Aug 2026· IMA Fungus· Vol 17· 0 citations· 127 references
Medicine
TL;DR
Combined mitogenomic and multi-locus phylogenomics clarified the phylogenetic placement of these taxa and provided timescale estimates for their divergence and enriches the mitogenomic resources of Phytophthora from pristine natural ecosystems.
Abstract
Abstract The genus Phytophthora (Oomycota) comprises highly destructive and widely distributed plant pathogens that threaten global agriculture and forest ecosystems; however, the evolutionary significance of intraspecific and interspecific mitogenomic variation within this genus remains poorly understood. In this study, complete mitochondrial genomes of 11 Phytophthora species, isolated from forest tree rhizospheres in the Qinling Mountains of China, were sequenced, assembled, and annotated to resolve their genetic diversity and evolutionary patterns. All 11 mitogenomes possess typical circular topologies, ranging in size from 37,502 bp (P. citrophthora) to 41,542 bp (P. cryptogea), with a uniform GC content averaging approximately 21.96%. The gene repertoire was highly conserved across all genomes, containing 34 core protein-coding genes (PCGs), two rRNA genes, 24–25 tRNA genes, and no introns. Selective pressure analysis showed that Ka/Ks ratios for all 34 core PCGs were significantly below 1 (ranging from 0.0096 to 0.1737), demonstrating that purifying selection drives mitochondrial genome evolution in Phytophthora. Combined mitogenomic and multi-locus phylogenomics clarified the phylogenetic placement of these taxa and provided timescale estimates for their divergence. Overall, this work enriches the mitogenomic resources of Phytophthora from pristine natural ecosystems and establishes a critical genomic baseline for accurate species identification, taxonomic revisions, and the study of evolutionary dynamics in oomycetes.
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 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.
Michael Gichuru Karendi, Caroline Njambi Ndungu, Elijah Mkala Mbadi et al.· Genetica· 0 citations
Background: Natural hybridisation is prevalent among Populus species in the Hengduan Mountains. Clarifying their interrelationships and hybrid formation mechanisms is critical for taxonomic classification and breeding of the genus.
Methods: This study sequenced the complete chloroplast genomes of three Populus species – P. lasiocarpa Oliv. (Sect. Leucoides Spach), P. gonggaensis N. Chao & J.R. He (Sect. Leucoides Spach), and P. cathayana Rehd. (Sect. Tacamahaca Spach) - to investigate their genetic relationships and evolutionary patterns.
Results: The chloroplast genome lengths were 156,554 bp (P. lasiocarpa), 156,494 bp (P. gonggaensis), and 156,812 bp (P. cathayana), with all sharing a 37% GC content and conserved quadripartite structure (large/small single-copy regions plus two inverted repeats). They contained 130 or 131 genes (85 or 86 protein-coding, 37 tRNA, 8 rRNA) and 129-142 simple sequence repeat (SSR) loci (primarily adenine/thymine-dominated mononucleotide repeats). Phylogenetic analysis revealed the three species form a monophyletic clade, with P. gonggaensis and P. cathayana showing close affinity.
Conclusions: Chloroplast evidence indicated that P. gonggaensis is maternally closely related to P. cathayana, supporting its maternal lineage from P. cathayana. Further nuclear genome evidence is needed to confirm the hybrid origin of this species.
Liangxing Zhang, Jia Mi, Xue-Qin Wan et al.· New Zealand Journal of Fores...· 0 citations
This study sequenced and comparatively analyzed the mitochondrial genomes of three agriculturally important Aulacophora pests: the polyphagous A. indica, the oligophagous A. lewisii, and the early-diverging A. nigripennis. All three mitogenomes contained the typical 37 genes with conserved gene order. However, total length varied substantially (15,258–18,766 bp), driven primarily by control region length variation. All species exhibited pronounced AT bias, and relative synonymous codon usage analysis revealed marked interspecific divergence. Phylogenetic analysis based on 13 protein-coding genes resolved A. nigripennis as the basal lineage and A. lewisii and A. indica as closely related sister species. Both widespread species displayed maximum haplotype diversity (Hd = 1.000); however, A. indica exhibited approximately 2.4-fold higher nucleotide diversity (Pi = 0.00478) than A. lewisii (Pi = 0.00198), indicating differential population genetic architectures between the two species. These findings established a comparative mitogenomic framework for Aulacophora and provide baseline data for future phylogenomic and phylogeographic investigations.
Liancheng Liu, Huanhuan Li, Gonghua Lin et al.· Life· 0 citations
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
Limeum is the sole genus of Limeaceae, comprising approximately 20 species distributed across Africa, Southwest Asia, and India. However, genomic resources for the family are limited, and phylogenetic relationships within the genus remain poorly understood. In this study, we sequenced, assembled, and analyzed the complete chloroplast genomes of six Limeum species to investigate their genomic characteristics and phylogenetic relationships. The chloroplast genomes ranged from 156,354 bp to 160,377 bp in length and exhibited the typical quadripartite structure. Each genome contained 131 genes, consisting of 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analyses identified 455 tandem repeats and 616 simple sequence repeats, revealing 16 highly variable regions that may serve as potential molecular markers for future studies. Phylogenetic analyses based on complete chloroplast genome sequences strongly supported the monophyly of Limeum and robustly resolved interspecific relationships within the genus. These results provide the first comprehensive plastome dataset for Limeum and a valuable genomic resource for species identification, genetic diversity assessment, phylogenetic reconstruction, and evolution studies of Limeum and the family Limeaceae.
Zheng-Lin He, Jin-Fei Xiao, Fei Zhao et al.· Korean Journal of Plant Taxo...· 0 citations
