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.
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.
Ying Huang, Shihao Jiang, Yanru Zhang et al.· Frontiers in Plant Science· 0 citations
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.
Wei Han, Kai Zhang, Yuanjin Zhao et al.· BMC Plant Biology· 0 citations
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.
Wenqiao Wang, Mujie Shen, Zhiwei Su et al.· Frontiers in Plant Science· 0 citations