A botanical renaissance: state-of-the-art DNA bar coding facilitates an Automated Identification Technology system for plants

Traditional taxonomic practices are insufficient on their own to cope with the growing need for accurate identifications. The recent development of DNA barcoding has been applied to plants. The next step is the development of a high-throughput Automated Identification Technology (AIT) system. Our research indicates that the efficacy of an AIT system equates with savings in time and funding. Given the potential interconnectivity of web-based applications, we suggest an AIT system for plants that uses several existing systems and suggest several applications where AIT could serve as a tool for biologists and for society at large.

[1]  M. Blaxter,et al.  Molecular taxonomics for biodiversity surveys: already a reality , 2003 .

[2]  H. Godfray.  Challenges for taxonomy , 2002, Nature.

[3]  Mark Blaxter,et al.  Molecular barcodes for soil nematode identification , 2002, Molecular ecology.

[4]  D. Stevenson,et al.  A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms , 2007, Cladistics : the international journal of the Willi Hennig Society.

[5]  M. O'Neill,et al.  Automated species identification: why not? , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[6]  P. Pheloung,et al.  A weed risk assessment model for use as a biosecurity tool evaluating plant introductions , 1999 .

[7]  G. Ramsay,et al.  PCR analysis of oilseed rape cultivars (Brassica napus L. ssp. oleifera) using 5′ -anchored simple sequence repeat (SSR) primers , 1996, Theoretical and Applied Genetics.

[8]  D. Janzen,et al.  Use of DNA barcodes to identify flowering plants. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Mehrdad Hajibabaei,et al.  A minimalist barcode can identify a specimen whose DNA is degraded , 2006 .

[10]  J. Nagaraju,et al.  DNA profiling of disputed chilli samples (Capsicum annum) using ISSR-PCR and FISSR-PCR marker assays. , 2001, Forensic science international.

[11]  David L. Erickson,et al.  A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region , 2007, PloS one.

[12]  H. C. J. Godfray.  Towards taxonomy's 'glorious revolution' , 2002, Nature.

[13]  A. Fazekas,et al.  Testing candidate plant barcode regions in the Myristicaceae , 2008, Molecular ecology resources.

[14]  A. Fazekas,et al.  DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach , 2006 .

[15]  Sujeevan Ratnasingham,et al.  Critical factors for assembling a high volume of DNA barcodes , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[16]  W. John Kress,et al.  300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants , 2006 .

[17]  Tobias Meckel,et al.  Live cell imaging of repetitive DNA sequences via GFP-tagged polydactyl zinc finger proteins , 2007, Nucleic acids research.

[18]  John A. Darling,et al.  DNA-based methods for monitoring invasive species: a review and prospectus , 2007, Biological Invasions.

[19]  D. L. Nanney,et al.  Genes and Phenes in Tetrahymena , 1982 .

[20]  K. Will,et al.  Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification , 2004, Cladistics : the international journal of the Willi Hennig Society.

[21]  Paul D N Hebert,et al.  DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[22]  C. W. Fetrow,et al.  Adulteration of dietary supplements. , 2003, American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists.

[23]  P. Hebert,et al.  DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. , 2007, Trends in genetics : TIG.

[24]  T. Deák.  Molecular taxonomy of yeasts. , 1999, Acta microbiologica et immunologica Hungarica.

[25]  P. Hebert,et al.  The promise of DNA barcoding for taxonomy. , 2005, Systematic biology.

[26]  Paul H. Williams,et al.  Promise and problems in applying quantitative complementary areas for representing the diversity of some Neotropical plants (families Dichapetalaceae, Lecythidaceae, Caryocaraceae, Chrysobalanaceae and Proteaceae) , 1996 .

[27]  G. Presting.  Identification of conserved regions in the plastid genome: implications for DNA barcoding and biological function , 2006 .

[28]  Lee,et al.  A worrying systematic decline. , 2000, Trends in ecology & evolution.

[29]  D. Janzen.  Setting up tropical biodiversity for conservation through non-damaging use: participation by parataxonomists , 2004 .

[30]  R. Hill,et al.  Taxonomic and systematic assessment of planktonic copepods using mitochondrial COI sequence variation and competitive, species-specific PCR , 1999, Hydrobiologia.

[31]  J. Bennetzen,et al.  Assessment of genetic diversity in dent and popcorn (Zea mays L.) inbred lines using inter-simple sequence repeat (ISSR) amplification , 1995, Molecular Breeding.

[32]  G. Lloyd-Jones,et al.  A molecular view of microbial diversity in a dynamic landfill in Québec. , 1998, FEMS microbiology letters.

[33]  A. Paterson,et al.  Mitochondrial COI and II provide useful markers for Wiseana (Lepidoptera: Hepialidae) species identification , 1999, Bulletin of Entomological Research.

[34]  M. Tobler,et al.  Implications of collection patterns of botanical specimens on their usefulness for conservation planning: an example of two neotropical plant families (Moraceae and Myristicaceae) in Peru , 2007, Biodiversity and Conservation.

[35]  H. Godfray,et al.  Introduction. Taxonomy for the twenty-first century. , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[36]  Nicolas Salamin,et al.  Land plants and DNA barcodes: short-term and long-term goals , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[37]  D. Janzen,et al.  Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[38]  D. Janzen,et al.  Now is the time. , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[39]  D. Tautz,et al.  A plea for DNA taxonomy , 2003 .

[40]  W. Kress,et al.  Amazonian biodiversity: assessing conservation priorities with taxonomic data , 1998, Biodiversity & Conservation.

[41]  David L. Erickson,et al.  DNA barcodes: Genes, genomics, and bioinformatics , 2008, Proceedings of the National Academy of Sciences.

[42]  N. Platnick,et al.  The intellectual content of taxonomy: a comment on DNA taxonomy , 2003 .

[43]  Thierry Vermat,et al.  Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding , 2006, Nucleic acids research.

[44]  Elizabeth Pennisi,et al.  Wanted: A Barcode for Plants , 2007, Science.

[45]  F. Muehlbauer,et al.  Inter-simple-sequence-repeat (ISSR) polymorphisms are useful for finding markers associated with disease resistance gene clusters , 1998, Theoretical and Applied Genetics.

[46]  Mark W. Chase,et al.  A proposal for a standardised protocol to barcode all land plants , 2007 .

[47]  Alessandro Minelli,et al.  DNA points the way ahead in taxonomy , 2002, Nature.

[48]  C. Kurtzman.  Molecular taxonomy of the yeasts , 1994, Yeast.

[49]  S. Trewick.  Mitochondrial DNA sequences support allozyme evidence for cryptic radiation of New Zealand Peripatoides (Onychophora) , 2000, Molecular ecology.

[50]  P. Raven,et al.  Taxonomy: Impediment or Expedient? , 2004, Science.

[51]  O. Hatzofe,et al.  The use of (GACA)4 PCR to sex Old World vultures (Aves: Accipitridae) , 1998 .

[52]  Jeremy R. deWaard,et al.  Biological identifications through DNA barcodes , 2003, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[53]  J. Vian,et al.  Partial sequencing of the cytochrome oxydase b subunit gene I: a tool for the identification of European species of blow flies for postmortem interval estimation. , 2000, Journal of forensic sciences.

[54]  N. Ivanova,et al.  Semi-automated, Membrane-Based Protocol for DNA Isolation from Plants , 2008, Plant Molecular Biology Reporter.

[55]  N. E. Stork,et al.  How many species are there? , 1993, Biodiversity & Conservation.

[56]  L. E. Morse,et al.  An Invasive Species Assessment Protocol: Evaluating Non-Native Plants for Their Impact on Biodiversity, Version 1 , 2004 .

[57]  N. Pace.  A molecular view of microbial diversity and the biosphere. , 1997, Science.

[58]  S. Emerson,et al.  A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[59]  W. Miller,et al.  Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis , 2006, Nucleic acids research.

[60]  Mehrdad Hajibabaei,et al.  Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring , 2007, BMC Biology.

[61]  M. Blaxter.  The promise of a DNA taxonomy. , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[62]  B. Groombridge.  Global biodiversity: status of the earth's living resources. , 1992 .

[63]  M. Branchard,et al.  Plant genomic instability detected by microsatellite-primers , 2000 .

[64]  James Mallet,et al.  Taxonomy: renaissance or Tower of Babel? , 2003 .

[65]  B. Nelson,et al.  Endemism centres, refugia and botanical collection density in Brazilian Amazonia , 1990, Nature.

[66]  S Hamels,et al.  Consensus PCR and microarray for diagnosis of the genus Staphylococcus, species, and methicillin resistance. , 2001, BioTechniques.

[67]  P. Hebert,et al.  bold: The Barcode of Life Data System (http://www.barcodinglife.org) , 2007, Molecular ecology notes.

[68]  E. Schuettpelz,et al.  Identifying fern gametophytes using DNA sequences , 2006 .

[69]  Robert M. May,et al.  How Many Species Are There on Earth? , 1988, Science.

[70]  David E. Richardson,et al.  High-throughput Species Identification: from Dna Isolation to Bioinformatics , 2006 .

[71]  J. Denslow,et al.  A Risk‐Assessment System for Screening Out Invasive Pest Plants from Hawaii and Other Pacific Islands , 2004 .

[72]  K. Wilson.  Molecular biology as a tool for taxonomy. , 1995, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.