Complete chloroplast genome of African Baobab (Adansonia digitata L.): structural characterization, comparative genomics, and phylogenetic placement within Malvaceae

Abstract

Chloroplast genomes are invaluable resources for plant genomic research, providing insights into genome evolution and molecular adaptation. With the growing scientific and economic interest in Adansonia digitata, a comprehensive characterization of its chloroplast is timely and necessary. A complete chloroplast genome of A. digitata was assembled, annotated, and characterized. Comparative structural analysis was conducted against other Adansonia species, and the assembly was validated through phylogenetic placement within Malvaceae. The assembled genome exhibits the canonical quadripartite organization, spanning 160,061 bp with a GC content of 36.88%, 79 protein-coding genes, 32 tRNAs, and 4 rRNAs. Repeat analysis identified 100 simple sequence repeat motifs, predominantly A/T-rich mononucleotide types (76%), alongside 50 long sequence repeats dominated by forward (26) and palindromic (17) repeats. Comparative analysis with other Adansonia species revealed conserved genome structure, with minor IR boundary shifts involving the ndhF gene, and ycf1 duplication in A. gregorii and A. grandidieri. Average nucleotide identity exceeded 99% across all Adansonia species, with near-complete similarity (ANI {approx} 99.96%) observed with the putative A. kilima. All predicted RNA editing events were nonsynonymous, dominated by C[->]U conversions (55.02%). Codon usage showed non-random synonymous preferences biased toward A/U-ending codons, driven primarily by mutational pressure with detectable gene-specific translational selection. Nucleotide diversity ({pi}) was higher in intergenic spacers (0.00490 {+/-} 0.00574) than in coding regions (0.00167 {+/-} 0.00199), with the majority of genomic regions showing no sequence variation ({pi} = 0). Substitution patterns indicated pervasive purifying selection, with relatively high but insignificant signals in matK, ycf1, accD, and rpoB. Phylogenomic analyses placed the assembled A. digitata chloroplast genome within the Adansonia lineage, consistent with its established systematic position. This study provides detailed insight into the chloroplast genome of A. digitata, and the findings will contribute towards advancing its genomic research.