Testing four candidate barcoding markers in temperate woody bamboos (Poaceae: Bambusoideae)

Journal of Systematics and Evolution

Volumn 50, Issue 6, 2012, Pages 527-539

  Cai, Zhao Ming ^a,b   Zhang, Yu Xiao ^a   Zhang, Li Na ^a   Gao, Lian Ming ^a   Li, De Zhu ^a  

^a KUNMING INSTITUTE OF BOTANY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

DNA barcoding; Internal transcribed spacer (ITS); MatK; RbcL; Temperate woody bamboos

Indexed keywords

EID: 84871260182     PISSN: 16744918     EISSN: 17596831     Source Type: Journal    
DOI: 10.1111/j.1759-6831.2012.00216.x     Document Type: Article

References (66)

1. Alvarez I, Wendel JF. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434.
2. Arca M, Hinsinger DD, Cruaud C, Tillier A, Bousquet J, Farscaria-Lacoste N. 2012. Deciduous tree and the application of universal DNA barcodes: a case study on the circumpolar Fraxinus. PLoS One 7: e34089.
3. Bergsten J, Bilton DT, Fujisawa T, Elliott M, Monaghan MT, Balke M, Hendrich L, Geijer J, Herrmann J, Foster GN, Ribera I, Nilsson AN, Barraclough TG, Vogler AP. 2012. The effect of geographical scale of sampling on DNA barcoding. Systematic Biology 61: 851-869.
4. Bouchenak-Khelladi Y, Salamin N, Savolainen V, Forest F, Bank Mvd Chase MW, Hodkinson TR. 2008. Large multi-gene phylogenetic trees of the grasses (Poaceae): Progress towards complete tribal and generic level sampling. Molecular Phylogenetics and Evolution 47: 488-505.
5. Bouchenak-Khelladi Y, Verboom GA, Savolainen V, Hodkinson TR. 2010. Biogeography of the grasses (Poaceae): a phylogenetic approach to reveal evolutionary history in geographical space and geological time. Botanical Journal of the Linnean Society 162: 543-557.
6. Bruni I, De Mattia F, Galimberti A, Galasso G, Banfi E, Casiraghi M, Labra M. 2010. Identification of poisonous plants by DNA barcoding approach. International Journal of Legal Medicine 124: 595-603.
7. Consortium for the Barcode of Life (CBOL) Plant Working Group. 2009. A DNA barcode for land plants. Proceedings of the National Academy of Sciences USA 106: 12 794-12 797.
8. Chase MW, Cowan RS, Hollingsworth PM, Van Den Berg C, Madrinan S, Petersen G, Seberg O, Jorgsensen T, Cameron KM, Carine M, Pedersen N, Hedderson T, Conrad F, Salazar G, Richardson JE, Hollingsworth ML, Barraclough TG, Kelly L, Wilkinson M. 2007. A proposal for a standardised protocol to barcode all land plants. Taxon 56: 295-299.
9. China Plant Barcode of Life (BOL) Group. 2011. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proceedings of the National Academy of Sciences USA 108: 19 641-19 646.
10. Cho Y, Mower JP, Qiu YL, Palmer JD. 2004. Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proceedings of the National Academy of Sciences USA 101: 17 741-17 746.
11. Cuénoud P, Savolainen V, Chatrou LW, Powell M, Grayer RJ, Chase MW. 2002. Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. American Journal of Botany 89: 132-144.
12. Das M, Bhattacharya S, Singh P, Filgueiras TS, Pal A. 2008. Bamboo taxonomy and diversity in the era of molecular markers. Advances in Botanical Research 47: 225-268.
13. Denduangboripant J, Cronk QCB. 2000. High intraindividual variation in internal transcribed spacer sequences in Aeschynanthus (Gesneriaceae): implications for phylogenetics. Proceedings of the Royal Society B: Biological Sciences 267: 1407-1415.
14. Dong WP, Liu J, Yu J, Wang L, Zhou SL. 2012. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS One 7: e35071.
15. Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
16. FayMF, Swensen SM, ChaseMW. 1997. Taxonomic affinities of Medusagyne oppositifolia (Medusagynaceae). KewBulletin 52: 111-120.
17. Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, Husband BC, Percy DM, Hajibabaei M, Spencer CHB. 2008. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS One 3: e2802.
18. Fazekas AJ, Kesanakurti PR, Burgess KS, Percy DM, Graham SW, Barrett SCH, Newmaster SG, Hajibabaei M, Husband BC. 2009. Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? Molecular Ecology Resources 9: 130-139.
19. Gao T, Yao H, Song JY, Liu C, Zhu YJ, Ma XY, Pang XH, Xu HX, Chen SL. 2010. Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2. Journal of Ethnopharmacology 130: 116-121.
20. Guo ZH, Chen YY, Li DZ. 2002. Phylogenetic studies on the Thamnocalamus group and its allies (Graminae: Bambusoideae) based on ITS sequence data. Molecular Phylogenetics and Evolution 22: 20-30.
21. Guo ZH, Chen YY, Li DZ, Yang JB. 2001. Genetic variation and evolution of the alpine bamboos (Poaceae: Bambusoideae) using DNA sequence data. Journal of Plant Research 114: 315-322.
22. He J, Wong KL, Shaw PC, Wang H, Li DZ. 2010. Identification of the medicinal plants in Aconitum L. by DNA barcoding technique. Planta Medica 76: 1622-1628.
23. Hebert PDN, Cywinska A, Ball SL, Dewaard JR. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 270: 313-321.
24. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W. 2004. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences USA 101: 14 812-14 817.
25. Hollingsworth ML, Andra Clark A, Forrest LL, Richardson J, Pennington R, Long DG, Cowan R, Chase MW, Gaudeul M, Hollingsworth PM. 2009. Selecting barcoding loci for plants: evaluation of seven candidate loci with species level sampling in three divergent groups of land plants. Molecular Ecology Resources 9: 439-457.
26. Hollingsworth PM, Graham SW, Little DP. 2011. Choosing and using a plant DNA barcode. PLoS One 6: e19254
27. Janzen DH. 1976. Why bamboos wait so long to flower. Annual Review of Ecology and Systematics 7: 347-391.
28. Janzen DH, Hajibabaei M, Burns JM, Hallwachs W, Remigio E, Hebert PDN. 2005. Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1835-1845.
29. Jiang ZH. 2007. Bamboo and rattan in the World. Beijing: China Forestry Publishing House.
30. Kress WJ, Erickson DL. 2007. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS One 2: e508.
31. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. 2005. Use of DNA barcodes to identify flowering plants. Proceedings of theNationalAcademy of Sciences USA 102: 8369-8374.
32. Lahaye R, Van Der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V. 2008. DNA barcoding the floras of biodiversity hotspots. Proceedings of theNationalAcademy of Sciences USA 105: 2923-2928.
33. Li DZ. 1997. The Flora of China Bambusoideae project: problems and current understanding of bamboo taxonomy in China. In: Chapman GP ed. The bamboos. London: Academic Press. 61-82.
34. Li DZ, Wang ZP, Zhu ZD, Xia NH, Jia LZ, Guo ZH, Yang GY, Stapleton CMA. 2006. Bambuseae (Poaceae). In: Wu ZY, Raven PH eds. Flora of China. Beijing: Science Press; St. Louis: Missouri Botanical Garden Press. 22: 7-180.
35. Liu J, Möller M, Gao LM, Zhang DQ, Li DZ. 2011. DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species. Molecular Ecology Resources 11: 89-100.
36. Meier R, Kwong S, Vaidya G, Ng PKL. 2006. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology 55: 715-728.
37. Möller M, Cronk QCB. 1997. Origin and relationships of Saintpaulia (Gesneriaceae) based on ribosomal DNA internal transcribed spacer (ITS) sequences. American Journal of Botany 84: 956-965.
38. Möller M, Kokubugata G, Jong K. 2008. Aspects of genome evolution in Gesneriaceae: patterns of 45S-nrDNA site evolution based on evidence from fluorescent in situ hybridisation (FISH). International Journal of Plant Sciences 169: 667-676.
39. Newmaster SG, Fazekas AJ, Ragupathy S. 2006. DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Canadian Journal of Botany 84: 335-341.
40. Newmaster SG, Fazekas AJ, Steeves RAD, Janovec J. 2008. Testing candidate plant barcode regions in the Myristicaceae. Molecular Ecology Resources 8: 480-490.
41. Ohrnberger D. 1999. The bamboos of the world: Annotated nomenclature and literature of the species and the higher and lower taxa. Amsterdam: Elsevier.
42. Peng S, Yang HQ, Li DZ. 2008. Highly heterogeneous generic delimitation within the temperate bamboo clade (Poaceae: Bambusoideae): evidence from GBSSI and ITS sequences. Taxon 57: 799-810.
43. Ragupathy S, Newmaster SG, Murugesan M, Balasubramaniam V. 2009. DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany study by the hill tribes of the Western Ghats in southern India. Molecular Ecology Resources 9: 164-171.
44. Ren BQ, Chen ZD. 2010. DNA barcoding plant life. Chinese Bulletin of Botany 45: 1-12.
45. Rowe K, Aplin PK, Baverstock RP, Mortz C. 2011. Recent and rapid speciation limited morphological disparity in the genus Rattus. Systematic Biology 60: 188-203.
46. Sang T, Crawford DJ, Stuessy TF. 1997. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84: 1120-1136.
47. Sass C, Little DP, Stevenson DW, Specht CD. 2007. DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads. PLoS One 2: e1154.
48. Shaw J, Lickey EB, Beck JT, Farmer SB, Liu WS, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL. 2005. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92: 142-168.
49. ShawJ, Lickey EB, Schilling EE, SmallRL. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. American Journal of Botany 94: 275-288.
50. Smith MA, Fisher BL, Hebert PDN. 2005.DNAbarcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1825-1834.
51. Smith SA, Donoghue MJ. 2008. Rates of molecular evolution are linked to life history in flowering plants. Science 322: 86-89.
52. Starr JR, Naczi RFC, Chouinard BN. 2009. Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae). Molecular Ecology Resources 9: 151-163.
53. Steven G. 2009. Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae). Molecular Ecology Resources 9: 172-180.
54. Sungkaew S, Stapleton CMA, Salamin N, Hodkinson TR. 2009. Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s. Journal of Plant Research 122: 95-108.
55. Swofford DL. 2002. PAUP. Phylogenetic analysis using parsimony (and other methods), version 4.0. Sunderland: Sinauer Associates.
56. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
57. Tate JA, Simpson BB. 2003. Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species. Systematic Botany 28: 723-737.
58. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
59. Triplett JK, Clark LG. 2010. Phylogeny of the temperate bamboos (Poaceae: Bambusoideae: Bambuseae) with an emphasis on Arundinaria and allies. Systematic Botany 35: 102-120.
60. Valentini A, Pompanon F, Taberlet P. 2009. DNA barcoding for ecologists. Trends in Ecology & Evolution 24: 110-117.
61. White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ eds. PCR protocols: a guide to methods and applications. San Diego: Academic Press. 315-322.
62. Yao H, Song JY, Liu C, Luo K, Han JP, Hansson B. 2010. Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS One 5: 370-375.
63. Yassin A, Capy P, Madi-Ravazzi L, Ogereau D, David JR. 2008. DNA barcode discovers two cryptic species and two geographical radiations in the invasive drosophilid Zaprionus indianus. Molecular Ecology Resources 8: 491-501.
64. Zeng CX, Zhang YX, Triplett JK, Yang JB, Li DZ. 2010. Large multi-locus plastid phylogeny of the tribe Arundinarieae (Poaceae: Bambusoideae) reveals ten major lineages and low rate of molecular divergence. Molecular Phylogenetics and Evolution 56: 821-839.
65. Zhang YJ, Ma PF, Li DZ. 2011. High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae). PLoS One 6: e20596.
66. Zhang YX, Zeng CX, Li DZ. 2012. Complex evolution in Arundinarieae (Poaceae: Bambusoideae): incongruence between plastid and nuclear GBSSI gene phylogenies. Molecular Phylogenetics and Evolution 63: 777-779.