Comparative chloroplast genome analysis and phylogenomics of Nigerian Aframomum (Zingiberaceae): insights into chloroplast genome evolution and species divergence.

BACKGROUND: Aframomum is a genus of ecologically and economically important plants in the Zingiberaceae family, yet its genomic evolution remains poorly understood. Previous chloroplast genome studies in the family have focused mainly on Asian genera such as Alpinia and Amomum, leaving the African lineage unexplored. METHODS: This study presents a comparative analysis of the complete chloroplast genomes of five Aframomum species, including A. alboviolaceum, A. angustifolium, A. daniellii, A. melegueta, and A. sceptrum. High-throughput Illumina sequencing was used to assemble the chloroplast genomes, which were annotated and analyzed for structural features, sequence divergence, codon usage, simple sequence repeats (SSRs), long repeats, and selection pressure on protein-coding genes. Phylogenetic relationships and divergence times were inferred using Bayesian methods implemented in MrBayes and BEAST2, respectively. RESULTS: All five chloroplast genomes exhibited a conserved quadripartite structure with genome sizes ranging from 161,101 bp to 166,130 bp, but displayed lineage-specific variation at inverted repeat/single-copy boundaries, particularly the expanded ycf1 and rps19 gene junctions in A. alboviolaceum. Comparative analyses revealed high sequence conservation, with notable divergence hotspots in non-coding regions, including ycf1-rps15, atpH-atpI, and trnT-trnL. Codon usage patterns indicated strong AT-bias, and selection analyses revealed that most genes are under purifying selection, whereas ycf1, rpoC2, and rpl16 show signals of positive selection, suggesting adaptive evolution in photosynthetic and translational functions. SSR analysis revealed predominantly A/T-rich mononucleotide repeats, with slight interspecific variation. Phylogenomic analysis strongly supported the monophyly of Aframomum and its close relationship to Amomum. Divergence time estimation indicates that Aframomum began diversifying around 26 Mya, with major radiation during the Miocene, contemporaneous with the African climatic shift that likely drove speciation. CONCLUSIONS: This study provides valuable insights into the chloroplast genome evolution and phylogeny of Aframomum, highlighting regions of high variability that are potential targets for molecular marker development. The results also reinforce the utility of chloroplast genome data in resolving evolutionary relationships and estimating divergence times within Zingiberaceae.