Plastome evidence repositions Abelmoschus ficulneus as a close relative of cultivated okra (Abelmoschus esculentus, Malvaceae)

Abstract

Introduction The genus Abelmoschus (Malvaceae) includes cultivated okra (A. esculentus), yet its phylogenetic relationships remain unresolved using limited molecular markers. Methods In this study, complete chloroplast genomes of A. esculentus and the first complete plastome of A. ficulneus were assembled and analyzed together with published plastomes of three additional Abelmoschus species and Hibiscus rosasinensis as an outgroup Results and Discussion Plastome sizes ranged from 163, 119 to 163, 503 bp, with conserved quadripartite structures and GC content (~36.7%). A total of 751 and 755 simple sequence repeats (SSRs) were identified in AE12 and AF01, respectively, with hexanucleotide repeats as the dominant class (~25%) and a consistent enrichment in the LSC region (~62–64%). Codon usage analysis of 64 codons revealed a conserved bias toward A/U-ending codons, with no substantial interspecific variation. IR boundary analysis identified a genus-specific feature, with rps3 consistently located within IR regions in Abelmoschus, in contrast to rpl2 in Hibiscus. Polymorphism analysis across 271 genomic regions identified nine hypervariable loci, all exhibiting five haplotypes (Hap = 5) and maximum haplotype diversity (Hd = 1). Nucleotide diversity was low overall (mean p = 0.00116). Phylogenetic reconstruction based on complete plastomes resolved two strongly supported clades (SH-like ≥ 0.99) and consistently placed A. ficulneus with A. esculentus. Hypervariable loci including ycf1, trnK–rps16, atpH–atpI, ndhF, and ndhF–rpl32 reproduced the full plastome topology. These results provide plastome-scale evidence refining the phylogenetic placement of A. ficulneus and identify validated loci for molecular marker development within Abelmoschus.