Chloroplast genome sequences from total DNA for plant identification
Open Access
- 27 August 2010
- journal article
- Published by Wiley in Plant Biotechnology Journal
- Vol. 9 (3), 328-333
- https://doi.org/10.1111/j.1467-7652.2010.00558.x
Abstract
Chloroplast DNA sequence data are a versatile tool for plant identification or barcoding and establishing genetic relationships among plant species. Different chloroplast loci have been utilized for use at close and distant evolutionary distances in plants, and no single locus has been identified that can distinguish between all plant species. Advances in DNA sequencing technology are providing new cost-effective options for genome comparisons on a much larger scale. Universal PCR amplification of chloroplast sequences or isolation of pure chloroplast fractions, however, are non-trivial. We now propose the analysis of chloroplast genome sequences from massively parallel sequencing (MPS) of total DNA as a simple and cost-effective option for plant barcoding, and analysis of plant relationships to guide gene discovery for biotechnology. We present chloroplast genome sequences of five grass species derived from MPS of total DNA. These data accurately established the phylogenetic relationships between the species, correcting an apparent error in the published rice sequence. The chloroplast genome may be the elusive single-locus DNA barcode for plants.Keywords
This publication has 34 references indexed in Scilit:
- Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomesBMC Biology, 2009
- Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in PanamaProceedings of the National Academy of Sciences of the United States of America, 2009
- Complete Chloroplast Genome Sequence of a Major Allogamous Forage Species, Perennial Ryegrass (Lolium perenne L.)DNA Research, 2009
- Evaluation of next generation sequencing platforms for population targeted sequencing studiesGenome Biology, 2009
- Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplifiedProceedings of the National Academy of Sciences of the United States of America, 2008
- Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technologyNucleic Acids Research, 2008
- DNA barcoding the floras of biodiversity hotspotsProceedings of the National Academy of Sciences of the United States of America, 2008
- DNA barcodes: Genes, genomics, and bioinformaticsProceedings of the National Academy of Sciences of the United States of America, 2008
- A database of PCR primers for the chloroplast genomes of higher plantsPlant Methods, 2007
- The map-based sequence of the rice genomeNature, 2005