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

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.

The complete chloroplast genome of Hedera helix (Araliaceae): comparative plastome analyses reveal divergence hotspots, selective constraints, and phylogenetic placement

Background Hedera helix: is an ecologically, horticulturally, and medicinally important member of Araliaceae. Although a genome sequence of this species has been reported, detailed chloroplast genome annotation and focused comparative plastome analysis of H. helix remain limited. This study aimed to assemble and annotate the complete chloroplast genome of H. helix and to evaluate its structural features, sequence variation, and phylogenetic position in a comparative family-level context. Methods Approximately 22 Gb of Illumina 150 bp paired-end data were generated for H. helix. The complete chloroplast genome was assembled de novo and annotated using standard plastome assembly and annotation pipelines. Comparative analyses included genome structure characterization, repeat and simple sequence repeat (SSR) detection, codon usage analysis, IR/SC boundary comparison, nucleotide diversity scanning, synteny assessment, and plastome-based phylogenetic reconstruction using representative Araliaceae taxa. Results The H. helix plastome is 156,688 bp in length and exhibits the typical quadripartite structure, comprising a large single-copy region of 86,626 bp, a small single-copy region of 18,180 bp, and two inverted repeats of 25,941 bp each, with an overall GC content of 37.99%. A total of 132 genes were annotated, including 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Repeat analyses identified 54 long repeats and 47 SSRs, most of which were A/T-rich. Codon usage analysis revealed a preference for codons ending in A or T. Comparative analyses showed that plastome structure and gene order were highly conserved across sampled Araliaceae species, with only minor variation at IR/SC junctions. Most protein-coding genes had Ka/Ks ratios consistent with purifying selection, whereas nucleotide diversity analysis identified several localized divergence hotspots, particularly in ycf1. Phylogenomic analysis based on plastome data strongly supported H. helix as sister to (H. rhombea + H. nepalensis var. sinensis). Conclusion This study provides a complete and curated plastome resource for H. helix and shows that its chloroplast genome is structurally conserved relative to other sampled Araliaceae plastomes. The identified SSRs and highly variable regions, especially ycf1, represent potential candidates for future marker development. In addition, the plastome-based phylogenetic results provide useful evidence for evaluating the placement of Hedera within Araliaceae.

Comparative plastid genomics of five Ormosia species (fabaceae): insights into structural variation and morphological homoplasy

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.

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.

The Complete Chloroplast Genome of Ficus gasparriniana var. laceratifolia Reveals Discordance Between Morphology-Based Classification and Plastid Phylogeny

This plastome provides a valuable genomic resource and reveals robust discordance between morphology-based classification and plastid phylogenetic placement in F. gasparriniana, providing a foundation for future nuclear-genomic and population-level tests of the alternative evolutionary scenarios underlying this discordance.