Complete chloroplast genomes of four Triumfetta species obtained from herbarium specimens: comparative analysis and identification of a synapomorphic inversion

The genus Triumfetta L. (Malvaceae) comprises about 177 species, several of which are of medicinal importance. However, genomic resources for this genus remain limited, with only ten chloroplast (cp.) genomes published to date. Here, we report the sequencing and de novo assembly of 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 objectives were to characterize cp. genome features, conduct comparative analyses with previously reported species, identify polymorphic loci, and reconstruct a preliminary phylogeny. The cp. genomes exhibited 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 (LSC) 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). Seven highly polymorphic loci were identified as potential DNA barcoding candidates, including two intergenic spacers (trnL-ccsA, ndhD-psaC), and five coding regions (clpP, rpl22, ycf1, rpl23, and ndhI). This study provides genomic resources for Triumfetta taxonomy, highlighting key structural variations and identifying molecular markers with potential applications in taxonomic research.