Complete chloroplast genome sequences of Dipterygium glaucum and Cleome chrysantha and other Cleomaceae Species, comparative analysis and phylogenetic relationships

Abstract

This current study presents, for the first time, the complete chloroplast genome of two Cleomaceae species: Dipterygium glaucum and Cleome chrysantha in order to evaluate the evolutionary relationship. The cp genome is 158,576 bp in length with 35.74% GC content in D. glaucum and 158,111 bp with 35.96% GC in C. chrysantha . Inverted repeats IR 26,209 bp, 26,251 bp each, LSC of 87,738 bp, 87,184 bp and SSC of 18,420 bp, 18,425 bp respectively. There are 136 genes in the genome, which includes 80 protein coding genes, 31 tRNA genes and four rRNA genes were observed in both chloroplast genomes. 117 genes are unique while the remaining 19 genes are duplicated in IR regions. The analysis of repeats shows that the cp genome includes all types of repeats with more frequent occurrences of palindromic; Also, this analysis indicates that the total number of simple sequence repeats (SSR) were 323 in D. glaucum , and 313 in C. chrysantha , of which the majority of the SSRs in these plastid genomes were mononucleotide repeats A/T which are located in the intergenic spacer. Moreover, the comparative analysis of the four cp sequences revealed four hotspot genes ( atpF, rpoC2, rps19 , and ycf1 ), these variable regions could be used as molecular makers for the species authentication as well as resources for inferring phylogenetic relationships of the species. All the relationships in the phylogenetic tree are with high support, this indicate that the complete chloroplast genome is a useful data for inferring phylogenetic relationship within the Cleomaceae and other families. The simple sequence repeats identified will be useful for identification, genetic diversity, and other evolutionary studies of the species. This study reported the first cp genome of the genus Dipterygium and Cleome . The finding of this study will be beneficial for biological disciplines such as evolutionary and genetic diversity studies of the species within the core Cleomaceae.

Gene Losses and Plastome Degradation in the Hemiparasitic Species Plicosepalus acaciae and Plicosepalus curviflorus: Comparative Analyses and Phylogenetic Relationships among Santalales Members

“…acaciae and P . curviflorus plastomes, while the remaining genes presented only one intron, which is consistent with previous reports in the chloroplast genome Macrosolen (Santalales) [ 31 ] and other cp genomes of angiosperms [ 32 , 33 ].…”

“…curviflorus , respectively. Similar results were reported in the chloroplast genomes of the order Santalales [ 31 ], as well in some species of angiosperms [ 32 , 33 ]. The results obtained from the present study show that in the plastid genome of P .…”

“…The plastome consists of many highly efficient genes capable of resolving phylogenetic issues at different levels of angiosperm taxonomy [ 33 , 57 , 58 , 59 ]. In this study, we found that P .…”

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

“…These similarities in codon choice also reveal the related relationship in the four species. The observed codon pattern is consistent with the CP genomes of Amomum [68], Panax [69], Dipterygium and Cleome [70], and various other species [71][72][73].…”

Comparative analysis of chloroplast genomes reveals phylogenetic relationships and intraspecific variation in the medicinal plant Isodon rubescens

“…Chloroplast DAN sequences are often used in phylogenetic studies and to measure the genetic diversity within a species [ 43 ]. Previous studies have shown that I .…”