Chloroplast Genomes of Four <i>Triumfetta</i> Species: Comparative Analysis and a Synapomorphic Inversion

The genus <i>Triumfetta</i> L. (Malvaceae) comprises approximately 177 species, several with medicinal properties. However, only ten chloroplast (cp) genomes have been published for this genus. We sequenced and <i>de novo</i> assembled complete cp genomes for four <i>Triumfetta</i> species (<i>Triumfetta annua</i> L., <i>Triumfetta cordifolia</i> A.Rich., <i>Triumfetta lappula</i> L., and <i>Triumfetta rhomboidea</i> Jacq.) using the Illumina NovaSeq 6000 platform. Our aims were to characterize their cp genome features, perform comparative analyses with previously published 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 in the large single-copy region comprising <i>trnC</i>, <i>petN</i>, <i>psbM</i>, <i>trnD</i>, <i>trnY</i>, and <i>trnE</i>. Codon usage analysis revealed a strong bias toward A/T-ending codons (RSCU &gt; 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 &gt; 1), most pronounced in the LSC (Ts/Tv = 1.29--1.35). Five highly polymorphic regions were identified as potential DNA barcoding candidates, including <i>rpl33-rps18</i>, <i>trnH-psbA</i>, <i>ccsA-ndhD</i>, <i>trnL-ccsA</i> and <i>ndhD-psaC</i>. This study provides genomic resources for <i>Triumfetta</i> 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.