Characterization of the complete plastome of Dysphania botrys, a candidate plant for cancer treatment

Abstract

Dysphania botrys belongs to Amaranthaceae and distributes in North Europe, Asia, and North America. It is a medicinal plant with diuretic, antispasmodic, carminative, antidiarrhoeic properties, and a candidate plant for cancer treatment. However, few studies focused on its phylogeny, and its taxonomic status is still controversial. To better understand the evolution of this species, the complete plastome of D. botrys was obtained by next-generation sequencing. It is the first plastome to be sequenced and reported in the genus Dysphania. The plastome is 152,055 bp in length, which consists of a large single-copy region (LSC, 83,769 bp; GC content: 34.7%), a small single-copy region (SSC, 17,916 bp; GC content: 30.1%), and a pair of inverted repeat regions (IRs, 25,185 bp; GC content: 42.7%). It harbors 112 unique genes, including 78 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes with an overall G þ C content of 36.8%. The phylogeny of Amaranthaceae based on the complete plastome sequences of 13 taxa showed that D. botrys belong to subfamily Chenopodioideae. Chenopodioideae, together with Betoideae formed a sister clade to the three subfamilies (Salicornioideae, Suaedoideae, and Salsoloideae), and this sister clade formed an evolutionary sister clade to Amaranthoideae. Our data will largely enrich the genetic information of Dysphania botrys and facilitate future studies on its evolutionary status.

Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives

“…The Caryophyllales, including B. vulgaris, contain canonical plastomes, harboring all hallmarks typical for angiosperm plastome sequences as described above [25,26]. For the wild beet species, until now, no plastome assembly is available, and of our investigated species, only the plastome sequence of B. vulgaris subsp.…”

Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives

“…Reasons for this may be recent species hybridization or incomplete lineage sorting (36,37). Therefore, the mitogenome seems to be mostly useful at higher taxonomic levels (25) and might not be the most suitable system for the beet and wild beet accessions investigated in this study.…”

“…Differences between the phylogenetic trees derived from different strategies and datasets (Figure 4C) may be explained by chance and/or by the use of the method (all splitstree results show high identities as indicated by all comparison metrics (Additional file S1D) while differences are larger when using different strategies [reads vs assemblies] in comparison to different datasets [chloroplasts vs. mitochondria]) or by real differences in the biological nature of mitochondria and chloroplasts. Mitochondrial DNA shows a low nucleotide substitution rate when compared to chloroplast DNA (25,35). Reasons for this may be recent species hybridization or incomplete lineage sorting (36,37).…”

“…II) An approach based on high-quality single-copy nuclear genes would require a minimum coverage of about 10x (25). Moreover, nuclear genes are often part of gene families and influenced by whole genome duplication events (14).…”

The complete chloroplast genome of Atriplex gmelinii C. A. Mey. ex Bong. (Amaranthaceae)

“… 2019a , 2019b ; Park et al. 2021 ), with the exception of Dysphania botrys (L.) Mosyakin & Clemants_2002, which has 83 genes (Chen and Yang 2018 ) and one Chenopodium album L._1753 (MF418659), which has 89 genes (Jashmi and Biseshwori 2017 ). The C. album (MF418659) may have been misidentified due to a different configuration from the rest of C. album (Park et al.…”