Species identification of Alnus (Betulaceae) using nrDNA and cpDNA genetic markers

Molecular Ecology Resources

Volumn 10, Issue 4, 2010, Pages 594-605

  Ren, Bao Qing ^a,b   Xiang, Xiao Guo ^a,b   Chen, Zhi Duan ^a  

^a INSTITUTE OF BOTANY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Alnus; DNA barcoding; ITS; Molecular identification; Morphological taxonomy; TrnH psbA

Indexed keywords

ALNUS; ALNUS FORMOSANA; ALNUS JAPONICA; ALNUS MARITIMA; BETULACEAE;

EID: 77954694153     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2009.02815.x     Document Type: Article

References (50)

1. Alvarez I, Wendel JF. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 2003, 29:417-434.
2. Benson DR, Silvester WB. Biology of Frankia strains, actinomycete symbionts of actinorhizal plants. Microbiological Reviews 1993, 57:293-319.
3. Bousquet J, Simon L, Lalonde M. DNA amplification from vegetative and sexual tissues of trees using polymerase chain-reaction. Canadian Journal of Forest Research-Revue Canadienne De Recherche Forestiere 1990, 20:254-257.
4. Bousquet J, Strauss SH, Li P. Complete congruence between morphological and rbcL-based molecular phylogenies in birches and related species (Betulaceae). Molecular Biology and Evolution 1992, 9:1076-1088.
5. Chase MW, Salamin N, Wilkinson M. Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 2005, 360:1889-1895.
6. Chase MW, Cowan RS, Hollingsworth PM. A proposal for a standardised protocol to barcode all land plants. Taxon 2007, 56:295-299.
7. Chen ZD. Phylogeny and phytogeography of Betulaceae. Acta Phytotaxonomic Sinica 1994, 32:101-153.
8. Chen ZD, Li JH. Phylogenetics and biogeography of Alnus (Betulaceae) inferred from sequences of nuclear ribosomal DNA its region. International Journal of Plant Sciences 2004, 165:325-335.
9. Chen ZD, Manchester SR, Sun HY. Phylogeny and evolution of the Betulaceae as inferred from DNA sequences, morphology, and paleobotany. American Journal of Botany 1999, 86:1168-1181.
10. Cowan RS, Chase MW, Kress WJ, Savolainen V. 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon 2006, 55:611-616.
11. DeSalle R. Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff. Conservation Biology 2006, 20:1545-1547.
12. Devey DS, Chase MW, Clarkson JJ. A stuttering start to plant DNA barcoding: microsatellites present a previously overlooked problem in non-coding plastid regions. Taxon 2009, 58:7-15.
13. Edwards D, Horn A, Taylor D, Savolain V, Hawkins JA. DNA barcoding of a large genus, Aspalathus L. (Fabaceae). Taxon 2008, 57:1317-1327.
14. Erickson DL, Spouge J, Resch A, Weigt LA, Kress WJ. DNA barcoding in land plants: developing standards to quantify and maximize success. Taxon 2008, 57:1304-1316.
15. Fazekas AJ, Burgess KS, Kesanakurti PR. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. Public Library of Science, ONE 2008, 3:e2802.
16. Ford CS, Ayres KL, Toomey N. Selection of candidate coding DNA barcoding regions for use on land plants. Botanical Journal of the Linnean Society 2009, 159:1-11.
17. Furlow JJ. The systematics of American species of Alnus (Betulaceae). Rhodora 1979, 81:151-248.
18. Govaerts R, Frodin DG. World Checklist and Bibliography of Fagales 1998, 17-35. Royal Botanical Garden, Kew, pp
19. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 2003, 52:696-704.
20. Haase M, Wilke T, Mildner P. Identifying species of Bythinella (Caenogastropoda: Rissooidea): a plea for an integrative approach. Zootaxa 2007, 1563:1-16.
21. Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics 2007, 23:167-172.
22. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows95/98/NT. Nucleic Acids Symposium Series 1999, 41:95-98.
23. Hebert PDN, Cywinska A, Ball SL, DeWaard JR. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B: Biological Sciences 2003, 270:313-321.
24. Hollingsworth PM, Forrest LL, Spouge JL. A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:12794-12797.
25. Huelsenbeck JP, Ronquist F. mrbayes: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
26. Kondo K, Shiba M, Yamaji H. Species identification of licorice using nrDNA and cpDNA genetic markers. Biological & Pharmaceutical Bulletin 2007, 30:1497-1502.
27. Kress WJ, Erickson DL. A two-locus global DNA barcode for land plant: the coding rbcL gene complements the non-coding trnH-psbA spacer region. Public Library of Science, ONE 2007, 2:e508.
28. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:8369-8374.
29. Kristiansen KA, Cilieborg M, Drabkova L. DNA taxonomy-the riddle of Oxychloe (Juncaceae). Systematic Botany 2005, 30:284-289.
30. Kumar S, Tamura K, Nei M. mega3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics 2004, 5:150-163.
31. Lahaye R, Van der Bank M, Bogarin D. DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:2923-2928.
32. Logacheva MD, Valiejo-Roman CM, Pimenov MG. ITS phylogeny of West Asian Heracleum species and related taxa of Umbelliferae-Tordylieae W.D.J. Koch, with notes on evolution of their psbA-trnH sequences. Plant Systematics and Evolution 2008, 270:139-157.
33. Murai S. Phytotaxonomical and geobotanical studies on genus Alnus in Japan III taxonomy of whole world species and distribution of each sect. Bulletin Government Forest Experimental Station of Japan 1964, 171:1-107.
34. Navarro E, Bousquet J, Moiroud A. Molecular phylogeny of Alnus (Betulaceae), inferred from nuclear ribosomal DNA ITS sequences. Plant and Soil 2003, 254:207-217.
35. Newmaster SG, Ragupathy S. Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae). Molecular Ecology Resources 2009, 9:172-180.
36. Newmaster SG, Fazekas AJ, Ragupathy S. DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Canadian Journal of Botany-Revue Canadienne De Botanique 2006, 84:335-341.
37. Newmaster SG, Fazekas AJ, Steeves RAD, Janovec J. Testing candidate plant barcode regions in the Myristicaceae. Molecular Ecology Resources 2008, 8:480-490.
38. Nitta JH. Exploring the utility of three plastid loci for biocoding the filmy ferns (Hymenophyllaceae) of Moorea. Taxon 2008, 57:725-736.
39. Presting GG. Identification of conserved regions in the plastid genome: implications for DNA barcoding and biological function. Canadian Journal of Botany-Revue Canadienne De Botanique 2006, 84:1434-1443.
40. Rach J, DeSalle R, Sarkar IN, Schierwater B, Hadrys H. Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proceedings of the Royal Society of London, Series B: Biological Sciences 2008, 275:237-247.
41. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003, 19:2496-2497.
42. Sass C, Littlle DP, Stevenson DW, Specht CD. DNA barcoding in the Cycadales: testing the potential of proposed barcoding marker for species identification of Cycads. Public Library of Science, ONE 2007, 11:e1154.
43. Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R. Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 2005, 360:1805-1811.
44. Seberg O, Petersen G. How many loci does it take to DNA barcode a Crocus? Public Library of Science, ONE 2009, 4:e4598.
45. Simmons MP, Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 2000, 49:369-381.
46. Smith MA, Fisher BL, Hebert PDN. DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 2005, 360:1825-1834.
47. Starr JR, Naczi RFC, Chouinard BN. Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae). Molecular Ecology Resources 2009, 9:151-163.
48. Swofford DL. paup*: Phylogenetic Analysis Using Parsimony (*and other methods) 2002, version 4.0b10, Sinauer, Sunderland
49. Thompson JD, Gibson TJ, Jeanmougin F, Higgins DG. The ClustalX windows interface: flexible strategies for multiple sequences alignment aided by quality analysis tools. Nucleic Acids Research 1997, 24:4876-4882.
50. Will KW, Mishler BD, Wheeler QD. The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biology 2005, 54:844-851.