Abstract
BackgroundMajority 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.ResultsThe 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.ConclusionBesides 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.
Highlights
Majority of the species within Senecioneae are classified in Senecio, making it the tribe’s largest genus
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
Eighteen genes were duplicated in the inverted repeat (IR) regions, with rps12 being uniquely positioned with its 5′ end exon at the large single copy (LSC) and the other is located in the IR regions
Summary
Majority of the species within Senecioneae are classified in Senecio, making it the tribe’s largest genus. The tribe is prominent for its size, and rich morphological and ecological diversity. It is mostly dominated by annual and perennial herbs, while the rest constitute shrubs, vines, trees, and epiphytes. It has a near cosmopolitan distribution, with southern Africa being one of its key diversity hotspot zones (Pelser et al 2007). Majority of the species in the tribe are placed in Senecio L., making it one of the largest genera of angiosperms, with over 1250 species (Nordenstam et al 2009). Its members are generally distinguished by style branches truncate with short sweeping hairs, separated stigmatic lines and sometimes with a median hair pencil, and with ecaudate anther bases and balusterform filament collar (Nordenstam 2007; Pelser et al 2007)
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