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

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.

Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

“…We speculate that relaxed neutral selection (Ka/Ks value around 1.0) and potential positive selection (Ka/Ks value greater than 1.0) of rpl23 , rpl36 , and rps7 in various species here reflects the highly diverse environments and adaptions of plants (Table S4). For gene ycf1 , it is one of the largest genes in chloroplast genome and usually has two functional copies [22,25], or one of the two copies was evolved to be a pseudogene in some plants [19,31–33] as well as in 11 mangroves ( Avicennia marina , Xylocarpus moluccensis , Hibiscus tiliaceus , Excoecaria agallocha , Bruguiera sexangula , Kandelia obovata , Rhizophora stylosa , Ceriops tagal , Sonneratia ovata , Pemphis acidula , Laguncularia racemose ). In this study, most species in Malpighiales including one mangrove Excoecaria agallocha , have ycf1 Ka/Ks values around or greater than 1.0, while about 0.4 in Malvales, Myrtales and Sapindales, and about 0.6 in Fabales and Lamiales, showing the diverse evolve rates in different species (Table S4, Figure 4).…”

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

“…This is likely to be due to the fact that the chloroplast genome does not contain enough information to attract researchers comparing with whole genome sequences. However, chloroplast genomes are occasionally useful for unravelling corresponding phylogenetic relationships based on the maternal lineage: e.g., Lindera genus [ 13 ], Fagopyrum genus [ 14 ], Potentilla genus [ 15 – 21 ], Pseudostellaria genus [ 22 – 26 ], and Dysphania genus [ 27 – 30 ]. Moreover, several studies that described assembled organelle genomes from NGS raw sequences generated with different purposes have been conducted [ 31 , 32 ].…”

Palyno‐morphological investigations of halophytic taxa of Amaranthaceae through SEM from Salt range of Northern Punjab, Pakistan

“…In past, some researchers included chenopodiaceae in the wider circumscription of Amaranthaceae and some authors have represented monophyly in their molecular studies in these families (Cuénoud et al, ; Judd, Campbell, Kellogg, Stevens, & Donoghue, ). The previous morphological and phylogenetic research revealed that Amaranthaceae and Chenopodiaceae had long been considered a single evolutionary lineage and were closely related families (Wang, Zhou, Bai, & Zhao, ). The AGP IV system in 2016 placed the family Amaranthaceae in order Caryophyllales and includes the plant species previously treated as family Chenopodiaceae.…”