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

Comparative Chloroplast Genomics and Phylogenetic Relationships of Poa angustifolia and Poa lipskyi (Poaceae)

Poa L. (Poaceae), comprising over 500 species, is taxonomically challenging due to morphological plasticity, hybridization, and polyploidy. To clarify plastome architecture and phylogenetic relationships within the genus, we sequenced and annotated complete chloroplast genomes of Poa angustifolia (accessions P10, P14) and Poa lipskyi (P17) from Uzbekistan. The three plastomes (135,310–135,609 bp) shared the typical quadripartite structure and an identical complement of 130 genes across self-replication, photosynthesis, and other functional categories. Codon usage and amino acid composition were highly conserved, with a consistent bias toward A/T-ending codons and leucine, isoleucine, glycine, and serine as the dominant residues. Sliding-window analysis identified two nucleotide-diversity hotspots, in the rpl32 – trnL -UAG and trnC -GCA– rpoB regions, and SSR profiling showed predominant mononucleotide A/T repeats alongside a few taxon-specific pentanucleotide motifs. Maximum-likelihood phylogenomic analysis placed the P. angustifolia accessions in a strongly supported clade sister to P. lipskyi , consistent with shared membership in sect. Poa. These results indicate that Poa plastomes are structurally conserved yet retain informative variable regions useful for phylogenetics and barcoding.

Assembly and comparative analysis of the complete mitochondrial genome of Viola philippica (Malpighiales, Violaceae)

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

This work offers novel insights into genomic diversity and evolutionary history of sampled Zehneria species, providing a critical molecular resource for future taxonomic and phylogenetic studies within Cucurbitaceae.

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

This study presents the largest plastome dataset for Chinese Begonia, identifies hypervariable markers, and resolves a specific taxonomic issue, clarifying the phylogenetic position.

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

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.

Characteristics, comparative genomics, and phylogenetic analysis of the chloroplast genome of Rosaplatyacantha

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.