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

Assembly, annotation, and comparative analysis of the first complete mitochondrial genome of Pennisetum sinese

Pennisetum sinese, a perennial grass central to “Juncao Technology,” holds considerable promise for non-grain biomass production and ecological restoration. Despite its agronomic value, the cytoplasmic genetic architecture of this species, particularly its mitochondrial genome, remains uncharacterized. Here, we present the first complete mitochondrial genome of the P. sinese assembled via hybrid long- and short-read sequencing. The genome adopts a multi-branched conformation spanning 405,186 bp with a GC content of 43.98%, and encodes 32 unique protein-coding genes, 20 tRNA genes, and three rRNA genes. We detected significant codon usage bias, abundant tandem repeats, and dispersed repeats. In addition, 24 chloroplast-derived homologous fragments totaling 13,053 bp were identified. Phylogenetic analysis confirms the placement of the P. sinese within the Poaceae clade, whereas synteny analysis reveals extensive structural rearrangements in its mitochondrial genome compared with closely related species. Furthermore, we predicted 454 C−to−U RNA editing sites. These findings establish a foundational genetic resource for P. sinese cytoplasmic inheritance and laying a foundation for future investigations into the molecular mechanisms underlying its high biomass yield and stress tolerance, informing future germplasm innovation.

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

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.

Comparative Chloroplast Genomics, Codon Usage Bias, and Phylogenetic Placement of Euonymus alatus

Euonymus alatus is a species of medicinal and ornamental value, yet high-quality chloroplast genome resources for this taxon remain scarce. The complete chloroplast genome of E. alatus was assembled and compared with 15 congeneric species to investigate genomic structure and evolutionary dynamics. The genome is 157,416 bp with a GC content of 37.3%, containing 131 genes and 156 repeats (67 tandem repeats, 49 dispersed repeats, and 40 SSRs). Divergence was concentrated in non-coding regions, with 14 hypervariable regions identified as potential markers. IR expansion occurred independently in E. fortunei and E. japonicus, while no genome-wide inversions were detected. 11 protein-coding genes were identified under positive selection, among which clpP exhibited the strongest signal, suggesting a possible role in adaptive evolution. Codon usage bias analysis revealed that both mutation pressure and natural selection shape codon usage patterns, with the latter playing a relatively prominent role; 17 optimal codons were identified. Phylogenetic analysis strongly supported E. alatus as sister to E. phellomanus. This study provides a valuable genomic resource for species authentication, phylogenetic revision, and breeding in this genus.

Comparative mitochondrial genome analysis undermine the established taxonomic status of Modiolatus flavidus

Comparative genomics and phylogenetic analysis of three Malvaceae species on the basis of chloroplast genomes

The Malvaceae family shows rich species diversity and has substantial economic and medicinal value. However, the frequent interspecific hybridization among members of this family has resulted in confused phylogenetic relationships among the groups, limiting the usefulness of traditional classification methods. This study aimed to investigate the phylogenetic relationships among selected taxa of Malvaceae by evaluating 23 chloroplast (CP) genomes, including three newly assembled CP genomes. Among these three genomes, the CP genome of Hibiscus schizopetalus L. was reported for the first time, while the CP genomes of Alcea rosea L. and Hibiscus grewiifolius L., which have been deposited in NCBI, were re-analyzed here alongside newly generated data for comparative purposes. In addition, 20 downloaded CP genomes encompassing 13 genera were analyzed using SNPs in whole CP genomes data. The results showed that the genomes ranged from 160,403 to 161,978 base pairs in length and consisted of small single copies (SSCs) and large single copies (LSCs) separated by two inverted repeat sequences (IRs), forming a typical quadripartite circular structure. The entire genome sequence showed relative conservation across species in terms of structure, GC content, codon usage, and gene composition. The mutation sites were mainly located in the LSC and SSC regions, and the variability in the non-coding regions was higher than that in the coding regions. The nucleotide polymorphism (Pi) analysis identified the non-coding regions such as ndhF-rpl32 and psbZ-trnG as high variable hotspots. A maximum likelihood phylogenetic tree was constructed based on SNPs in whole CP genomes data. The phylogenetic analysis divided these 23 species into five highly supported clades. It also revealed a close sister-group relationship between Abelmoschus and Hibiscus species, suggesting that Hibiscus may have a separate lineage from okra species. In conclusion, the increasing availability of CP genome resources will enhance our understanding of the classification and evolutionary patterns of the Malvaceae family. The development of molecular markers will provide important molecular evidence for precise identification and classification revision of plants in this family.

The complete chloroplast genome of Artocarpus gongshanensis (Moraceae)

Abstract The chloroplast genome of Artocarpus gongshanensis S. K. Wu ex C. Y. Wu & S. S. Chang 1989, a threatened species endemic to China, was sequenced for the first time using Illumina NovaSeq 6000. The complete chloroplast genome assembly reveals a quadripartite structure with a total length of 160,174 bp, consisting of a large single-copy (LSC) region (89,311 bp) and a small single-copy (SSC) region (19,489 bp), separated by two inverted repeat (IR) regions (25,687 bp each). Phylogenetic reconstruction based on chloroplast genome data strongly supports that A. gongshanensis forms a sister clade with A. hypargyreus. Comparative genomic analyses demonstrate that the structural organization of A. gongshanensis chloroplast genome is conserved with other Artocarpus species. This newly characterized chloroplast genome provides critical molecular data for resolving taxonomic uncertainties within the genus and establishing evidence-based conservation measures for this threatened plant.