DOI: 10.5061/dryad.qrfj6q5rc
title: Complete chloroplast genomes of Desmidorchis penicillata (Deflers) Plowes and Desmidorchis retrospiciens Ehrenb: Comparative and phylogenetic analyses among subtribe Stapeliinae (Ceropegieae, Asclepiadoideae, Apocynaceae)

description: 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.
description: # Complete chloroplast genomes of Desmidorchis penicillata (Deflers)
 Plowes and Desmidorchis retrospiciens Ehrenb: Comparative and phylogenetic
 analyses among subtribe Stapeliinae (Ceropegieae, Asclepiadoideae,
 Apocynaceae)
 [https://doi.org/10.5061/dryad.qrfj6q5rc](https://doi.org/10.5061/dryad.qrfj6q5rc) ## Description of the data and file structure ### Files and variables #### File: Ceropegieae\_Data\_matrix.fas **Description:** FASTA format file containing aligned sequences of the 77 protein-coding genes from from 11 chloroplast genomes representing the entire Ceropegieae tribe, which includes the subtribes Anisotominae, Heterostemminae, Leptadeniinae, and Stapeliinae. In addition, three genomes from tribe Marsdenieae serve as outgroup taxa. This matrix was used for phylogenetic analyses to elucidate the phylogenetic placement of *Desmidorchis penicillatus and D. retrospiciens* within subtribe Stapeliinae and tribe Ceropegieae. The dataset was constructed using genomic sequences generated in this study and sourced from GenBank (see supporting information Table S1 for details) and is intended for comparative genomics and evolutionary studies. ## Sharing/Access Information Links to other publicly accessible locations of the data: * [GenBank Sequence Data](https://www.ncbi.nlm.nih.gov/genbank/) ## Code/Software * **Alignment software**: MUSCLE V.3.8.4 (Edgar, 2004), used for sequence alignment within Geneious Prime® (Kearse et al., 2012). * **Phylogenetic analysis tools**: RAxML V.8.2.12 for Maximum Likelihood analysis and MrBayes V.3.2.7 for Bayesian Inference. * **Visualization software**: iTOL V.6.5.8 for tree annotation and visualization. The genes were individually aligned using default parameters in MUSCLE and concatenated into a single matrix. This matrix is ready for phylogenetic analyses, as conducted using Maximum Likelihood (ML) and Bayesian Inference (BI) methods. For those interested in reproducing the analyses, we recommend using the same versions of software and parameters as mentioned above.