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.
Abstract
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.
The utility of plastid genome data for resolving deep-level phylogenetic relationships within Hamamelidaceae is highlighted, providing a robust framework for future taxonomic and evolutionary studies of this globally distributed and taxonomically complex family.
Sadaf Habib, Yong Shi, Jie Zhang et al.· Frontiers in Plant Science· 0 citations
The results indicate that while the Ormosia plastomes retain the typical angiosperm quadripartite structure, they show a substantial expansion of the inverted repeat (IR) regions compared to the sister lineage of core genistoids (represented by Lupinus and Sophora), with the boundaries extending to the clpP gene.
Shihong Zhang, Fengcheng Deng, Yixiong Zhao et al.· Plant Systematics and Evolut...· 0 citations
Phylogenetic analyses recovered Veronica as a well-supported monophyletic lineage and clarified the plastid positions of the three newly sequenced species, providing 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
This study presents the largest plastome dataset for Chinese Begonia, identifies hypervariable markers, and resolves a specific taxonomic issue, clarifying the phylogenetic position.
Yang Huang, Wenxiu Tang, Secai Huang et al.· BMC Genomics· 0 citations
Background Rosa platyacantha is a rose species endemic to the high-altitude regions of Xinjiang in China. To date, no complete chloroplast genome has been reported for this species, limiting our understanding of its genomic characteristics and phylogenetic relationships within the genus Rosa. Methods This study employed Sequencing by Synthesis (SBS) technology to achieve the first complete sequencing, assembly, and annotation of the R. platyacantha chloroplast genome. Comparative genomics and phylogeny analyses were then conducted using this data alongside chloroplast genome data from other Rosa species. Results The chloroplast genome of R. platyacantha spans 157,133 bp, and it annotates 132 genes and has a total guanine cytosine (GC) content of 37.21%. Fifty-one simple sequence repeat (SSR) loci were identified, predominantly adenine/thymine (A/T)-type mononucleotide repeats. Codon usage preference analysis revealed a marked bias towards synonymous codons ending in adenine/uracil (A/U). Compared to closely related species, R. platyacantha exhibited higher nucleotide diversity (Pi) in non-coding regions and the large single copy (LSC) and small single copy (SSC) region. Potential adaptive hot spots were identified at ycf3-trnS -GCU (Pi = 0.29005), trnC-GCA, trnT-UGU, and trnV-UAC. Rose genus chloroplast genomes are generally conserved, with most species exhibiting identical inverted repeat regions a and b (IRa and IRb) lengths. However, only R. acicularis shows a 62 bp difference, and the associated fragment length of the duplicated gene ycf1 varies between species from 1,108 to 1,117 bp. Phylogeny analysis revealed that R. platyacantha did not cluster with the sympatric R. fedtschenkoana. This finding confirms their distant evolutionary relationship at the genome level, providing new insights into the evolutionary and dispersal pathways of Rosa species within the unique habitats of northwest China.
Gang Lu, Mengmeng Yu, Fazu Xu et al.· PeerJ· 0 citations