Chloroplast genomes of six Aloe species: Insights into genetic variation and evolutionary patterns

Aloe is a highly diverse genus of succulent plants with important pharmacological, medicinal, and commercial importance. However, the limited availability of genomic resources has constrained evolutionary and comparative genomics studies of this genus. To address this problem, we sequenced and assembled the first comprehensive chloroplast genome sequences of six Aloe species (Aloe barberae, Aloe excelsa, Aloe marlothii, Aloe perfoliata, Aloe glauca, and Aloe tenuifolia) using a high-throughput whole-genome sequencing approach. The total length of the assembled chloroplast genomes varied from 152,383 to 154,127 bp, exhibiting a conserved quadripartite structure comprising 131 genes. Comparative genomic analyses revealed the loss of the rpl32 and infA genes across all the sampled species except for Aloe arborescens, suggesting lineage-specific gene retention. Furthermore, we identified eight protein-coding genes under positive selection and five intergenic regions with significant variability, which hold potential for molecular species identification (DNA barcoding) and phylogenetic studies. Phylogenetic reconstruction revealed robust branch support values, validating the monophyletic status of the Aloe genus and updating the sister clade of Aloe vera, which was previously close to Aloe maculata. These findings offer insights into genetic variation, gene loss, and potential evolutionary patterns, contributing to future phylogenetic and conservation research.