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

Abstract

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.

Comparative analysis of the complete chloroplast genomic sequence and chemical components of Cinnamomum micranthum and Cinnamomum kanehirae

“…Most of the repeat events occurred in IGS in both species. This is in accordance with findings in other plants (Do et al 2013;Ma et al 2013;Su et al 2014;Zhang et al 2014;Cho et al 2015). In comparison with two other Lauraceae species, Machilus balansae and M. yunnanensis, the number of repeats (with lengths of > 20 bp) varied from 39 to 41 (Song et al 2015).…”

“…The two IR sequences were reversed and complementary; the assembly software could not combine these three contigs as one contig. This result is similar to the assembly of the Tartary buckwheat (Fagopyrum tataricum) cp genome based on NGS (Cho et al 2015). The three long contigs revealed about 10-15-bp overlap between each of their flanking regions and then were manually assembled as a single circular cp genome.…”

Application of InDel markers based on the chloroplast genome sequences for authentication and traceability of tartary and common buckwheat

“…The method presented here utilises the InDel evolutionary hotspots compared between F. tataricum and F. esculentum in our previous study. Totally, six InDel regions which are identical among accessions of each species showed (Cho et al 2015). Based on this, five InDel markers were chosen to study their application in the authentication of the two buckwheat species.…”

“…The InDel markers used in this study were identified by comparing the chloroplast genome sequences of Tartary and common buckwheat in our previous study (Cho et al 2015). Among the total seven InDel patterns identified, five InDel markers (InDel_01, 03, 04, 05, 06) were used in this study to check their application in the authentication of buckwheat.…”

“…In this view, the study presented here shows the application of InDel (insertion/deletion) markers based on the chloroplast genome sequences of Tartary and common buckwheat to evaluate and distinguish the trace amounts of these buckwheat species in food products. The InDel markers used in this study were identified by comparing the chloroplast genome sequences of Tartary and common buckwheat in our previous study (Cho et al 2015).…”