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

Insights into phylogenetic relationships of Veronica species (Plantaginaceae) based on comparative chloroplast genomics

Veronica L. is one of the most species-rich genera in Plantaginaceae and several species have medicinal, horticultural, or ecological value. In this study, the complete chloroplast genomes of three Veronica species were assembled and annotated using Illumina sequencing data. The plastomes exhibited a typical quadripartite structures, with total lengths of 150,202 bp for Veronica biloba L., 151,159 bp for Veronica ciliata Fisch. and 151,098 bp for Veronica vandellioides Maxim. Each genome contained 130–132 unique genes, including 86–87 protein-coding genes, 36–37 tRNA genes, and 8 rRNA genes. Comparative analyses of 24 Veronica plastomes indicated that the IR/SC junctions were largely conserved, although slight boundary shifts occurred around rps19, ndhF, and ycf1. Forward, palindromic, complement, and reverse repeats were detected, and A/T mononucleotide repeats were the dominant SSR type. Nucleotide diversity analysis identified rpl32-trnL, trnK-rps16, rpl32, ycf1, ndhF, accD, matK, and rpoB as highly variable regions. Phylogenetic analyses recovered Veronica as a well-supported monophyletic lineage and clarified the plastid positions of the three newly sequenced species. Divergence time estimation suggested that the estimation suggested of Veronica was around 14.9 Ma, with V. biloba, V. ciliata and V. vandellioides diverging approximately 3.9 Ma, 0.6 Ma, and 6.9 Ma, respectively. Because the analyses were based on plastid genomes, the inferred topology should be interpreted as chloroplast phylogenetic evidence rather than a complete species-history reconstruction. These results provide plastome resources and molecular evidence for taxonomy, species identification, and future evolutionary studies of Veronica.

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

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

BACKGROUND Mosses are key components of terrestrial ecosystems and provide important systems for studying plant diversity, adaptation, and genome evolution. Lewinskya is a species-rich moss genus in Orthotrichaceae, but species delimitation and phylogenetic reconstruction within the genus remain difficult because diagnostic characters are often subtle or convergent. Chloroplast genomes can provide useful genomic resources and complementary evidence for comparative and systematic studies. This study aimed to generate new Lewinskya plastome resources and evaluate plastome structure, sequence variation, codon usage, and plastid-based phylogenetic relationships in the genus. RESULTS Five newly sampled Lewinskya chloroplast genomes were assembled from genome-skimming data, including three circular plastome assemblies and two high-quality single-scaffold assemblies. Together with the published plastome of L. incana, the six Lewinskya plastomes ranged from 122,258 to 123,526 bp and showed conserved genome organization, gene content, GC composition, and inverted repeat boundaries. Each plastome encoded 128 genes, including 83 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. A total of 520-542 simple sequence repeats were detected per plastome, with mononucleotide repeats being dominant and most repeats located in the large single-copy region. Comparative analyses revealed no large-scale rearrangements, but several localized divergence regions were detected. Nucleotide diversity analysis identified 11 highly variable regions, including five genic regions (rps18, rpl22, infA, rpl32 and rps3) and six intergenic spacers, most of which were located in the large single-copy region. Codon usage patterns were highly similar among species and showed a preference for A/T-ending codons. Phylogenetic analyses based on 78 plastid protein-coding genes from 26 Orthotrichaceae plastomes strongly supported the sampled Lewinskya species as a clade, although some deeper relationships within the genus remained weakly resolved. CONCLUSIONS 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. The identified repeat loci and highly variable regions provide candidate markers for future species identification and population-level studies. Plastome-scale data offer useful evidence for Lewinskya systematics, but broader taxon sampling and integration with nuclear genomic and morphological evidence will be needed to resolve difficult interspecific relationships.

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

Comparative plastome analyses and phylogenetic insights of Stellaria (Caryophyllaceae)

Stellaria (Caryophyllaceae) comprises approximately 112 species globally, with China serving as a significant center of diversity hosting about 64 species. Despite its taxonomic importance, the genus remains insufficiently studied in China. Previous phylogenetic studies relying on limited DNA barcodes produced weakly supported inferences, while those based on chloroplast genomes are currently lacking. Here, we characterize the chloroplast genome structure and reconstruct its highly resolved infrageneric phylogeny using 60 newly sequenced plastomes. All plastomes displayed a conserved quadripartite structure, with lengths varying from 147,205 bp to 149,409 bp, GC contents ranging from 36.6% to 36.7%, and gene counts spanning 128 to 129 genes. Codon usage patterns were highly conserved with leucine encoded by UUA exhibiting the highest relative synonymous codon usage. A total of 55–74 simple sequence repeats and 42–64 long repeats were detected. Three hypervariable regions—petN-psbM, trnP-rpl33, and ycf1 were identified as promising candidate DNA barcodes. Phylogenomic analysis resolved Stellaria into three strongly supported major clades and 15 well-defined subclades. The results are largely consistent with the established phylogeny of Stellaria. However, we observed certain discrepancies within specific clades. We propose some suggestions for these clades and species based on morphological and molecular evidence. This study provides the first comprehensive phylogenetic framework for Stellaria based on the chloroplast genome, establishing a robust foundation for future taxonomic revisions and evolutionary studies.

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

12 plastomes representing major Mentha species, hybrid taxa, and unresolved accessions are analyzed to characterize plastome structure, repeat composition, sequence divergence, phylogenetic relationships, and plastid RNA editing.