Land plants and DNA barcodes: short-term and long-term goals.

Details

Serval ID
serval:BIB_E7E94D739675
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Land plants and DNA barcodes: short-term and long-term goals.
Journal
Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Author(s)
Chase M.W., Salamin N., Wilkinson M., Dunwell J.M., Kesanakurthi R.P., Haidar N., Savolainen V.
ISSN
0962-8436 (Print)
ISSN-L
0962-8436
Publication state
Published
Issued date
2005
Peer-reviewed
Oui
Volume
360
Number
1462
Pages
1889-1895
Language
english
Abstract
Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low levels of variability and (ii) the typically used land plant plastid phylogenetic markers (e.g. rbcL, trnL-F, etc.) appear to have too little variation. However, no one has assessed how well current phylogenetic resources might work in the context of identification (versus phylogeny reconstruction). In this paper, we make such an assessment, particularly with two of the markers commonly sequenced in land plant phylogenetic studies, plastid rbcL and internal transcribed spacers of the large subunits of nuclear ribosomal DNA (ITS), and find that both of these DNA regions perform well even though the data currently available in GenBank/EBI were not produced to be used as barcodes and BLAST searches are not an ideal tool for this purpose. These results bode well for the use of even more variable regions of plastid DNA (such as, for example, psbA-trnH) as barcodes, once they have been widely sequenced. In the short term, efforts to bring land plant barcoding up to the standards being used now in other organisms should make swift progress. There are two categories of DNA barcode users, scientists in fields other than taxonomy and taxonomists. For the former, the use of mitochondrial and plastid DNA, the two most easily assessed genomes, is at least in the short term a useful tool that permits them to get on with their studies, which depend on knowing roughly which species or species groups they are dealing with, but these same DNA regions have important drawbacks for use in taxonomic studies (i.e. studies designed to elucidate species limits). For these purposes, DNA markers from uniparentally (usually maternally) inherited genomes can only provide half of the story required to improve taxonomic standards being used in DNA barcoding. In the long term, we will need to develop more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability; these would permit the detection of hybrids and permit researchers to identify the 'genetic gaps' that are useful in assessing species limits.
Keywords
Automatic Data Processing/methods, Biodiversity, Classification/methods, Computational Biology/methods, DNA/genetics, DNA, Ribosomal Spacer/genetics, Databases, Genetic, Molecular Diagnostic Techniques/methods, Plants/genetics, Ribulose-Bisphosphate Carboxylase/genetics, Species Specificity
Pubmed
Web of science
Create date
24/01/2008 18:41
Last modification date
20/08/2019 16:10
Usage data