Comparative Analysis Of Chloroplast Genomes Of Five Senecio Species From Mount Kenya

The genus Senecio is composed of nearly cosmopolitan species with the Antarctica being the only region where they are absent.The genus has a number of economically important species including some infamous weeds and others that contain toxic bioactive substances due to the presence of pyrrolizidine alkaloids.In Kenya,there are a number of Senecio species which have shown great diversity in Mount Kenya region although other species have been distributed in other mountains in the country.A large number of species coupled with complex and diverse life history and morphology have greatly impacted taxonomic and evolutionary studies in this genus.The study of Senecio is an opening to determine the evolutionary relationship of the species,especially in Mt Kenya region since it has great diversity and habitat of the majority of the Senecio species while in China,it contributes to the database of the molecular research among the Senecio species.Therefore,the complete chloroplast genome was aimed at analyzing the genome features and phylogeny to evaluate the evolutionary relationships among the species.We also aimed at analyzing the formation of microsatellite markers which is an essential guide in determining the appropriate species for intraspecific microsatellite marker formation.The phylogenetic analysis was aimed at determining the evolutionary relationships among the Senecio species with reference to other closely related species in the genus Senecio.This study employed high throughput sequencing technology to sequence the first complete plastid genomes of five species of Senecio.We also employed the use of other bioinformatic tools such as the genome annotation using an online program Dual Organellar Genome Annotator for annotation,sequences alignment with Mauve software,Predictive RNA editors for plants for RNA editing,MIcroSAtellite identification tool for the analysis of microsatellites and phylogenetic analysis was conducted with RAxML.The chloroplast genomes of the Senecio species showed no remarkable difference in sene contents and organization.However,the entire chloroplast genome sizes were observed ranging from 151,191 bp(Senecio purtschelleri)to 151,413 bp(Senecio keniophytuw).Each of the genomes contained a total of 87 protein-coding genes,8 rRNA genes,and 34 tRNA genes.The highest frequency of intraspecific microsatellite markers was recorded in Senecio keniophytum and Senecio roseiflorns.The phylogenetic analysis resulted in a cluster of the five Senecio species with Jacobaea vulgaris as the closest relative based on the sampled taxa,confirming the potential of complete genome sequence data to carry out further evolutionary analysis at all taxonomic levels within the Asteraceae family.The highest divergence hotspots were realized in the intergeneric regions then followed by the coding regions.Microsatellites developed during the analysis are important for the more hybridization studies in the genus.In conclusion,we noted that some Senecio species are related to one another genetically despite the morphological differences observed among the species.For instance,the genome structure with similar gene arrangements was observed to be the same among all the five Senecio species.These differences were concluded to have risen from the mutational changes among the species which was later observed during the analysis of editing sites among the Senecio species.The sequence data generated in this study will provide the much-needed resources for future molecular studies within the genus which will be an important guide in ex-situ conservation of the species.There is a need for further studies of the evolutionary relationships among the Senecio species since only a few representative species were used in our study.We also recommended for further hybridization studies for the Senecio species in Mount Kenya in the future studies.