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

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  • Liu, Chang
    • Other Affiliation: 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
  • Liang, Dong
    • Other Affiliation: School of Computer Science & Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100191, P.R.China
  • Gao, Ting
    • Other Affiliation: College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, P.R. China
  • Pang, Xiaohui
    • Other Affiliation: 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
  • Song, Jingyuan
    • Other Affiliation: 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
  • Yao, Hui
    • Other Affiliation: 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
  • Han, Jianping
    • Other Affiliation: 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
  • Liu, Zhihua
    • Other Affiliation: 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
  • Guan, Xiaojun
    • Affiliation: School of Medicine, Curriculum in Bioinformatics and Computational Biology
  • Jiang, Kun
    • Other Affiliation: Pidit Ltd, 192 West Grant Ave, Edison, NJ 08820, USA
  • Li, Huan
    • Other Affiliation: School of Computer Science & Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100191, P.R.China
  • Chen, Shilin
    • Other Affiliation: 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
Abstract
  • Abstract 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.
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  • Article
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  • In Copyright
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  • Chang Liu et al.; licensee BioMed Central Ltd.
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  • English
Is the article or chapter peer-reviewed?
  • Yes
Bibliographic citation
  • BMC Bioinformatics. 2011 Nov 30;12(Suppl 13):S4
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  • BioMed Central Ltd
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  • Open Access
Date uploaded
  • August 23, 2012

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