Plant DNA barcoding using chloroplast genome sequences

Chloroplast DNA sequence data have played a critical role in the development of plant DNA barcodes. While the mitochondrial locus CO1 is well accepted as an efficient DNA barcode for animals, no single locus has been identified that can discriminate between all plant species. There has been considerable debate about the selection of the most suitable chloroplast loci, and the two-locus (matK and rbcL) plant barcode proposed in 2009 remains problematic for some plant groups. Recent advances in DNA sequencing technology are providing opportunities for whole genome sequence comparisons. Assembly of chloroplast genome sequences from massively parallel sequencing (MPS) of total DNA circumvents PCR-based issues such as amplification and primer universality. Access to the whole chloroplast genome will provide many more informative sites and has the potential to improve plant identification within and among even closely related species. We present chloroplast genome sequences recovered from MPS of total DNA for a wide range of species including wild rice relatives, eucalypts and sugarcane. The analysis of chloroplast genome sequences is rapidly becoming a simple, accurate and cost effective option for DNA barcoding and plant identification. Is the chloroplast genome the elusive single-locus DNA barcode for plants?