DNA Barcoding in Plants & Its Potential Applications

Today, barcodes conceived by Bernard Silver, a graduate student at Drexel Institute of Technology in Philadelphia, PA, and his friends Norman Woodland and Jordin Johanson in 1948 are used universally. They play a critical role for identification purposes, relational information, and tracking  Botany at Dairy Farm. They are especially useful because scanners are relatively inexpensive, extremely accurate and highly efficient at obtaining and transmitting information from barcodes and their databases.

Natural barcodes (a short strand of deoxyribonucleic acid (DNA) (the genetic code unique to each living organism and some viruses) that consists of between 300-800 base pairs (bps) – Adenine (A)-Thymidine (T), and Cytosine (C)-Guanine (G)) that can be represented by different colors) also exist and are well established in the animal kingdom. Through sequencing of the cytochrome oxidase 1 (CO1) gene (inspired by biologist Paul Hebert’s futile efforts dating back to the 1970s to identify 2000 species of moth in Papua New Guinea (because of their taxonomic and morphological similarities), his “retreat to water fleas” (of which there are only 200 species) and subsequent 2003 paper in which he described “the diversity of life as a ‘harsh burden’ to biologists” and suggested, “every species on earth… be assigned a simple DNA bar code so it would be easy to tell them apart” as written in Scanning Life (National Geographic, May 2010)), which is present in the mitochondrial DNA of every multi-cellular organism, scientists are able to readily determine phylogeny (identification) on a molecular level and store it in databases for easy retrieval. Per P. M. Hollingsworth, DNA bar-coding plants in biodiversity hot spots: Progress and outstanding questions (Heredity, 9 April 2008) “DNA bar-coding is now routinely used for organismal identification” in animals and “has contributed to the discovery of new species. ”

However, per Mark W. Chase, Nicolas Salamin, Mike Wilkinson, James M. Dunwell, Rao Prasad Kesanakurthi, Nadia Haidar, and Vincent Savolainen, Land plants and DNA barcodes: short-term and long-term goals (Philosophical Transactions Of the Royal Society, 2005) this has not been the case with plants until recently since their CO1 gene does not have the ability to serve as a barcode gene and because they “have had the reputation of being problematic for DNA bar-coding” due to “low levels of variability” and lack of variation in “plastid phylogenetic markers. ” This view prevailed until 2008 when a team led by Dr. Vincent Savolainen of Imperial College London’s Department of Life Sciences and the Royal Botanic Gardens, Kew, studied the functionality of the megakaryocyte-associated tyrosine-protein kinase (matK) gene located in the intron of trnK chloroplast genes found in plant leaves. Their research found that the matK gene (which “contained significant species-level genetic variability and divergence, conserved flanking sites for developing PCR (polymerase chain reaction, a process that enables scientists to produce millions of copies of a specific DNA sequence in about two hours while bypassing the need to use bacteria to amplify DNA) primers for wide taxonomic application, [and] a short sequence length… to facilitate… DNA extraction and amplification”) as reported by W. John Kress and David L. Erickson, DNA barcodes: Genes, genomics, and bioinformatics (PNAS. Vol. 105, No. 8. 26 February 2008) and in Polymerase Chain Reaction (PCR) (Gene Almanac. Dolan DNA Learning Center and Cold Spring Harbor Laboratory, Inc. 2009) could be used to differentiate between at least 90% of all plants, including those that appeared identical to the human eye, known as cryptic species because of their identical appearance and genetic differences.

The matK gene, though, was found ineffective in distinguishing between up to 10% of plant species because of two major factors:

1. When variation resulting from “rapid bursts of speciation” was small, and
2. Based on Anna-Marie Lever’s article, DNA ‘barcode’ revealed in plants (BBC News, 6 February 2008), when plants were hybrids whose genome was rearranged through natural and artificial cross-breeding, which “confuse[d] matK gene information”

When discovery that the matK gene could serve as a natural barcode in plants was made, its location was consistent with that in animals – the barcode genes in both are located in cellular energy centers outside the nucleus (mitochondria serve as “tiny powerhouses” in animal cells while chloroplasts are involved in plant photosynthesis) since per Anna-Marie Lever, DNA ‘barcode’ revealed in plants, “nuclear genes usually evolve too rapidly to distinguish between [organisms] of the same species. ” However, consistent with mitochronidrial genes in animals, “chloroplast genes [in plants] evolve at a slower rate, allowing for [distinguishment between the same species, and] fast enough for differences to occur in the DNA code between species. ”

The only exception between plants and animals is the range of effectiveness for their respective barcode genes. The CO1 gene can be effectively used to determine and record phylogeny in nearly 100% of animal species while the matK gene is ineffective in about 10% of plant species. The key reason for the 90% effective range with regard to the matK gene can be attributed to natural crossbreeding, which is significantly more common to plants than animals. Because of this, matK gene information needs to be supplemented by data from another gene. Although studies utilizing trnH-psbA genes that share similar characteristics to matK showed promise (when sequencing of matK and trnH-psbA was utilized involving plants of the nutmeg family (Myristicaceae) the effective range for correct identification rose to approximately 95%), a panel of 52 leading barcoding scientists opted on using the ribulose-bisphosphate carboxylase (rbcL) gene (also located in plant chloroplasts) outlined in a 2009 paper published in Proceedings of the National Academy of Sciences as reported by Daniel Cressey, DNA barcodes for plants a step closer (Nature, 27 July 2009), to effectively complete the barcode for the 10% group.

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