This study characterized six Pachypleurum plastomes and highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions, and provided a framework for Pachypleurum and improved the taxonomic system of the Apiaceae family.
Abstract
Phylogenomic data rich in informative loci can significantly improve the support and resolution of phylogenetic tree and has been proven to be an effective tool for studying plant taxonomy and phylogeny. The genus Pachypleurum Ledeb., belonging to subfamily Apioideae (Apiaceae), comprises approximately seven species worldwide (six in China). Due to the long-standing taxonomic ambiguity of this genus, it is urgent need for investigation. In this current study, we obtained six Pachypleurum plastomes and performed comprehensively comparative analyses. The results showed that six Pachypleurum plastomes were conserved in genome structure, gene number, gene arrangement, codon bias and SSRs, but varied in genome size, GC content and SC/IR boundaries. These findings indicated that Pachypleurum plastomes showed both conservation and diversity. In addition, nine mutation hotspot regions (matK, rps16, atpF, clpP, ndhE, trnH-psbA, psbK-psbI, accD-psaI, ycf4-cemA) were identified that can serve as potential DNA barcodes for species identification within the genus Pachypleurum. Phylogenetic analyses based on 79 commonly shared PCGs and ITS sequences robustly supported that the non-monophyly of Pachypleurum and six Pachypleurum members fell into two clades: Selineae and Acronema Clade. The phylogenetic results also showed that Chinese Pachypleurum taxa may be circumscribed to only one species (P. alpinum) and other five species previously placed in this genus may be transferred out this genus and the systematic position of them were also discussed. Finally, combined with plastome comparison, phylogenetic analyses and morphological characteristics, we discussed the morphological delimitation of Pachypleurum genus. This study characterized six Pachypleurum plastomes and highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions. In conclusion, our study not only enriched the data on the plastomes of Pachypleurum, but also provided a framework for Pachypleurum and improved the taxonomic system of the Apiaceae family.
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.
Hui-Long Li, Wen Deng, Chen-Xuan Yang et al.· BMC Plant Biology· 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
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.
Yang Huang, Wenxiu Tang, Secai Huang et al.· BMC Genomics· 0 citations
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 whole-plastome phylogeny recovered Bupleurum as monophyletic relative to Chamaesium, and only one of seven multi-accession operational binomial groups was monophyletic, and only one showed a positive local barcode gap.
Yujie He, Mingxuan Wu, Aohan Wang et al.· Frontiers in Plant Science· 0 citations