Biodiv Sci ›› 2008, Vol. 16 ›› Issue (5): 417-425. DOI: 10.3724/SP.J.1003.2008.08215
Special Issue: 物种形成与系统进化
• Reviews • Next Articles
Shuping Ning1,3, Haifei Yan1, Gang Hao2, Xuejun Ge1,*()
Received:
2008-08-23
Accepted:
2008-09-18
Online:
2008-09-20
Published:
2008-09-20
Contact:
Xuejun Ge
Shuping Ning, Haifei Yan, Gang Hao, Xuejun Ge. Current advances of DNA barcoding study in plants[J]. Biodiv Sci, 2008, 16(5): 417-425.
Gene | Primer | Direction | Sequence 5′→3′ |
---|---|---|---|
matK | 2.1 | f | CCTATCCATCTGGAAATCTTAG |
2.1a | f | ATCCATCTGGAAATCTTAGTTC | |
5 | r | GTTCTAGCACAAGAAAGTCG | |
3.2 | r | CTTCCTCTGTAAAGAATTC | |
2.1-Myristicaceae | f | CCTATCCATCTGGATATCTTGG | |
5-Myristicaceae | r | GTTCTAGCACACGAAAATCG | |
390F | f | CGATCTATTCATTCAATATTTC | |
1326R | r | TCTAGCACACGAAAGTCGAAGT | |
Angiosperms-KIM | F | ATCCATCTGGAAATCTTAGTTC | |
r | GTTCTAGCACAAGAAAGTCG | ||
Plants-KIM | f | CRATCWATTCATTCAATATT | |
r | CGTACAGTACTTTTGTGTTT | ||
matK_Kew | f | AATATCCAAATACCAAATCC | |
r | ACCCAGTCCATCTGGAAATCTTGGTTC | ||
trnH-psbA | psbA3 | f | GTTATGCATGAACGTAATGCTC |
trnH-05 | r | CGCGCATGGTGGATTCACAATCC | |
rbcL-a | f | ATGTCACCACAAACAGAGACTAAAGC | |
r | GTYAAATCAAGTCCACCYCG | ||
f | ATGTCACCACAAACAGAGACTAAAGC | ||
r | CTTCTGCTACAAATAAGAATCGATCTC | ||
atpF-atpH_KIM | atpF | ACTCGCACACACTCCCTTTCC | |
atpH | GCTTTTATGGAAGCTTTAACAAT | ||
psbK-psbI_KIM | psbK | TTAGCCTTTGTTTGGCAAG | |
psbI | AGAGTTTGAGAGTAAGCAT |
Table 1 Different primers for several plant barcoding regions
Gene | Primer | Direction | Sequence 5′→3′ |
---|---|---|---|
matK | 2.1 | f | CCTATCCATCTGGAAATCTTAG |
2.1a | f | ATCCATCTGGAAATCTTAGTTC | |
5 | r | GTTCTAGCACAAGAAAGTCG | |
3.2 | r | CTTCCTCTGTAAAGAATTC | |
2.1-Myristicaceae | f | CCTATCCATCTGGATATCTTGG | |
5-Myristicaceae | r | GTTCTAGCACACGAAAATCG | |
390F | f | CGATCTATTCATTCAATATTTC | |
1326R | r | TCTAGCACACGAAAGTCGAAGT | |
Angiosperms-KIM | F | ATCCATCTGGAAATCTTAGTTC | |
r | GTTCTAGCACAAGAAAGTCG | ||
Plants-KIM | f | CRATCWATTCATTCAATATT | |
r | CGTACAGTACTTTTGTGTTT | ||
matK_Kew | f | AATATCCAAATACCAAATCC | |
r | ACCCAGTCCATCTGGAAATCTTGGTTC | ||
trnH-psbA | psbA3 | f | GTTATGCATGAACGTAATGCTC |
trnH-05 | r | CGCGCATGGTGGATTCACAATCC | |
rbcL-a | f | ATGTCACCACAAACAGAGACTAAAGC | |
r | GTYAAATCAAGTCCACCYCG | ||
f | ATGTCACCACAAACAGAGACTAAAGC | ||
r | CTTCTGCTACAAATAAGAATCGATCTC | ||
atpF-atpH_KIM | atpF | ACTCGCACACACTCCCTTTCC | |
atpH | GCTTTTATGGAAGCTTTAACAAT | ||
psbK-psbI_KIM | psbK | TTAGCCTTTGTTTGGCAAG | |
psbI | AGAGTTTGAGAGTAAGCAT |
[1] |
Aldrich JBW, Cherney E, Merlin LC (1988) The role of insertions/deletions in the evolution of the intergenic region between psbA and trnH in the chloroplast genome. Current Genetics, 14,137-146.
URL PMID |
[2] | Allander T, Emerson SU, Engle RE, Purcell RH, Bukh J (2001) A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proceedings of the National Academy of Sciences, USA, 98,11609-11614. |
[3] | Brown B, Emberson RM, Paterson AM (1999) Mitochondrial COI and II provide useful markers for Weiseana (Lepidoptera, Hepialidae) species identification. Bulletin of Entomological Research, 89,287-294. |
[4] | 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 TAJ, Conrad F, Salazar GA, 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. |
[5] | Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, Haidar N, Savolainen V (2005) Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of the Royal Society B: Biological Sciences, 360,1889-1895. |
[6] | Cowan RS, Chase MW, Kress WJ, Savolainen V (2006) 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon, 55,611-616. |
[7] | Doukakis P, Birstein VJ, Ruban GI, Desalle R (1999) Molecular genetic analysis among subspecies of two Eurasian sturgeon species, Acipenser baerii and A. stellatus. Molecular Ecology, 8,S117-S127. |
[8] |
Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, Husband BC, Percy DM, Hajibabaei M, Barrett SCH (2008) Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PloS One, 3,e2802.
DOI URL PMID |
[9] | Frézal L, Leblois R (2008) Four years of DNA barcoding: current advances and prospects. Infection, Genetics and Evolution, 8,727-736. |
[10] | Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences,USA, 103,968-971. |
[11] |
Hamels S, Gala JL, Dufour S, Vannuffel P, Zammatteo N, Remacle J (2001) Consensus PCR and microarray for diagnosis of the genus Staphylococcus, species, and methicillin resistance. Biotechniques, 31,1364-1372.
URL PMID |
[12] | Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003a) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B: Biological Sciences, 270,313-321. |
[13] | Hebert PDN, Ratnasingham S, deWaard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London Series B: Biological Sciences, 270,S96-S99. |
[14] | Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. Plos Biology, 2,1657-1663. |
[15] |
Hollingsworth PM (2008) DNA barcoding plants in biodiversity hot spots: Progress and outstanding questions. Heredity, 101,1-2.
URL PMID |
[16] | Jackson RB, Moore LA, Hoffmann WA, Pockman WT, Linder CR (1999) Ecosystem rooting depth determined with caves and DNA. Proceedings of the National Academy of Sciences,USA, 96,11387-11392. |
[17] | 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. |
[18] | Kress WJ, Erickson DL (2008) DNA barcodes: Genes, genomics, and bioinformatics. Proceedings of the National Academy of Sciences,USA, 105,2761-2762. |
[19] | Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences,USA, 102,8369-8374. |
[20] | Lahaye R, Savolainen V, Duthoit S, Maurin O, Bank Mvd (2008a) A test of psbK-psbI and atpF-atpH as potential plant DNA barcodes using the flora of the Kruger National Park as a model system (South Africa). Available from Nature Precedings, <http://hdl.handle.net/10101/npre.12008.11896.10101>. |
[21] | Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, barraclough TG, Vincent S (2008b) DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences,USA, 105,2923-2928. |
[22] | Logacheva MD, Valiejo-Roman CM, Pimenov MG (2008) 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, 270,139-157. |
[23] | Mallet J, Willmott K (2003) Taxonomy: renaissance or Tower of Babel? Trends in Ecology & Evolution, 18,57-59. |
[24] |
Meier RS, 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.
URL PMID |
[25] | Meyer CP, Paulay G (2005) DNA barcoding: Error rates based on comprehensive sampling. PloS Biology, 3,2229-2238. |
[26] | 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. |
[27] |
Newmaster SG, Fazekas AJ, Steeves RAD, Janovec J (2008) Testing candidate plant barcode regions in the Myristicaceae. Molecular Ecology Resources, 8,480-490.
URL PMID |
[28] | Niesters HG, Goessens WH, Meis JF, Quint WG (1993) Rapid, polymerase chain reaction-based identification assays for Candida species. Journal of Clinical Microbiology, 31,904-910. |
[29] |
Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science, 276,734-740.
DOI URL PMID |
[30] | Pennisi E (2007) Wanted: A barcode for plants. Science, 318,190-191. |
[31] | Presting GG (2006) Identification of conserved regions in the plastid genome: implications for DNA barcoding and biological function. Canadian Journal of Botany, 84,1434-1443. |
[32] | Ratnasingham S, Hebert PDN (2007) Bold: the barcode of life data system (). Molecular Ecology Notes, 7,355-364. |
[33] |
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.
DOI URL PMID |
[34] | Schindel DE, Miller SE (2005) DNA barcoding a useful tool for taxonomists. Nature, 435,17. |
[35] | 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, 92,142-166. |
[36] | Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier G, Brochmann C, Willerslev E (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding . Nucleic Acids Research, 35,8. |
[37] |
Vincent S, Vian JM, Carlotti MP (2000) 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. Journal of Forensic Sciences, 45,820-823.
URL PMID |
[38] | Wells JD, Pape T, Sperling FAH (2001) DNA-based identification and molecular systematics of forensically important sarcophagidae (Diptera). Journal of Forensic Sciences, 46,1098-1102. |
[39] | Wells JD, Sperling FAH (2001) DNA-based identification of forensically important Chrysomyinae (Diptera: Calliphoridae). Forensic Science International, 120,110-115. |
[40] |
Whipple IG, Barkworth ME, Bushman BS (2007) Molecular insights into the taxonomy of Glyceria (Poaceae: Meliceae) in North America . American Journal of Botany, 94,551-557.
URL PMID |
[41] |
Yancy HF, Zemlak TS, Mason JA, Washington JD, Tenge BJ, Nguyen NLT, Barnett JD, Savary WE, Hill WE, Moore MM, Fry FS, Randolph SC, Rogers PL, Hebert PDN (2008) Potential use of DNA barcodes in regulatory science: Applications of the regulatory fish encyclopedia. Journal of Food Protection, 71,210-217.
DOI URL PMID |
[42] | Yoo HS, Eah JY, Kim JS, Kim YJ, Min MS, Paek WK, Lee H, Kim CB (2006) DNA barcoding Korean birds. Molecules and Cells, 22,323-327. |
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