to see which regions could be amplified and provide discrimination. Although the actual data are not shown in this short update, they summarize their results by proposing three chloroplast gene regions as a standard barcode for land plants: two coding regions, matK and rpoC1, and, either a third coding region, rpoB, or the non-coding psbA-trnH spacer region.

In June 2007 PLoS ONE, Kress and Erikcson, Smithsonian Institution, examine nine potential loci (8 plastid regions which includes the four final candidates in the Taxon paper, and nuclear gene ITS). In this analysis, as in Chase et al report, there are two steps: first, does the region amplify with a standard set of primers, and second, if so, does the sequence enable discrimination of closely-related species. In the 48 pairs of species examined, only two loci, trnH-psbA and rbcL-a exhibited more than 90% success with standard primers.  Based on this admittedly small sample, the authors propose a “two-locus global DNA barcode for land plants” in which “rbcL-a provides a strong recognition anchor that will place an unidentified specimen into a family, genus, and sometimes species; the highly variable trnH-psbA spacer will futher narrow the corrrect species identification where rbcL-a lacks discrimination power.”

These are promising starts towards a standardized DNA barcode for land plants. More tests are needed, including analysis of variation within species, as both studies used single specimens for each target species.

This entry was posted on Thursday, July 19th, 2007 at 8:17 pm and is filed under General. You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed.

2 Responses to “Mapping routes for DNA barcoding land plants”

  1. Indoor Plants Says:

    This is extremely interesting, was this done via haplotype mapping or is this only possible in animals?

  2. Mark Stoeckle Says:

    Standards for DNA barcoding of land plants will be announced in Proc Natl Acad Sci USA in July 2009.

Contact: mark.stoeckle@rockefeller.edu

About this site

This web site is an outgrowth of the Taxonomy, DNA, and Barcode of Life meeting held at Banbury Center, Cold Spring Harbor Laboratory, September 9-12, 2003. It is designed and managed by Mark Stoeckle, Perrin Meyer, and Jason Yung at the Program for the Human Environment (PHE) at The Rockefeller University.

About the Program for the Human Environment

The involvement of the Program for the Human Environment in DNA barcoding dates to Jesse Ausubel's attendance in February 2002 at a conference in Nova Scotia organized by the Canadian Center for Marine Biodiversity. At the conference, Paul Hebert presented for the first time his concept of large-scale DNA barcoding for species identification. Impressed by the potential for this technology to address difficult challenges in the Census of Marine Life, Jesse agreed with Paul on encouraging a conference to explore the contribution taxonomy and DNA could make to the Census as well as other large-scale terrestrial efforts. In his capacity as a Program Director of the Sloan Foundation, Jesse turned to the Banbury Conference Center of Cold Spring Harbor Laboratory, whose leader Jan Witkowski prepared a strong proposal to explore both the scientific reliability of barcoding and the processes that might bring it to broad application. Concurrently, PHE researcher Mark Stoeckle began to work with the Hebert lab on analytic studies of barcoding in birds. Our involvement in barcoding now takes 3 forms: assisting the organizational development of the Consortium for the Barcode of Life and the Barcode of Life Initiative; contributing to the scientific development of the field, especially by studies in birds, and contributing to public understanding of the science and technology of barcoding and its applications through improved visualization techniques and preparation of brochures and other broadly accessible means, including this website. While the Sloan Foundation continues to support CBOL through a grant to the Smithsonian Institution, it does not provide financial support for barcoding research itself or support to the PHE for its research in this field.