DOI: 10.3724/SP.J.1143.2010.09234

Acta Botanica Yunnanica (云南植物研究) 2010/32:3 PP.239-249

The Preliminary Study on DNA Barcoding of Mosses----A Case of Part of Genera of Meteoriaceae

We compared the performances of the candidate loci for moss DNA barcoding and the primers used in amplifying the loci. Primers for three coded loci (matK, rps4 and rbcL-a) and four non-coded loci (atpB-rbcL, atpF-H, psbK-I and trnH-psbA) of the chloroplast genome, one from the mitochondrial genome (nad5), and one from the nucleus genome (ITS2) were evaluated. Seventy-four samples representing 14 species belonging to five genera of Trachypodoaceae (or Meteoriaceae) were screened. All primers for matK and a pair of primers for trnH-psbA failed. Low successes were encountered with the primers for atpF-H and psbK-I. The primers for psbK-I produced several bands and the PCR products of atpF-H were difficult to sequence. The powers of the remaining six loci were compared using the variability, identification success and the resolutions. It was found that ITS2 is the most promising candidate for DNA barcoding for mosses. Among the chloroplast genes, atpB-rbcL exhibited the highest resolution. Although trnH-psbA is very variable, it is too short to be an ideal barcode alone. Combinations of chloroplast genes were also tried and Ps of both atpB-rbcL+trnH-psbA and rbcL-a++trnH-psbA were 64% using NJ method. More additions of loci did not increase the resolution. No barcoding gap exists for all these loci. Phylogenetic analyses were carried out prior to the DNA barcoding evaluation and some taxonomic problems do exist. This study exemplifies the necessity of correct species delimitation and the adoption of both plastid and nuclear loci in plant DNA barcoding.

Key words:DNA barcode,Resolution,Meteoriaceae,Loci,Mosses

ReleaseDate:2014-07-21 15:19:51

Buck WR, 1994. A new attempt at understanding the Meteoriaceae [J].Journal of the Hattori Botanical Laboratory, 75: 51—72

Chase MW, Cowan RS et al, 2007. A proposal for a standardised protocol to barcode all land plants [J]. Taxon, 56 (2): 295—299

Doyle JJ, Doyle JL, 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue [J]. Phytochemical Bulletin, 19: 11—15

Draper I, Hedenas L, Grimm GW, 2007. Molecular and morphological incongruence in European species of Isothecium (Bryophyta) [J]. Molecular Phylogenetics and Evolution, 42: 700—716

Excoffier L, Smouse PE, Quattro JM, 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data [J]. Genetics, 131: 479—491

Excoffier L, Laval G, Schneider S, 2005. Arlequin (version 30): An integrated software package for population genetics data analysis [J]. Evolutionary Bioinformatics Online, 1: 47—50

Fazekas AJ, Burgess KS, Kesanakurti PR et al, 2008. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally Well [J]. PLoS One, 3: 7, e2802

Frey W, Fischer E, Stech M, 2009. Syllabus of Plant Families: Bryophytes and Seedless Vascular Plant [M]. Berlin, Stuttgart: Gebrüder Borntraeger

Gradstein SR, Churchill SP, Salazar-Allen N, 2001. Guide to the Bryophtes of Tropical America [M]. Memoirs of the New York Botanical Garden. New York: New York Botanical Garden Press, 86: 1—577

Hedenas L, Huttunen S, Shevock JR et al, 2009. Homalothecium calofornicum (Brachytheciaceae), a new endemic species to the California Floristic Province, Pacific Coast of North America [J]. The Bryologist, 112 (3): 593—604

Hillingsworth ML, Clark AA, Forrest LL et al, 2009. Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants [J]. Molecular Ecology Resources, 9: 439—457

Kress WJ, Wurdack KJ, Zimmer EA et al, 2005. Use of DNA barcodes to identify flowering plants [J]. Proceedings of the National Academy of Sciences of the United States of America, 102: 8369—8374

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 [J]. PloS One, 2: e508

Kress WJ, Erickson DL, 2008. DNA barcodes: Genes, genomics, and bioinformatics [J]. Proceedings of the National Academy of Sciences of the United States of America, 105: 2761—2762

Lahaye R, Savolainen V, Duthoit S et al, 2008a. A test of psbK-psbI and atpF-H as potential plant DNA barcodes using the flora of the Kruger National Park as a model system (South Africa) [OL]. Nature Precedings,

Lahaye R, van der Bank M, Bogarin D et al, 2008b. DNA barcoding the floras of biodiversity hotspots [J]. Proceedings of the National Academy of Sciences of the United States of America,105: 2923—2928

Larkin MA, Blackshields G, 2007. Clustal W and Clustal X version 20 [J]. Applications Note, 23: 2947—2948

Meier R, Kwong S, Vaidya G et al, 2006. Barcoding and Taxonomy in Diptera: A Tale of High Intraspecific Variability and Low Identification Success [J]. Systematic Biology, 55 (5): 715—728

Newmadter SG, Fazekas AJ, Steeves RAD et al, 2008. Testing candidate plant barcode regions in the Myristicaceae [J]. Molecular Ecology Resources, 8: 480—490

Pennisi E, 2007. Wanted: A barcode for plants [J]. Science, 318: 190—191

Rambaut A, 1996. Se-Al: sequence alignment editor. Available at http://evolvezoooxacuk/

Redfearn PL, Tan BC, He S, 1996. A newly updated and annotated checklist of Chinese Mosses [J]. Journ Hattori Bot Lab, 79: 163—357

Sass C, Little DP, Stevenson DM et al, 2007. DNA barcoding in the Cycadales: Testing the potential of proposed barcoding markers for species identification of Cycads [J]. PLoS ONE, 2 (11): e1154. (doi:101371/journalpone0001154)

Starr JR, Naczi RFC, Chouinard BN, 2009. Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae) [J]. Molecular Ecology Resources, 9:151—163

Swofford DL, 2003. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods) [M]. Version 4., Sunderland, Massachusetts: Sinauer Associates