Complete chloroplast genomes of Desmidorchis penicillata (Deflers) Plowes and Desmidorchis retrospiciens Ehrenb: Comparative and phylogenetic analyses among subtribe Stapeliinae (Ceropegieae, Asclepiadoideae, Apocynaceae)

The succulent shrubs Desmidorchis penicillata and D. retrospiciens, part
of the taxonomically challenging genus Desmidorchis, are well-known for
their ecological resilience and medicinal significance. This study
sequences the first complete chloroplast genomes of these species,
shedding light on their genomic characteristics and evolutionary
relationships. The circular genomes of D. penicillata (161,776 bp) and D.
retrospiciens (162,277 bp) display a quadripartite structure typical of
angiosperms. Gene content, order, and GC content are consistent, featuring
114 unique genes, including 80 protein-coding, 30 transfer RNAs, and four
ribosomal RNAs genes. Codon usage analysis underscores A/U-rich
preferences, while RNA editing sites, predominantly in ndhB and ndhD
genes, suggest post-transcriptional modifications. Analysis of long
repeated sequences reveals a predominance of forward and palindromic
repeats. Simple sequence repeats (SSRs), particularly A/T motifs, are
abundant, with high presence of mononucleotide, offering potential
molecular markers. Comparative analysis with their relatives in subtribe
Stapeliinae identifies mutational hotspots such as ycf1, ndhF,
trnG(GCC)-trnfM(CGA) and ndhG-ndhI that could be potential DNA barcoding
markers. The inverted repeat (IR) boundaries analysis revealed an
expansion of IR on the small single copy region, leading to the formation
of a pseudogene. Overall, substitution rate analysis indicated purifying
selection, with a few genes (rpl22, clpP and rps11) showing signatures of
positive selection. Additionally, the phylogenetic analysis positioned
Desmidorchis within the Stapeliinae clade and strongly supported the
sister relationship between D. penicillata and D. retrospiciens. This
study provides comprehensive molecular data for future research in
Desmidorchis.