May 26, 2011 | Peter M. Hollingsworth, Sean W. Graham, Damon P. Little
This review discusses the selection and use of plant DNA barcodes. DNA barcoding aims to create a shared resource of DNA sequences for organism identification and taxonomic clarification. While successful in animals using the COI gene, establishing a standardized plant barcode has been challenging. The review outlines the process of selecting and refining plant barcodes, evaluates factors influencing their discriminatory power, and describes early applications and major projects. It also outlines the tools needed for plant DNA barcoding to advance.
The selection of a core barcode involves choosing standard loci that can be sequenced reliably. The COI gene is suitable for animals but not for plants due to low nucleotide substitution rates in plant mitochondrial genomes. Instead, researchers have looked outside mitochondrial genomes and found that multiple markers are often needed for adequate species discrimination. The rbcL+matK barcode was proposed as a core barcode due to its ease of amplification and discriminatory power. However, challenges remain, including the need for improved matK primers and the lower discrimination success of rbcL+matK in plants compared to COI in animals.
The review discusses the development of supplementary markers and the use of non-coding regions like trnH-psbA and nrITS for plant barcoding. It also highlights the challenges of using nrITS, including paralogy, polymorphic sites, and sequence quality issues. Alternative sources of markers, such as complete plastid genomes and low copy nuclear genes, are also discussed. The review emphasizes the need for continued research and development of tools to improve the efficiency and accuracy of plant DNA barcoding. The use of DNA barcoding in practical applications, such as species identification and ecological forensics, is also explored. The review concludes with the importance of developing robust reference libraries and supporting infrastructure for widespread use of plant DNA barcoding.This review discusses the selection and use of plant DNA barcodes. DNA barcoding aims to create a shared resource of DNA sequences for organism identification and taxonomic clarification. While successful in animals using the COI gene, establishing a standardized plant barcode has been challenging. The review outlines the process of selecting and refining plant barcodes, evaluates factors influencing their discriminatory power, and describes early applications and major projects. It also outlines the tools needed for plant DNA barcoding to advance.
The selection of a core barcode involves choosing standard loci that can be sequenced reliably. The COI gene is suitable for animals but not for plants due to low nucleotide substitution rates in plant mitochondrial genomes. Instead, researchers have looked outside mitochondrial genomes and found that multiple markers are often needed for adequate species discrimination. The rbcL+matK barcode was proposed as a core barcode due to its ease of amplification and discriminatory power. However, challenges remain, including the need for improved matK primers and the lower discrimination success of rbcL+matK in plants compared to COI in animals.
The review discusses the development of supplementary markers and the use of non-coding regions like trnH-psbA and nrITS for plant barcoding. It also highlights the challenges of using nrITS, including paralogy, polymorphic sites, and sequence quality issues. Alternative sources of markers, such as complete plastid genomes and low copy nuclear genes, are also discussed. The review emphasizes the need for continued research and development of tools to improve the efficiency and accuracy of plant DNA barcoding. The use of DNA barcoding in practical applications, such as species identification and ecological forensics, is also explored. The review concludes with the importance of developing robust reference libraries and supporting infrastructure for widespread use of plant DNA barcoding.