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Jan, 2023;23 (1): 106-117.

Accurate identification of taxon-specific molecular markers in plants based on DNA signature sequence.

Zhongyi Hua, Chao Jiang, Shuhui Song, Dongmei Tian, Ziyuan Chen, Yan Jin, Yuyang Zhao, Junhui Zhou, Zhang Zhang, Luqi Huang, Yuan Yuan
Author Information
  1. Zhongyi Hua: National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China. ORCID
  2. Chao Jiang: National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China.
  3. Shuhui Song: China National Center for Bioinformation, Beijing, China.
  4. Dongmei Tian: China National Center for Bioinformation, Beijing, China.
  5. Ziyuan Chen: National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China.
  6. Yan Jin: National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China.
  7. Yuyang Zhao: National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China.
  8. Junhui Zhou: National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China.
  9. Zhang Zhang: China National Center for Bioinformation, Beijing, China.
  10. Luqi Huang: National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China.
  11. Yuan Yuan: National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing, China.
PMID: 35951477 DOI: 10.1111/1755-0998.13697

Abstract

Accurate identification of plants remains a significant challenge for taxonomists and is the basis for plant diversity conservation. Although DNA barcoding methods are commonly used for plant identification, these are limited by the low amplification success and low discriminative power of selected genomic regions. In this study, we developed a k-mer-based approach, the DNA signature sequence (DSS), to accurately identify plant taxon-specific markers, especially at the species level. DSS is a constant-length nucleotide sequence capable of identifying a taxon and distinguishing it from other taxa. In this study, we performed the first large-scale study of DSS markers in plants. DSS candidates of 3899 angiosperm plant species were calculated based on a chloroplast data set with 4356 assemblies. Using Sanger sequencing of PCR amplicons and high-throughput sequencing, DSSs were validated in four and 165 species, respectively. Based on this, the universality of the DSSs was over 79.38%. Several indicators influencing DSS marker identification and detection have also been evaluated, and common criteria for DSS application in plant identification have been proposed.

Keywords

DNA signature sequence chloroplast genome plants species identification

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Grants

  1. 2060302/Key project at central government level for the ability establishment of sustainable use for valuable Chinese medicine resources
  2. CI2021B014/CI2021A041/Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences
  3. 2018FY10080002/Special Funds for Basic Resources Investigation Research of the Ministry of Science and Technology
  4. 2019YFC1711000/The National Key Research and Development Program of China

MeSH Term

Plants
High-Throughput Nucleotide Sequencing
Genetic Markers
Magnoliopsida
Polymerase Chain Reaction
Sequence Analysis, DNA
DNA Barcoding, Taxonomic
DNA, Plant
Phylogeny

Chemicals

Genetic Markers
DNA, Plant
Journal Article

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