Complete Chloroplast Genomes of Four Triumfetta Species from Herbarium Specimens: Comparative Analysis and Identification of a Synapomorphic Inversion

The genus Triumfetta L. (Malvaceae) includes about 177 species, including some medicinal species. However, genomic resources for the genus remain limited, with only ten chloroplast (cp) genomes published to date. We sequenced and de novo assembled complete cp genomes for four Triumfetta species (Triumfetta annua L., Triumfetta cordifolia A.Rich., Triumfetta lappula L., and Triumfetta rhomboidea Jacq.) using the Illumina NovaSeq 6000 platform. Our aims were to characterize their cp genome features, perform comparative analyses with reported species, identify polymorphic loci, and reconstruct a preliminary phylogeny. The cp genomes displayed the typical quadripartite structure, ranging from 159,245 to 160,604 bp, and contained 112 unique genes (78 protein-coding, 30 tRNA, and 4 rRNA). Comparative analysis revealed a six-gene synapomorphic inversion (trnC, petN, psbM, trnD, trnY, and trnE) in the large single-copy region. Codon usage analysis revealed a strong bias toward A/T-ending codons (RSCU > 1). Leucine was the most abundant amino acid, while cysteine was the least abundant. Simple sequence repeat analysis identified 63–81 repeats, with a predominance of mononucleotide A/T repeats. Nucleotide substitution analysis revealed a transition bias across all regions (Ts/Tv > 1), most pronounced in the LSC (Ts/Tv = 1.29–1.35). Five highly polymorphic regions were identified as potential DNA barcoding candidates, including rpl33-rps18, trnH-psbA, ccsA-ndhD, trnL-ccsA, and ndhD-psaC. This study provides genomic resources for Triumfetta taxonomy, highlighting key structural variations and identifying molecular markers with potential applications in taxonomic research. These findings provide valuable phylogenetic markers for future systematic and conservation studies.