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Background  Majority of the species within Senecioneae are classified in  Senecio , making it the tribe’s largest genus. Certain intergeneric relationships within the tribe are vaguely defined, with the genus  Senecio  being partly linked to this ambiguity. Infrageneric relationships within  Senecio  remain largely unknown and consequently, the genus has undergone continuous expansion and contraction over the recent past due to addition and removal of taxa.  Dendrosenecio , an endemic genus in Africa, is one of its segregate genera. To heighten the understanding of species divergence and phylogeny within the tribe, the complete chloroplast genomes of the first five  Senecio  and six  Dendrosenecio  species were sequenced and analyzed in this study.    Results  The entire length of the complete chloroplast genomes was ~ 150 kb and ~ 151 kb in  Dendrosenecio  and  Senecio  respectively. Characterization of the 11 chloroplast genomes revealed a significant degree of similarity particularly in their organization, gene content, repetitive sequence composition and patterns of codon usage. The chloroplast genomes encoded an equal number of unique genes out of which 80 were protein-coding genes, 30 transfer ribonucleic acid, and four ribosomal ribonucleic acid genes. Based on comparative sequence analyses, the level of divergence was lower in  Dendrosenecio . A total of 331 and 340 microsatellites were detected in  Senecio  and  Dendrosenecio,  respectively. Out of which, 25 and five chloroplast microsatellites (cpSSR) were identified as potentially valuable molecular markers. Also, through whole chloroplast genome comparisons and DNA polymorphism tests, ten divergent hotspots were identified. Potential primers were designed creating genomic tools to further molecular studies within the tribe. Intergeneric relationships within the tribe were firmly resolved using genome-scale dataset in partitioned and unpartitioned schemes. Two main clades, corresponding to two subtribes within the Senecioneae, were formed with the genus  Ligularia  forming a single clade while the other had  Dendrosenecio, Pericallis, Senecio  and  Jacobaea . A sister relationship was revealed between  Dendrosenecio  and  Pericallis  whereas  Senecio,  and  Jacobaea  were closely placed in a different clade.    Conclusion  Besides emphasizing on the potential of chloroplast genome data in resolving intergeneric relationships within Senecioneae, this study provides genomic resources to facilitate species identification and phylogenetic reconstructions within the respective genera.    Electronic supplementary material  The online version of this article (10.1186/s40529-019-0265-y) contains supplementary material, which is available to authorized users.

Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics