Complete chloroplast genomes of Desmidorchis penicillata (Deflers) Plowes and Desmidorchis retrospiciens Ehrenb: Comparative and phylogenetic analyses among subtribe Stapeliinae (Ceropegieae, Asclepiadoideae, Apocynaceae)
Data files
Sep 12, 2024 version files 1.04 MB
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Ceropegieae_Data_matrix.fas
1.04 MB
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README.md
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Abstract
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.
README: 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
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:
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.