This study presents the first complete V. philippica mitogenome, providing insights into its genetic evolution and a scientific basis for elucidating the species’ phylogenetic relationships and genetic diversity.
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.
Xiaobing Hu, Dan Zhu, Xin Ning et al.· Frontiers in Plant Science· 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
The first complete mitogenome of Eurostus validus is reported and indicates that both mutation pressure and natural selection shape codon usage bias, with natural selection playing a dominant role.
Dongkai Liu, Chao Xue, Yingyin Gao· Journal of the Entomological...· 0 citations
This study employed Sequencing by Synthesis (SBS) technology to achieve the first complete sequencing, assembly, and annotation of the R. platyacantha chloroplast genome, 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
We employed second-generation sequencing technology to determine the complete mitochondrial genome of Mioscirtus w. wagneri (Eversmann, 1859), which is the first species reported in the genus Mioscirtus. The mitochondrial genome spans 15,632 base pairs and encodes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and an AT-rich control region (D-loop region). The nucleotide composition exhibits a strongly A+T bias (75.6%). Among the 13 PCGs, 27 codons exhibited higher usage frequencies, predominantly with A/U endings. All tRNA genes adopt the canonical cloverleaf secondary structure, except for tRNASer(AGN), which lacks the dihydrouridine (DHU) arm. Nucleotide diversity and evolutionary rate analyses across mitogenomes of Oedipodinae revealed pervasive purifying selection acting on all 13 PCGs (Ka/Ks < 1). Among these, ND2 exhibited the highest nucleotide diversity, whereas ND4L exhibited the lowest. Phylogenetic analyses were conducted based on the concatenated nucleotide sequences of all 13 PCGs, using both Maximum likelihood (ML) and Bayesian inference (BI) frameworks, which produced an identical topology strongly supported M. w. wagneri as a monophyletic lineage within the subfamily Oedipodinae. This lineage formed a sister group relationship with species of the genus Celes and shared a most recent common ancestor with species of the genus Oedipoda, together constituting the tribe Oedipodini. This phylogenetic relationship is consistent with traditional morphology-based classifications. These findings expand the currently sparse mitogenomic resource for the subfamily Oedipodinae and provide a robust genetic foundation for future studies on the population genetics and evolutionary history of M. w. wagneri.
Introduction Russula (Russulaceae, Basidiomycota) is a widely distributed genus of ectomycorrhizal fungi. Methods In this study, we assembled and annotated the complete mitochondrial genomes (mitogenomes) of six Russula species. Results The mitogenomes ranged from 41,017 bp (R. hookeri) to 57,170 bp (R. aff. cessans). This size variation appears to be partly influenced by intron content, as the smallest genome (R. hookeri) lacks introns in the cox1 gene. All mitogenomes contained 15 core protein-coding genes (PCGs) (atp6, atp8, atp9, cob, cox1-cox3, nad1-nad6, nad4L, and rps3), two rRNA genes, and 25–27 tRNA genes, with the largest intergenic spacer consistently located between rrnL and nad6. Codon usage showed a strong bias toward A/U-ending codons, with UUA (Leu) and AGA (Arg) exhibiting the highest relative synonymous codon usage (RSCU) values. Notably, trnM was newly annotated in the trnE-trnL region across all six species. Selective pressure analysis revealed that 14 of the 15 core PCGs were under purifying selection (Ka/Ks < 1), while rps3 showed elevated Ka/Ks values in some species, suggesting possible relaxed or positive selection. Phylogenetic analysis based on 57 mitochondrial sequences resolved the relationships among the six Russula species. Discussion This study enriches the mitogenomic resources of Russulaceae and provides a foundation for future phylogenetic and evolutionary studies of Russula.
Xianyi Wang, Huangxue Luo, Qun Luo et al.· Frontiers in Microbiology· 0 citations
We use cookies to run the site and, with your consent, for analytics and to show ads.
See our Cookie Policy.
