Comprehensive plastome variation and RNA editing in Mentha: insights into phylogenetic relationships and candidate DNA barcodes

Comparative plastome analyses of Lewinskya (Orthotrichaceae): insights into genome structure, molecular evolution, and phylogenetic relationships.

The newly assembled Lewinskya plastomes expand genomic resources for Orthotrichaceae and show that chloroplast genome evolution in the sampled species is structurally conservative but contains informative localized variation.

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

Hamamelidaceae, within the order Saxifragales, comprises 27 genera and approximately 120 species. The family has a pantropical and temperate distribution across the Americas, Asia, Africa, and Australia. Previous molecular investigations, constrained by limited taxon sampling and inadequate genetic markers, supported a five-subfamily classification system. However, these studies predominantly focused on Asian taxa, resulting in poor resolution of the evolutionary relationships among American, African, and Australian genera. To address these sampling gaps, we employed near-complete generic sampling (26 of 27 genera) to investigate plastome architecture, structural variation, and phylogenetic relationships. We newly sequenced and assembled 15 plastid genomes representing geographically and taxonomically underrepresented genera and analyzed them alongside 59 publicly available plastomes retrieved from GenBank. Plastid genomes exhibited conserved quadripartite architecture with sizes ranging from 158, 076 bp to 160, 814 bp, minimal structural variation, consistent GC content (37.7-38.2%), and identical gene order. Inverted repeat (IR) regions had limited size variation (26, 211-26, 429 bp). Simple sequence repeat (SSR) distribution (2, 219 loci) showed no clear correlation with the genus-level phylogenetic relationships. We identified ten hypervariable regions, including coding sequences ( accD, ycf1, clpP, ndhF , and rpl22 ) and intergenic spacers ( rpl33-rps18 , the trnG-UCC intron, trnH-GUG-psbA, accD-psaI , and petA-psbJ ), as promising candidate regions for future applications in species delimitation and phylogenetic studies. Phylogenetic analyses revealed largely congruent topologies across datasets and methods, providing improved resolution and strong support for most subfamilial and tribal relationships compared with previous studies. This study highlights the utility of plastid genome data for resolving deep-level phylogenetic relationships within Hamamelidaceae. The genome architecture reflects the high conservation of plastid genomes, while the identified mutation hotspots represent potential resources for future taxonomic and phylogenetic studies. Our results support the existing subfamily classification while improving geographical coverage and generic representation, providing a robust framework for future taxonomic and evolutionary studies of this globally distributed and taxonomically complex family.

Comparative genomics of Begonia chloroplasts: insights into molecular evolution, species identification, and phylogeny

Begonia , a hyperdiverse genus with ecological and medicinal values, confronts challenges in species identification and phylogenetic resolution due to remarkable morphological plasticity and ambiguous taxonomic boundaries. Chloroplast genomes (plastomes) serve as powerful molecular tools for addressing these issues, yet comprehensive plastomic data for Chinese Begonia species remain insufficient. This study presents the largest plastome dataset for Chinese Begonia (76 plastomes total), identifies hypervariable markers, and resolves a specific taxonomic issue, clarifying the phylogenetic position. We sequenced and assembled plastomes of 25 Chinese Begonia species, integrating 51 public plastomes for comparative analyses, including plastome structure, repeat dynamics, codon usage, nucleotide polymorphism, phylogenetics (ML/BI), and positive selection ( Ka/Ks , BEB tests). All 25 assembled plastomes exhibited a conserved quadripartite structures (167,365 − 169,901 bp) with 142–143 genes. Eleven hypervariable regions (e.g., ycf1 , petB , ndhF-rpl32 ) were identified as potential DNA barcodes. Phylogenetic tree aligned with geographic distributions, clarifying taxonomic positions (e.g., B. mashanica ). Five genes ( matK , ndhB , ndhD , rps8 , and rps15 ) showed candidate signals of positive selection, suggesting candidate loci for shade adaptation that require functional validation. This study enriches Begonia plastome resources, provides reliable molecular markers for species authentication, and sheds light on adaptive evolution. The findings support sustainable utilization of medicinal Begonia and advancing genus-level evolutionary and taxonomic research.

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

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

The genus Myricaria (Tamaricaceae) comprises shrubs widely distributed across arid and high-altitude regions of Eurasia, with China representing an important diversity center, particularly in the Qinghai–Tibetan Plateau and adjacent areas. To investigate plastome evolution and phylogenetic relationships within this genus, we sequenced and comparatively analyzed complete plastomes of five Myricaria species from China, together with those of Reaumuria as an outgroup. All plastomes exhibited a typical quadripartite structure and highly conserved gene composition, containing 127–135 genes, indicating strong structural stability across the genus. Despite the overall conservation of plastome architecture, minor size differences were observed and were mainly associated with contraction and expansion of inverted repeat (IR) boundaries. Comparative analyses revealed heterogeneous patterns of sequence divergence, with nucleotide variation primarily concentrated in intergenic regions and a limited number of protein-coding genes, whereas IR regions showed relatively high conservation. Simple sequence repeats (SSRs) and long repeats displayed species-specific distribution patterns, contributing to localized plastome variation. Sliding window analysis identified several mutation hotspots mainly located in single-copy regions, suggesting their potential utility for species identification and phylogenetic studies. Phylogenomic analyses based on complete plastome sequences strongly supported the monophyly of Myricaria and resolved major relationships among sampled species. However, limited resolution among some closely related taxa suggests recent diversification and possible incomplete lineage sorting. 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 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.