| Today, barcodes conceived by Bernard Silver, a | | | | greatest loss of plylogentically useful data) to capture |
| graduate student at Drexel Institute of Technology in | | | | their evolutionary links. The other, reported by Hiroaki |
| Philadelphia, PA, and his friends Norman Woodland and | | | | Setoguchi, Takeshi Asakawa Osawa, Jean-Christophe |
| Jordin Johanson in 1948 are used universally. They | | | | Pintaud, Tanguy Jaffré, and Jean-Marie Veillon in |
| play a critical role for identification purposes, relational | | | | Phylogenetic relationships within Araucariaceae based |
| information, and tracking. They are especially useful | | | | on rbcL gene sequences (American Journal of |
| because scanners are relatively inexpensive, | | | | Botany, 1998) utilized rbcL gene sequencing to |
| extremely accurate and highly efficient at obtaining | | | | successfully determine the pylogenetic relationship |
| and transmitting information from barcodes and their | | | | between 29 species of Araucariaceae (a sample |
| databases. | | | | representing nearly every existing species of the |
| Natural barcodes (a short strand of deoxyribonucleic | | | | ancient family of conifers that achieved maximum |
| acid (DNA) (the genetic code unique to each living | | | | diversification during the Jurassic (c. 199.6± 0.6 to |
| organism and some viruses) that consists of | | | | 145.5± 4 million years ago (Ma) and Cretaceous |
| between 300-800 base pairs (bps) - Adenine | | | | periods (c. 145.5 ± 4 to 65.5 ± 0.3 Ma)). |
| (A)-Thymidine (T), and Cytosine (C)-Guanine (G)) | | | | During the study that led to the discovery that a |
| that can be represented by different colors) also | | | | plant's matK gene could serve as a primary barcode |
| exist and are well established in the animal kingdom. | | | | gene, Dr. Savolainen's team compared eight potential |
| Through sequencing of the cytochrome oxidase 1 | | | | candidate genes and analyzed more than 1600 plant |
| (CO1) gene (inspired by biologist Paul Hebert's futile | | | | DNA samples obtained from the tropical forests of |
| efforts dating back to the 1970s to identify 2000 | | | | Costa Rica and the temperate region of Kruger |
| species of moth in Papua New Guinea (because of | | | | National Park, South Africa, two of the world's leading |
| their taxonomic and morphological similarities), his | | | | biodiversity hotspots. |
| "retreat to water fleas" (of which there are only 200 | | | | Through sequencing of the matK gene (which has a |
| species) and subsequent 2003 paper in which he | | | | slightly different code for plants of different species |
| described "the diversity of life as a 'harsh burden' to | | | | and a near identical code for plants of the same |
| biologists" and suggested, "every species on Earth... | | | | species), they were able to distinguish between a |
| be assigned a simple DNA bar code so it would be | | | | thousand orchid species - plants known for their |
| easy to tell them apart" as written in Scanning Life | | | | difficulty to differentiate because of their near |
| (National Geographic, May 2010)), which is present in | | | | identical appearance, especially when sterile. |
| the mitochondrial DNA of every multi-cellular | | | | Consequently, per Plant DNA 'Barcode' identified |
| organism, scientists are able to readily determine | | | | (Medical News Today, 6 February 2008), "...what was |
| phylogeny (identification) on a molecular level and | | | | previously assumed to be one species of orchid was |
| store it in databases for easy retrieval. Per P.M. | | | | [found to be] two distinct species that live on |
| Hollingsworth, DNA bar-coding plants in biodiversity | | | | different slopes of the mountains [with] differently |
| hot spots: Progress and outstanding questions | | | | shaped flowers adapted for different pollinating |
| (Heredity, 9 April 2008) "DNA bar-coding is now | | | | insects." |
| routinely used for organismal identification" in animals | | | | Scientific analysis, in which the matK gene was |
| and "has contributed to the discovery of new | | | | divided into five sectors has determined that the |
| species." | | | | sector 3 (known as 3') region is the most effective |
| However, per Mark W. Chase, Nicolas Salamin, Mike | | | | area in providing useful phylogenetic information. |
| Wilkinson, James M. Dunwell, Rao Prasad | | | | When broken down further, 140 out of the 306 bps |
| Kesanakurthi, Nadia Haidar, and Vincent Savolainen, | | | | of the 3' region were phylogenetically informative. |
| Land plants and DNA barcodes: short-term and | | | | Establishment of the matK gene's barcode function |
| long-term goals (Philosophical Transactions Of The | | | | supplemented by use of the rbcL gene, represents a |
| Royal Society, 2005) this has not been the case with | | | | major breakthrough in plant science since it offers a |
| plants until recently since their CO1 gene does not | | | | diverse range of potential applications that can be |
| have the ability to serve as a barcode gene and | | | | used by scientists and plant taxonomists |
| because they "have had the reputation of being | | | | systematists as well as an opportunity to close the |
| problematic for DNA bar-coding" due to "low levels of | | | | large gap that presently exists between plant and |
| variability" and lack of variation in "plastid phylogenetic | | | | animal barcoding. |
| markers." This view prevailed until 2008 when a team | | | | Such potential applications include but are not limited |
| led by Dr. Vincent Savolainen of Imperial College | | | | to: |
| London's Department of Life Sciences and The Royal | | | | 1. Accurate identification of plant species, especially |
| Botanic Gardens, Kew, studied the functionality of | | | | those of cryptic species that are difficult to |
| the megakaryocyte-associated tyrosine-protein | | | | differentiate that could potentially lead to discovery |
| kinase (matK) gene located in the intron of trnK | | | | of new species. Presently as stated by Anna-Marie |
| chloroplast genes found in plant leaves. Their research | | | | Lever, DNA 'barcode' revealed in plants only a "few |
| found that the matK gene (which "contained | | | | experts [can] accurately identify the plant |
| significant species-level genetic variability and | | | | composition of biodiverse hotspots." |
| divergence, conserved flanking sites for developing | | | | 2. Accurate identification of botanic components in |
| PCR (polymerase chain reaction, a process that | | | | foods and medicines. |
| enables scientists to produce millions of copies of a | | | | 3. Detection of undesirable plant material in processed |
| specific DNA sequence in about two hours while | | | | foods by health inspectors. |
| bypassing the need to use bacteria to amplify DNA) | | | | 4. Tracking of plant species (e.g. migration). |
| primers for wide taxonomic application, [and] a short | | | | 5. Locating of endangered species for habitat |
| sequence length... to facilitate... DNA extraction and | | | | preservation. |
| amplification") as reported by W. John Kress and | | | | 6. Detection of illegal transport/trade of endangered |
| David L. Erickson, DNA barcodes: Genes, genomics, | | | | species to protect them from potential harm. |
| and bioinformatics (PNAS. Vol. 105, No. 8. 26 February | | | | 7. Confirmation or identification of plant-insect |
| 2008) and in Polymerase Chain Reaction (PCR) (Gene | | | | associations. |
| Almanac. Dolan DNA Learning Center and Cold Spring | | | | 8. Expansion and facilitation of botanical medical |
| Harbor Laboratory, Inc. 2009) could be used to | | | | research. |
| differentiate between at least 90% of all plants, | | | | However, before this can be achieved, the following |
| including those that appeared identical to the human | | | | steps must be taken: |
| eye, known as cryptic species because of their | | | | 1. Establishment of a genetic database that can be |
| identical appearance and genetic differences. | | | | uploaded into a portable scanner so that data can be |
| The matK gene, though, was found ineffective in | | | | readily available based on the analysis of a mere leaf |
| distinguishing between up to 10% of plant species | | | | tissue sample. To enhance identification of known |
| because of two major factors: | | | | species and speed up discovery of new species, such |
| 1. When variation resulting from "rapid bursts of | | | | a database must be massive and available online. |
| speciation" was small, and | | | | 2. Establishment of a search method or algorithm to |
| 2. Based on Anna-Marie Lever's article, DNA 'barcode' | | | | search and access DNA barcode information from an |
| revealed in plants (BBC News, 6 February 2008), | | | | online database. |
| when plants were hybrids whose genome was | | | | 3. Establishment of a set of reference standards |
| rearranged through natural and artificial | | | | (which includes barcoding based solely on bp |
| cross-breeding, which "confuse[d] matK gene | | | | extractions from matK and rbcL genes) utilizing |
| information" | | | | existing plant DNA specimens held at botanical |
| When discovery that the matK gene could serve as | | | | gardens, herbariums, museums and other DNA |
| a natural barcode in plants was made, its location was | | | | repositories. For example, the Consortium for the |
| consistent with that in animals - the barcode genes in | | | | Barcode of Life based at the Smithsonian Institution's |
| both are located in cellular energy centers outside the | | | | National Museum of Natural History in Washington, |
| nucleus (mitochondria serve as "tiny powerhouses" in | | | | D.C. has identified over two million of the estimated |
| animal cells while chloroplasts are involved in plant | | | | ten million species of plants, animals, and fungi (many |
| photosynthesis) since per Anna-Marie Lever, DNA | | | | still unnamed) while the Royal Botanic Gardens, Kew |
| 'barcode' revealed in plants, "nuclear genes usually | | | | currently holds 23,000+ plant DNA samples. This is |
| evolve too rapidly to distinguish between [organisms] | | | | especially important since fresh collection efforts |
| of the same species." However, consistent with | | | | aimed at obtaining the DNA of every plant species, |
| mitochronidrial genes in animals, "chloroplast genes [in | | | | are impractical since they would require significant |
| plants] evolve at a slower rate, allowing for | | | | effort and time. |
| [distinguishment between the same species, and] fast | | | | 4. Collection efforts conducted in accordance with |
| enough for differences to occur in the DNA code | | | | international laws (e.g. Convention of Biological |
| between species." | | | | Diversity) to protect habitats and ensure specimen |
| The only exception between plants and animals is the | | | | integrity. Per W. John Kress and David L. Erickson, |
| range of effectiveness for their respective barcode | | | | DNA barcodes: Genes, genomics, and bioinformatics, |
| genes. The CO1 gene can be effectively used to | | | | such collection efforts are necessary since existing |
| determine and record phylogeny in nearly 100% of | | | | specimens are limited in quantity and may consist of |
| animal species while the matK gene is ineffective in | | | | degraded DNA. Currently collection efforts are being |
| about 10% of plant species. The key reason for the | | | | made in temperate (Plummers Island, MD and New |
| 90% effective range with regard to the matK gene | | | | York City, among others) and tropical (Forest |
| can be attributed to natural crossbreeding, which is | | | | Dynamics Plot, Panama, among others) regions. |
| significantly more common to plants than animals. | | | | With a stamp of approval from the United Nations |
| Because of this, matK gene information needs to be | | | | that declared 2010 "the International Year of |
| supplemented by data from another gene. Although | | | | Biodiversity," vigorous global efforts aimed at |
| studies utilizing trnH-psbA genes that share similar | | | | barcoding 500,000 out of the 1.7 million named |
| characteristics to matK showed promise (when | | | | species of plants, animals, and fungi by 2015, are |
| sequencing of matK and trnH-psbA was utilized | | | | being pursued by international teams of scientists as |
| involving plants of the nutmeg family (Myristicaceae) | | | | well as by groups/projects such as the Consortium |
| the effective range for correct identification rose to | | | | for the Barcode of Life and soon, the International |
| approximately 95%), a panel of 52 leading barcoding | | | | Barcode of Life (iBol) project, which is slated to |
| scientists opted on using the ribulose-bisphosphate | | | | launch in July 2010. Furthermore, Paul Hebert, the |
| carboxylase (rbcL) gene (also located in plant | | | | biologist who inspired the barcode movement and a |
| chloroplasts) outlined in a 2009 paper published in | | | | major participant in the iBol project, per Scanning Life |
| Proceedings of the National Academy of Sciences as | | | | (National Geographic, May 2010) declared, "the |
| reported by Daniel Cressey, DNA barcodes for plants | | | | approach is scalable to the planet [so that by 2025 |
| a step closer (Nature, 27 July 2009), to effectively | | | | every] species humans encounter frequently will |
| complete the barcode for the 10% group. | | | | [have been] barcoded." |
| While discovery of the phylogenetic usefulness of | | | | With regard to plants, as technology is enhanced to |
| the matK gene is relatively novel, studies indicating | | | | exploit the genetic code of matK and rbcL genes |
| the phylogenetic usefulness of the rbcL gene date | | | | through the establishment of a uniform database, |
| back as far as 1986 when Jane Aldrich, Barry | | | | production of inexpensive portable scanners capable |
| Cherney, Ellis Merlin and Jeff Palmer reported in | | | | of analyzing leaf/tissue samples and matching the |
| Nucleic Acids Research that sequencing of rbcL genes | | | | DNA barcode with database information, the field of |
| showed petunia and tobacco and alfalfa and peas are | | | | botanical phylogenetics and research will benefit |
| 97.3% and 94.1% genetically identical when comparing | | | | greatly especially since plant identification and |
| their bps. | | | | classification will be available to more than a few |
| Additional studies, to name two, added further | | | | experts. In addition, such identification and |
| evidence of the phylogenetic usefulness of the rbcL | | | | classification will be more accurate than that provided |
| gene. One, reported by Mitsuyasu Hasebe, | | | | by sole reliance on visual examination and physical |
| Tomokyuki Omori, Miyuki Nakazawa, Toshio Sano, | | | | morphology (especially with regard to cryptic species) |
| Masahiro Kato, and Kunio Iwatsuki in rbcL Gene | | | | while endangered species will be able to be easily |
| sequences provide evidence for the evolutionary | | | | tracked and better protected, and people will have |
| lineages of leptosporangiate ferns (Proceedings of | | | | greater assurance pertaining to the food, drinks, and |
| the National Academy of Sciences, June 1994) utilized | | | | or medicine they consume. |
| PCR-amplified rbcL fragments in 58 species of | | | | Additional References: |
| leptosporangiate ferns, which belong to the | | | | José A. Jurado-Rivera, Alfried P. Vogler, Chris A.M. |
| pteridophyte class (vascular plants that produce | | | | Reid, Eduard Petitpierre, and Jesús Gómez-Zurita. |
| spores to reproduce in lieu of flowers and seeds) | | | | DNA barcoding insect-host plant associations. The |
| which has the longest evolutionary history of any | | | | Royal Society. 17 October 2008. |
| vascular land plant (consequently enduring the | | | | |