PTIGS-IdIt, a system for species identification by DNA sequences of the psbA-trnH intergenic spacer region

详细信息    查看全文

• 作者：Chang Liu (1)
  Dong Liang (2)
  Ting Gao (3)
  Xiaohui Pang (1)
  Jingyuan Song (1)
  Hui Yao (1)
  Jianping Han (1)
  Zhihua Liu (1)
  Xiaojun Guan (4)
  Kun Jiang (5)
  Huan Li (2)
  Shilin Chen (1)
  
• 刊名：BMC Bioinformatics
• 出版年：2011
• 出版时间：December 2011
• 年：2011
• 卷：12
• 期：13-supp
• 全文大小：158KB
• 参考文献：1. Chen S, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, Gao T, Pang X, / et al.: Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. / PloS one 2010,5(1):e8613. CrossRef
  2. Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, van der Bank M, Chase MW, Cowan RS, Erickson DL, / et al.: A DNA barcode for land plants. / Proceedings of the National Academy of Sciences of the United States of America 2009,106(31):12794-2797. CrossRef
  3. 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(23):8369-374. CrossRef
  4. Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V: DNA barcoding the floras of biodiversity hotspots. / Proceedings of the National Academy of Sciences of the United States of America 2008,105(8):2923-928. CrossRef
  5. Sass C, Little DP, Stevenson DW, Specht CD: DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads. / PloS one 2007,2(11):e1154. CrossRef
  6. Yao H, Song J, Liu C, Luo K, Han J, Li Y, Pang X, Xu H, Zhu Y, Xiao P, / et al.: Use of ITS2 region as the universal DNA barcode for plants and animals. / PloS one 2010.,5(10): epublish
  7. Chase MW, Cowan RS, Hollingsworth PM, van den Berg C, Madrián S, Petersen G, Seberg O, Jorgsensen T, Cameron KM, Carine M: A proposal for a standardised protocol to barcode all land plants. / Taxon 2007,56(2):295-99.
  8. Newmaster SG, Fazekas AJ, Steeves RAD, Janovec J: Testing candidate plant barcode regions in the Myristicaceae. / Mol Ecol Resour 2008,8(3):480-90. CrossRef
  9. Shaw J, Lickey EB, Schilling EE, Small RL: Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. / Am J Bot 2007,94(3):275-88. CrossRef
  10. Yao H, Song JY, Ma XY, Liu C, Li Y, Xu HX, Han JP, Duan LS, Chen SL: Identification of Dendrobium species by a candidate DNA barcode sequence: the chloroplast psbA-trnH intergenic region. / Planta medica 2009,75(6):667-69. CrossRef
  11. ?torchová H, Olson MS: The architecture of the chloroplast psb A-trn H non-coding region in angiosperms. / Plant Syst Evol 2007,268(1):235-56. CrossRef
  12. Little DP, Stevenson DW: A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms. / Cladistics 2007,23(1):1-1. CrossRef
  13. Austerlitz F, David O, Schaeffer B, Bleakley K, Olteanu M, Leblois R, Veuille M, Laredo C: DNA barcode analysis: a comparison of phylogenetic and statistical classification methods. / BMC bioinformatics 2009,10(Suppl 14):S10. CrossRef
  14. Chu KH, Xu M, Li CP: Rapid DNA barcoding analysis of large datasets using the composition vector method. / BMC bioinformatics 2009,10(Suppl 14):S8. CrossRef
  15. Eddy SR: Profile hidden Markov models. / Bioinformatics (Oxford, England) 1998,14(9):755-63. CrossRef
  16. Krogh A, Brown M, Mian IS, Sjolander K, Haussler D: Hidden Markov models in computational biology. Applications to protein modeling. / Journal of molecular biology 1994,235(5):1501-531. CrossRef
  17. Aldrich J, Cherney BW, Merlin E, Christopherson L: The role of insertions/deletions in the evolution of the intergenic region between psbA and trnH in the chloroplast genome. / Current genetics 1988,14(2):137-46. CrossRef
  18. Hamilton MB, Braverman JM, Soria-Hernanz DF: Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in new world species of the Lecythidaceae. / Molecular biology and evolution 2003,20(10):1710-721. CrossRef
  19. Whitlock BA, Hale AM, Groff PA: Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode. / PloS one 2010,5(7):e11533. CrossRef
  20. Batzoglou S: The many faces of sequence alignment. / Briefings in bioinformatics 2005,6(1):6-2. CrossRef
  21. Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S: Glocal alignment: finding rearrangements during alignment. / Bioinformatics (Oxford, England) 2003,19(Suppl 1):i54-2. CrossRef
  22. Huang X: On global sequence alignment. / Bioinformatics (Oxford, England) 1994,10(3):227-35. CrossRef
  23. Ristad ES, Yianilos PN: Learning string-edit distance. / IEEE trans Pattern Anal Mach Intell 1998,20(5):522-32. CrossRef
  24. Uliel S, Fliess A, Amir A, Unger R: A simple algorithm for detecting circular permutations in proteins. / Bioinformatics (Oxford, England) 1999,15(11):930-36. CrossRef
  25. Eddy SR: What is dynamic programming? / Nature Biotec 2004,22(7):909-10. CrossRef
  
• 作者单位：Chang Liu (1)
  Dong Liang (2)
  Ting Gao (3)
  Xiaohui Pang (1)
  Jingyuan Song (1)
  Hui Yao (1)
  Jianping Han (1)
  Zhihua Liu (1)
  Xiaojun Guan (4)
  Kun Jiang (5)
  Huan Li (2)
  Shilin Chen (1)
  
  1. The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, P. R. China
  2. School of Computer Science & Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing, 100191, P.R.China
  3. College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, P.R. China
  4. Center for BioInformatics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
  5. Pidit Ltd, 192 West Grant Ave, Edison, NJ, 08820, USA
  
• ISSN：1471-2105

文摘

Background DNA barcoding technology, which uses a short piece of DNA sequence to identify species, has wide ranges of applications. Until today, a universal DNA barcode marker for plants remains elusive. The rbcL and matK regions have been proposed as the “core barcode-for plants and the ITS2 and psbA-trnH intergenic spacer (PTIGS) regions were later added as supplemental barcodes. The use of PTIGS region as a supplemental barcode has been limited by the lack of computational tools that can handle significant insertions and deletions in the PTIGS sequences. Here, we compared the most commonly used alignment-based and alignment-free methods and developed a web server to allow the biologists to carry out PTIGS-based DNA barcoding analyses. Results First, we compared several alignment-based methods such as BLAST and those calculating P distance and Edit distance, alignment-free methods Di-Nucleotide Frequency Profile (DNFP) and their combinations. We found that the DNFP and Edit-distance methods increased the identification success rate to ~80%, 20% higher than the most commonly used BLAST method. Second, the combined methods showed overall better success rate and performance. Last, we have developed a web server that allows (1) retrieving various sub-regions and the consensus sequences of PTIGS, (2) annotating novel PTIGS sequences, (3) determining species identity by PTIGS sequences using eight methods, and (4) examining identification efficiency and performance of the eight methods for various taxonomy groups. Conclusions The Edit distance and the DNFP methods have the highest discrimination powers. Hybrid methods can be used to achieve significant improvement in performance. These methods can be extended to applications using the core barcodes and the other supplemental DNA barcode ITS2. To our knowledge, the web server developed here is the only one that allows species determination based on PTIGS sequences. The web server can be accessed at http://psba-trnh-plantidit.dnsalias.org.