Identification of effective DNA barcodes for Triticum plants through chloroplast genome-wide analysis

The Egyptian flora is rich with a large number of Triticum plants, which are very difficult to discriminate between in the early developmental stages. This study assesses the significance of using two DNA Barcoding loci (matK and rbcL) in distinguishing between 18 different Triticum accessions in Egypt. We isolated and sequenced 15 rbcL and six matK fragments, but our analysis of the resultant sequences demonstrated a limited ability of matK and rbcL in distinguishing between Triticum accessions. Therefore, we pursued a bioinformatics approach to determine the most useful loci which may be used as DNA barcodes for the Triticum spp. We obtained the 10 available chloroplast genomes of the 10 Triticum species and sub-species from NCBI, and performed chloroplast genome-wide analysis to find the potential barcode loci. A total of 134 chloroplast genes, gene combinations, intergenic regions and intergenic region combinations were tested using a Tree-based method. We were unable to discriminate between Triticum species by using chloroplast genes, gene combinations and intergenic regions. However, a combination of the intergenic region (trnfM-trnT) with either (trnD-psbM), (petN-trnC), (matK-rps16) or (rbcL-psaI) demonstrated a very high discrimination capacity, suggesting their utilization as DNA barcodes for the Triticum plants. Furthermore, our novel DNA barcodes demonstrated high discrimination capacity for other Poaceae members.

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

[2]  C. van den Berg,et al.  DNA barcoding in Atlantic Forest plants: What is the best marker for Sapotaceae species identification? , 2014, Genetics and molecular biology.

[3]  V. Täckholm,et al.  Flora of Egypt. , 1954 .

[4]  R. Soreng,et al.  A laboratory guide for generating DNA barcodes in grasses: a case study of Leptochloa s.l. (Poaceae: Chloridoideae) , 2014 .

[5]  Sara El-Metwally,et al.  Next Generation Sequencing Technologies and Challenges in Sequence Assembly , 2014, SpringerBriefs in Systems Biology.

[6]  Wenpan Dong,et al.  Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding , 2012, PloS one.

[7]  Damon P. Little,et al.  Choosing and Using a Plant DNA Barcode , 2011, PloS one.

[8]  P. Hollingsworth.  Refining the DNA barcode for land plants , 2011, Proceedings of the National Academy of Sciences.

[9]  Jerrold I. Davis,et al.  Phylogeny of the Grasses (Poaceae) Revisited , 2007 .

[10]  Shiliang Zhou,et al.  ycf1, the most promising plastid DNA barcode of land plants , 2015, Scientific Reports.

[11]  Richard Cronn,et al.  Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes , 2009, BMC Biology.

[12]  E. Kellogg.  BEYOND TAXONOMY: PROSPECTS FOR UNDERSTANDING MORPHOLOGICAL DIVERSITY IN THE GRASSES (POACEAE) , 2006 .

[13]  Bin Wang,et al.  The complete chloroplast genome sequence of Alocasia macrorrhizos , 2016, Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis.

[14]  J. Vogel,et al.  Use of rbcL and trnL-F as a Two-Locus DNA Barcode for Identification of NW-European Ferns: An Ecological Perspective , 2011, PloS one.

[15]  Shilin Chen,et al.  Plant DNA barcoding: from gene to genome , 2015, Biological reviews of the Cambridge Philosophical Society.

[16]  H. Khan,et al.  Comparative Evaluation of PCR Success with Universal Primers of Maturase K (matK) and Ribulose-1, 5-Bisphosphate Carboxylase Oxygenase Large Subunit (rbcL) for Barcoding of Some Arid Plants , 2011 .

[17]  L. Consaul,et al.  DNA Barcoding the Canadian Arctic Flora: Core Plastid Barcodes (rbcL + matK) for 490 Vascular Plant Species , 2013, PloS one.

[18]  R. Poudel,et al.  High universality of matK primers for barcoding gymnosperms , 2011 .

[19]  P. Catalán,et al.  A DNA Barcoding Method to Discriminate between the Model Plant Brachypodium distachyon and Its Close Relatives B. stacei and B. hybridum (Poaceae) , 2012, PloS one.

[20]  Sara El-Metwally,et al.  New Horizons in Next-Generation Sequencing , 2014 .

[21]  Pang-Chui Shaw,et al.  Identification of herbal medicinal materials using DNA barcodes , 2011 .

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

[23]  Molecular Identification of Pooideae, Poaceae in Korea , 2015 .

[24]  M. Ashfaq,et al.  Evaluating the capacity of plant DNA barcodes to discriminate species of cotton (Gossypium: Malvaceae) , 2013, Molecular ecology resources.

[25]  Sylvie Duthoit,et al.  DNA barcoding the floras of biodiversity hotspots , 2008, Proceedings of the National Academy of Sciences.

[26]  David L. Erickson,et al.  DNA barcodes for ecology, evolution, and conservation. , 2015, Trends in ecology & evolution.

[27]  D. Little,et al.  DNA barcoding: a new tool for palm taxonomists? , 2011, Annals of botany.

[28]  Osama Ouda,et al.  FN-Identify: Novel Restriction Enzymes-Based Method for Bacterial Identification in Absence of Genome Sequencing , 2015, Adv. Bioinformatics.

[29]  S. Arabia,et al.  SELECTION OF CHLOROPLAST DNA MARKERS FOR THE DEVELOPMENT OF DNA BARCODE AND RECONSTRUCTION OF PHYLOGENY OF SENECIO ASIRENSIS BOULOS AND J.R.I. WOOD , 2013 .

[30]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[31]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[32]  J. Shaw,et al.  The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. , 2005, American journal of botany.

[33]  Arun Kumar Pandey,et al.  The changing epitome of species identification - DNA barcoding. , 2014, Saudi journal of biological sciences.

[34]  Prospects of barcoding the Italian wild dendroflora: oaks reveal severe limitations to tracking species identity , 2011, Molecular ecology resources.

[35]  Shiliang Zhou,et al.  New universal matK primers for DNA barcoding angiosperms , 2011 .

[36]  Kareem A. Mosa,et al.  Limited resources of genome sequencing in developing countries: Challenges and solutions , 2016, Applied & translational genomics.

[37]  M. Simmons,et al.  Application of DNA barcodes in Hedyotis L. (Spermacoceae, Rubiaceae) , 2011 .

[38]  S. Ramalingam,et al.  DNA barcoding: a genomic-based tool for authentication of phytomedicinals and its products , 2015 .

[39]  Amanda Ciprandi Pires,et al.  DNA barcoding and traditional taxonomy unified through Integrative Taxonomy: a view that challenges the debate questioning both methodologies , 2010 .

[40]  I. Kirsch.  Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Preface. , 2011, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[41]  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.

[42]  C. Millar,et al.  Genetic diversity within species , 1996 .

[43]  A. Galimberti,et al.  Integrated taxonomy: traditional approach and DNA barcoding for the identification of filarioid worms and related parasites (Nematoda) , 2009, Frontiers in Zoology.

[44]  B. Barrett,et al.  DNA fingerprinting and genetic relationships among white clover cultivars , 2022 .

[45]  M. Govindaraj,et al.  Importance of Genetic Diversity Assessment in Crop Plants and Its Recent Advances: An Overview of Its Analytical Perspectives , 2015, Genetics research international.

[46]  Douglas W. Yu,et al.  Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. , 2013, Ecology letters.

[47]  B. Allen,et al.  Survey and DNA Barcoding of Poaceae in Flat Rock Cedar Glades and Barrens State Natural Area, Murfreesboro, Tennessee , 2011 .

[48]  J. Felsenstein,et al.  A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. , 1994, Molecular biology and evolution.

[49]  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.

[50]  W. John Kress,et al.  A DNA barcode for land plants , 2009, Proceedings of the National Academy of Sciences.

[51]  S. Graham,et al.  Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well , 2008, PloS one.

[52]  Q. Cronk,et al.  Botany without borders: barcoding in focus , 2008, Molecular ecology.

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

[54]  Pradhyumna K. Singh,et al.  Universal Plant DNA Barcode Loci May Not Work in Complex Groups: A Case Study with Indian Berberis Species , 2010, PloS one.

[55]  J. Dopazo,et al.  A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus , 2015, Molecular biology and evolution.

[56]  T. Borsch,et al.  Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA , 2009, Plant Systematics and Evolution.

[57]  T. Hodkinson,et al.  New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins. , 2012, The New phytologist.

[58]  M. Chase,et al.  Selection of candidate coding DNA barcoding regions for use on land plants , 2009 .

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

[60]  Lianming Gao,et al.  Testing four candidate barcoding markers in temperate woody bamboos (Poaceae: Bambusoideae) , 2012 .

[61]  A. Schüßler,et al.  DNA barcoding of arbuscular mycorrhizal fungi. , 2010, The New phytologist.

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

[63]  Jeffrey P. Mower,et al.  Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[64]  K. Chen,et al.  Evaluation of candidate barcoding markers in Orinus (Poaceae). , 2016, Genetics and molecular research : GMR.

[65]  Rajeev Kumar Sarma,et al.  Phylogenetic analysis of chloroplast matK gene from Zingiberaceae for plant DNA barcoding , 2008, Bioinformation.

[66]  C. M. Culumber.  DNA barcoding of western North American taxa: Leymus (Poaceae) and Lepidium (Brassicaceae) , 2007 .

[67]  M. Rosenberg,et al.  Multiple sequence alignment accuracy and phylogenetic inference. , 2006, Systematic biology.

[68]  Joey Shaw,et al.  Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. , 2007, American journal of botany.

[69]  W. Zhang,et al.  Phylogeny of the grass family (Poaceae) from rpl16 intron sequence data. , 2000, Molecular phylogenetics and evolution.

[70]  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.

[71]  M. Stoeckle.  Taxonomy, DNA, and the Bar Code of Life , 2003 .

[72]  Q. Cronk,et al.  Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA. , 2012, American journal of botany.