<div>Background: Comparative study of the complete chloroplast genomes of some species in the Subtribe Asclepiadeae was conducted to evaluate the variations and similarities between the species and to resolve the phylogenetic relationship within the subtribe. P. tomentosa has been used for medicinal uses in Saudi Arabia, Middle East, Africa and Brazil. It is used often in cosmetics and tanning industries, although it&rsquo;s very well utilized as a traditional medicine in many civilizations. 
 
Methods: The genomes were compared using Mvista Bioinformatics tools to evaluate the inverted repeats (IR), large single copy (LSC) and small single copy (SSC) regions and also the border junctions were visualized with IR scope to express the expansion and contraction of the circular genome structure. While SSR markers were determined using the Reputer program, the genome map was done using OGDRAW (OrganellarGenomeDRAW). 
 
Result: Observed variations of the Mvista alignments is mainly at the coding regions of the sequences, while IR borders were varied at the SSC region of A. nivea genome; with ycf1 and rps19 due to evolutionary events. The genome sizes of C. procera are 166,010 bp, P. tomentosa 164,213bp, A. nivea 161,592 bp and C. wilfordii 161,180 bp. GC contents of A. nivea, C. wilfordii and P. tomentosa are 38% respectively; while C. procera is the least with 37%.; total SSR markers as well as the circular genome map were presented in this study.</div>

Comparative Chloroplast Genome Analysis and Evolutionary Relationships in Some Species of Asclepiadeae, Apocynaceae