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Genetic Divergence and Phylogenetic Relationships of Catharanthus roseus Cultivars: Insights from Chloroplast Genomic Analysis and DNA Barcoding
Abstract
Context: This investigation elucidates the genetic heterogeneity and phylogenetic affinities among eight cultivars of Catharanthus roseus, with particular emphasis on petal color and morphological variations. Aims: The primary objective is to elucidate the genetic disparities and evolutionary trajectories among these cultivars, thereby augmenting our comprehension of their genomic architecture and phylogenetic lineages. Methods: The genomic DNA of the cultivars underwent sequencing, assembly, and annotation utilizing sophisticated bioinformatic tools such as NOVOPlasty and GeSeq. Subsequent sequence alignment was executed using the MAFFT (Multiple Alignment using Fast Fourier Transform) algorithm to facilitate a comparative analysis. Key Results: The results revealed minimal plastome size variation among cultivars, ranging from 154,928 bp to 155,066 bp. Notably, Group 1 cultivars (coded 1, 6, and 8) exhibited elongated, flatter petals, while Group 2 cultivars (coded 2, 3, 4, 5, and 7) displayed broader, more orbicular petals. Sequence-based analysis unveiled significant variations in photosynthesis-related genes, revealing distinct single nucleotide polymorphism (SNP) frequencies and insertion/deletion (Indel) patterns between the two groups. Codon usage analysis did not identify significant discrepancies, suggesting that chloroplast-derived codon usage is not a reliable speciation marker in this context. While simple sequence repeat (SSR) biomarkers displayed variability, they did not provide substantive insights into the speciation process. Phylogenetic relationships were elucidated through DNA barcoding and analysis of key plastid markers such as matK, rbcL, and trnL. The trnL gene demonstrated superior efficacy in clustering cultivars based on petal morphology. Phylogenetic trees constructed from these markers revealed close genetic relationships within the same tribe, while C. roseus exhibited genetic distinctiveness from other species within its tribe and family. Conclusions: This study provides comprehensive chloroplast genome assemblies for C. roseus cultivars, significantly advancing our understanding of their genetic diversity and phylogenetic relationships. Implications: The findings enhance our comprehension of speciation mechanisms within the Apocynaceae family and offer important insights for the refinement of taxonomic frameworks. By providing more accurate species delineation, this work contributes to a deeper evolutionary perspective on the diversification of C. roseus and related species
CP24363 Accepted 08 January 2025
© CSIRO 2025
