Plastome evolution and phylogenomic insights from representative taxa across all nine subfamilies of Malvaceae.

Comparative plastome analysis and plastomic phylogeny of Moraceae with expanded species-level sampling.

Phylogenetic reconstruction based on complete plastome sequences strongly supported the monophyly of all seven recognized tribes of Moraceae, recovered the non-monophyly of Streblus, and placed Maclura within Chlorophoreae, consistent with recent nuclear and plastid phylogenomic frameworks.

Plastid genome evolution and phylogenomics with broad taxon sampling: insights into intrafamilial classification of Hamamelidaceae

The utility of plastid genome data for resolving deep-level phylogenetic relationships within Hamamelidaceae is highlighted, providing a robust framework for future taxonomic and evolutionary studies of this globally distributed and taxonomically complex family.

Plastome characterization of Embelia ribes Burm. f. (Myrsinoideae: Primulaceae): comparative analysis and phylogenetic inference

Comparative chloroplast genomics and phylogenomic insights into the genus Zehneria (Cucurbitaceae)

This work offers novel insights into genomic diversity and evolutionary history of sampled Zehneria species, providing a critical molecular resource for future taxonomic and phylogenetic studies within Cucurbitaceae.

Comparative plastome analysis and phylogenetic relationships of Chinese Myricaria species (Tamaricaceae)

Overall, Myricaria plastomes show a pattern of highly conserved genome structure coupled with localized sequence divergence, providing valuable resources for phylogenetic resolution, species identification, and plastome evolutionary studies.

Comparative genomics, phylogenomic reconstruction and divergence time analysis of 32 Delphinium species based on complete chloroplast genomes

Delphinium , characterized by distinctive spurred flowers, comprises numerous high-altitude endemic species with significant ornamental and medicinal value. However, the intrageneric phylogenetic relationships and evolutionary history of Delphinium have remained poorly resolved, primarily due to the limited variability of traditional DNA markers and complex morphological homoplasy. In this study, complete chloroplast genomes of three Delphinium spp. were sequenced and combined with those of 29 Delphinium spp. publicly available plastomes to conduct a comprehensive phylogenomic analysis and divergence time estimation. The Delphinium plastomes exhibited a highly conserved quadripartite structure, with genome sizes ranging from 153,769 to 157,339 bp. Comparative genomic analyses revealed 2,426 SSRs, and although narrow variable windows ( π > 0.02) were detected within or adjacent to five loci ( ndhA - ndhH , ycf2 , trnG - trnfM - rps14 , rrn23 , trnI ), their overall sequences remained highly conserved at the species level. Given their moderate overall divergence and reduced substitution saturation, these five loci are suitable for higher-level phylogeny, whereas conventional DNA barcodes and SSC-derived regions remain more effective for species-level discrimination. Phylogenomic reconstruction based on whole plastomes robustly supported the monophyly of Delphinium and resolved six well-supported primary clades, outperforming concatenated protein-coding genes in topological resolution. Furthermore, divergence time estimation revealed that the Delphinium crown group originated in the early Eocene (ca. 53.23 Ma; 95% HPD: 51.68-54.77 Ma). An initial major lineage divergence occurred during the Oligocene (ca. 28.53 Ma) driven by global cooling, followed by exPLoSive diversification during the Pliocene and Pleistocene (e.g., rapid radiation of core clades at 3.47 Ma). This recent rapid radiation was likely triggered by the intense uplift of the Qinghai-Tibet Plateau and recurrent Northern Hemisphere glaciations. Collectively, our study provides new insights into the plastome evolution and phylogeny of Delphinium , offering a robust evolutionary framework for understanding its diversification and facilitating future population genetic analyses.