Genome size estimation, chloroplast genome characterization, and comparative analysis of Opuntia ficus-indica and O. pubescens reveal phylogenetic relationships within the genus Opuntia

Abstract

The genus Opuntia has great ecological and socioeconomic relevance, but its chloroplast genomes exhibit high evolutionary dynamism that generates phylogenetic inconsistencies. This study estimates the genome size and compared the complete chloroplast genomes of O. ficus-indica and O. pubescens to clarify their structure and evolutionary position. DNA was sequenced using the Illumina NovaSeq 6000 platform for de novo and guided assembly and annotation. Structural comparisons, sequence repeats, and codon usage bias were evaluated across 18 species, and a phylogenetic reconstruction of 37 species was performed using Maximum Likelihood, Maximum Parsimony, and Bayesian inference. The plastomes have lengths of 152,730 bp and 150,927 bp, containing 139 and 137 genes, respectively. Four types of structural rearrangements with a low degree of conservation were identified, driven by contractions in the inverted repeat regions. Additionally, abundant repeated sequences and a highly conserved codon usage bias were found. Phylogenetically, O. ficus-indica clustered within the Basilares clade and O. pubescens in the Nopalea clade. These findings evidence the marked evolutionary dynamism in Opuntia and provide valuable chloroplast genomic data for future research on genetic diversity and speciation.