Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships

Xumei Wang,Guoqing Bai,Tao Zhou,Yuemei Zhao

doi:10.1038/s41598-018-30398-6

Xumei Wang, Guoqing Bai + Show 2 more

Open Access

https://doi.org/10.1038/s41598-018-30398-6

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Abstract

Fagopyrum dibotrys, belongs to Polygonaceae family, is one of national key conserved wild plants of China with important medicinal and economic values. Here, the complete chloroplast (cp) genome sequence of F. dibotrys is reported. The cp genome size is 159,919 bp with a typical quadripartite structure and consisting of a pair of inverted repeat regions (30,738 bp) separated by large single copy region (85,134 bp) and small single copy region (13,309 bp). Sequencing analyses indicated that the cp genome encodes 131 genes, including 80 protein-coding genes, 28 tRNA genes and 4 rRNA genes. The genome structure, gene order and codon usage are typical of angiosperm cp genomes. We also identified 48 simple sequence repeats (SSR) loci, fewer of them are distributed in the protein-coding sequences compared to the noncoding regions. Comparison of F. dibotrys cp genome to other Polygonaceae cp genomes indicated the inverted repeats (IRs) and coding regions were more conserved than single copy and noncoding regions, and several variation hotspots were detected. Coding gene sequence divergence analyses indicated that five genes (ndhK, petL rpoC2, ycf1, ycf2) were subject to positive selection. Phylogenetic analysis among 42 species based on cp genomes and 50 protein-coding genes indicated a close relationship between F. dibotrys and F. tataricum. In summary, the complete cp genome sequence of F. dibotrys reported in this study will provide useful plastid genomic resources for population genetics and pave the way for resolving phylogenetic relationships of order Caryophyllales.

Highlights

Fagopyrum dibotrys, belongs to Polygonaceae family, is one of national key conserved wild plants of China with important medicinal and economic values
The complete cp genome of F. dibotrys was 159,919 bp in length and contained a pair of inverted repeats (IRs) (30,738 bp) which were separated by a small single copy (SSC) region (13,309 bp) and a large single copy (LSC) region (85,134 bp) (Fig. 1)
We found that all Fagopyrum species formed one monophyletic clade along with three Rumiceae species, and F. dibotrys was related to F. tataricum, as in the phylogeny reported by Zhou et al.[54] using ITS and matK

Summary

Introduction

Belongs to Polygonaceae family, is one of national key conserved wild plants of China with important medicinal and economic values. The complete cp genome sequence of F. dibotrys reported in this study will provide useful plastid genomic resources for population genetics and pave the way for resolving phylogenetic relationships of order Caryophyllales. The angiosperm chloroplast (cp) genome is more conserved than the nuclear and mitochondrial genome; typically its structure is quadripartite, containing a pair of inverted repeats (IRs), a large single-copy (LSC) region, and a small single-copy (SSC) region[1]. Combined with high costs of traditional Sanger sequencing, only a small portion of the cp genomes were obtained, which are insufficient for determining evolutionary relationships and applying on plant phylogenetic and genomic studies. F. dibotrys has been designated as a national key conserved wild plant of China by the State Council of Traditional Chinese Medicine and listed in the National Important Wild Conservation Plants in China[13]

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