Aug 2026· IMA Fungus· Vol 17· 0 citations· 157 references
Medicine
TL;DR
Conordance of codon usage and functional gene abundance with phylogeny is revealed, along with diverse host- and lifestyle-associated adaptive strategies in this important group of plant pathogens.
Abstract
Abstract Colletotrichum spp. are widespread fungal pathogens that cause anthracnose in numerous economically important crops and, exhibiting extensive taxonomic, host plant, and lifestyle diversity. Here, we analyzed the genome sequences of 150 strains representing 97 species across 15 species complexes and four singletons, including and integrating both newly assembled and publicly available genomes. Phylogenomic investigation clarified the taxonomy of Colletotrichum and resolved misidentifications. We identified variations in genome architecture contributed by phylogenetic lineages, host types, and lifestyles, with transposable element proliferation playing significant roles. Interestingly, codon usage bias followed phylogenetic patterns, with species complexes forming distinct clusters and exhibiting a significant bistable co-evolutionary relationship with tRNA genes. Functional gene repertoires displayed coordinated shifts, with higher abundance in broad host-range species complexes and in strains associated with woody or dicotyledonous hosts. Although most functional categories retained strong phylogenetic signals, co-occurrence analysis of weak-signal categories identified modules related to host cell wall disruption, fungal cell wall remodeling, and virulence that were significantly associated with ecological differentiation. Evolutionary trajectories and gene family dynamics further revealed divergent ecological strategies, with oxidative versus rapid-response detoxification in woody- and herbaceous-associated lineages, respectively. The diversifications were accompanied by woody-specific expansion of GH39 and alkaline proteases and progressive differentiation of pectin-degrading capacity, including contraction in woody lineages and divergence between dicot- and monocot-associated herbaceous lineages. The C. gloeosporioides species complex emerged with a comprehensive expansion of detoxification and cell wall-degrading capacities, likely contributing to its broad host range. In contrast, endophytic lineages exhibited convergent gene family contraction in adhesion and cell wall remodeling. Together, this study revealed concordance of codon usage and functional gene abundance with phylogeny, along with diverse host- and lifestyle-associated adaptive strategies in this important group of plant pathogens.
The genus Erwinia comprises a diverse group of bacteria associated with plants, insects, and the environment, including several economically important phytopathogens. The genus has been revised taxonomically many times, yet a thorough and genome-wide assessment of its evolutionary relationships and genomic diversity has been lacking. In this research, we carried out an extensive phylogenomic and comparative genomic analyses of the genus Erwinia using 104 genomes including historically important strains. Genome-wide analyses integrating average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), core-genome phylogenomics, pan-genome analysis, and comparative genomics resolved evolutionary relationships across the genus and identified multiple taxonomic inconsistencies. The pan-genome analysis revealed a relatively small core genome alongside an extensive accessory genome, underscoring the substantial genomic plasticity and ongoing diversification within the genus. The comparative analyses further showed pronounced lineage-specific variation in secretion systems, exopolysaccharide biosynthetic loci, flagellar gene clusters, genomic islands, prophages, and iron acquisition systems, suggesting that virulence-associated determinants have evolved through differential gene gain, loss, and conservation across distinct lineages, thereby facilitating host and ecological niche adaptation. This lineage-specific variation indicates that pathogenicity in the genus is not driven by a single conserved set of virulence determinants but instead reflects distinct combinations of virulence-associated genes. These findings refine the genomic framework of the genus Erwinia, provide evidence for taxonomic revision of several lineages, and improve our understanding of the evolutionary relationships, genomic diversification, and lineage-specific adaptations associated with host interactions and ecological specialization. Impact Statement This study provides the first comprehensive genome-wide phylogenomic framework for the genus Erwinia, integrating taxonomy, pan-genome diversity, virulence-associated determinants, and mobile genetic elements across all 18 currently recognized species. Analyses resolve evolutionary relationships, uncover multiple taxonomic inconsistencies, identify previously unrecognized species-level lineages, including a putative novel Erwinia species PL328 isolated from Cornus florida (dogwood), and reveal lineage-specific genomic features. These findings establish a valuable genomic foundation for future studies of Erwinia evolution, taxonomy, and plant-microbe interactions. Data Summary Genomes sequenced in this study were submitted to the NCBI database under the accession numbers: JCBCPT000000000
Nimisha Maurya, S. Dobhal, George W. Sundin et al.· bioRxiv· 0 citations
These findings provide new insights into the genomic basis of ecological adaptation and metabolic diversification in Pseudoalteromonas, supporting the role of pigmentation as a proxy for enhanced biosynthetic potential, while carbohydrate utilization capabilities evolve more independently and offering a framework for targeted bioprospecting of marine-derived metabolites with industrial and environmental applications.
Jéssica Scherer, Renato Kulakowski Corá, Diego Bonatto et al.· Marine Biotechnology· 0 citations
Collectively, FMT fungi illustrate how divergent ecological strategies can emerge through differential modification and regulatory deployment of a shared hypocrealean genomic toolkit.
Raymond J. St. Leger, Huiyu Sheng, Alexander X Hafer· Microbiology and Molecular B...· 0 citations
New methodologies were examined, including genome scanning, advanced assembly tools such as GetOrganelle, and multispecies merger phylogenetic reconstruction, highlighting the necessity of multi-genome integration, the application of pan-plastome methodologies, and the expanding possibilities of chloroplast synthetic biology and genome editing to improve agriculture.
Shaima Mahfood Ebrahim Abdulrahman, M. Karaismailoğlu· Bartın University Internatio...· 0 citations
Introduction Fish nocardiosis is a chronic and economically significant bacterial disease in aquaculture, yet its genomic basis remains poorly resolved beyond single-species studies. It remains unclear whether fish-associated Nocardia share conserved persistence-associated features or exhibit lineage-specific genomic diversification. Materials and methods We conducted a comparative genomic analysis of 22 Nocardia genomes, including 20 N. seriolae isolates and single representatives of N. salmonicida and N. crassostreae. Genome-wide analyses included phylogenomics, gene-content comparison, pangenome analysis, functional annotation, virulence-associated homolog screening, genomic island detection, and secondary biosynthetic gene cluster prediction. Results The conserved genome core was enriched in central metabolism, lipid-associated cell envelope biogenesis, iron acquisition, and stress-response pathways. Virulence-associated homologs were dominated by persistence-associated and metabolic functions, whereas classical toxin systems were limited, although several transport- and secretion-associated homologs were detected, consistent with their potential contribution to host interaction and intracellular persistence. Phylogenomic and gene-content analyses revealed clear species-level divergence but limited host-associated structuring within N. seriolae. Pangenome analysis supported a robust open pangenome structure (γ = 0.386), with extensive accessory gene diversity enriched in regulatory functions, mobile genetic elements, and secondary metabolic pathways. Genomic islands were dominated by insertion-sequence-associated genes, recombinases, regulators, and hypothetical proteins, whereas prophage- and toxin-related signatures were rare. Secondary metabolite analysis revealed extensive biosynthetic diversity, with most biosynthetic gene clusters showing low similarity to characterized reference pathways. However, ectoine- and nocobactin-associated pathways were broadly conserved. Conclusion These genome findings are consistent with a persistence-associated pathogenicity model in which fish-associated Nocardia, particularly N. seriolae, may depend more on metabolic resilience, stress adaptation, iron acquisition, and accessory genome plasticity than on classical toxin-mediated virulence. Collectively, the results highlight the importance of accessory genome diversification, iron acquisition, and stress adaptation in shaping host-associated lifestyles and provide a comparative genomic foundation for future functional investigations and aquaculture disease-management strategies.
Kiran Kumar Eripogu, P. Maharathi, Wen-Hsiung Li· Frontiers in Microbiology· 0 citations
The pantropical genus Diospyros L. (Ebenaceae) includes many economically valuable species prized for ebony timber and edible fruits. However, its high species diversity and morphological similarity pose significant challenges for understanding its evolutionary history. Previous phylogenetic studies have suggested a rapid adaptive radiation in Diospyros, but relationships among major lineages remain poorly resolved. Here, we reconstruct a comprehensive species-level phylogeny for Chinese Diospyros using whole genome sequencing data from 69 individuals representing 65 species. Phylogenomic analyses of a concatenated nuclear SNP matrix recovered six strongly supported major clades. Notably, we found substantial cytonuclear discordance between nuclear and plastid phylogenies. To investigate this conflict, we conducted extensive gene-tree concordance analyses (Phytop, MSCquartets) and quantified introgression and incomplete lineage sorting (ILS) using Dsuite, QuIB, and PhyloNet. These analyses revealed widespread, statistically significant gene-tree conflict, particularly at deep nodes. Our results demonstrate that the evolutionary history of Chinese Diospyros has been likely shaped by deep ILS-a probable genomic signature of rapid early radiation-alongside localized ancient hybridization, most prominently within the morphologically diverse Asian clade F. Recent gene flow appears to have played a limited role, although the relative contributions of ILS and introgression remain challenging to fully disentangle. These findings provide insights into the drivers of cytonuclear discordance and offer a robust phylogenetic framework for understanding the mechanistic role of ILS in diversification, with implications for adaptive radiation dynamics in species-rich tropical lineages.
