Complete Chloroplast Genome Sequence of Tartary Buckwheat (Fagopyrum tataricum) and Comparative Analysis with Common Buckwheat (F. esculentum)

PLoS One. 2015 May 12;10(5):e0125332. doi: 10.1371/journal.pone.0125332. eCollection 2015.


We report the chloroplast (cp) genome sequence of tartary buckwheat (Fagopyrum tataricum) obtained by next-generation sequencing technology and compared this with the previously reported common buckwheat (F. esculentum ssp. ancestrale) cp genome. The cp genome of F. tataricum has a total sequence length of 159,272 bp, which is 327 bp shorter than the common buckwheat cp genome. The cp gene content, order, and orientation are similar to those of common buckwheat, but with some structural variation at tandem and palindromic repeat frequencies and junction areas. A total of seven InDels (around 100 bp) were found within the intergenic sequences and the ycf1 gene. Copy number variation of the 21-bp tandem repeat varied in F. tataricum (four repeats) and F. esculentum (one repeat), and the InDel of the ycf1 gene was 63 bp long. Nucleotide and amino acid have highly conserved coding sequence with about 98% homology and four genes--rpoC2, ycf3, accD, and clpP--have high synonymous (Ks) value. PCR based InDel markers were applied to diverse genetic resources of F. tataricum and F. esculentum, and the amplicon size was identical to that expected in silico. Therefore, these InDel markers are informative biomarkers to practically distinguish raw or processed buckwheat products derived from F. tataricum and F. esculentum.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Chloroplasts / genetics*
  • Conserved Sequence
  • Evolution, Molecular
  • Fagopyrum / classification*
  • Fagopyrum / cytology
  • Fagopyrum / genetics*
  • Genetic Markers / genetics
  • Genetic Variation
  • Genome, Chloroplast*
  • INDEL Mutation
  • Sequence Analysis, DNA


  • Genetic Markers

Grants and funding

This study was supported by a grant from the “Cooperative Research Program for Agriculture Science and Technology Development, (Project Title: Development of DNA markers linked to agricultural traits for buckwheat breeding, Project No. PJ009246),” Rural Development Administration, Republic of Korea. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.