This work reconstructed the evolutionary history of the bacterial glycoside hydrolase subfamily GH5-40 across leafhoppers (Cicadellidae) and identified 87 GH5-40 genes encoding 113 catalytic domains across 23 leafhopper species, with copy numbers ranging from 1 to 19 genes per genome.
Abstract
Horizontal gene transfer from bacteria is a known source of metabolic novelty in insects, yet how these acquisitions diversify and persist over evolutionary time scales remains poorly understood. Here, we reconstructed the evolutionary history of the bacterial glycoside hydrolase subfamily GH5-40 across leafhoppers (Cicadellidae). We annotated 24 genomes and identified 87 GH5-40 genes encoding 113 catalytic domains across 23 leafhopper species, with copy numbers ranging from 1 to 19 genes per genome. Maximum-likelihood phylogenetic analyses recovered all leafhopper GH5-40 domains as a single clade nested within Actinobacteria, supporting one ancestral acquisition followed by extensive lineage-specific duplication of both genes and catalytic domains. Seventeen genes encode 2 to 4 tandem catalytic domains connected by disordered linkers, and a four-domain architecture recurs independently in two divergent leafhopper subfamilies. Recombinant enzymes from distantly related species displayed contrasting substrate preferences for β-glucans and β-mannans in vitro, despite GH5-40 enzymes being classically characterized as endo-β-1,4-mannanases.
Cellulose is an important polysaccharide that constitutes all plant cell walls, giving them strength and stability. The plant cellulose synthase (CESA) gene family, which encodes the catalytic subunits of cellulose synthesis complexes (CSCs), has diversified independently in several plant lineages, providing an interesting model for understanding selection for gene duplication. Here we quantified the presence of CESA genes across mosses to understand how the process of gene family diversification occurred in this group and how it parallels diversification in other groups. We first examined the CESA gene family in eight species of mosses across seven families for which whole genome assemblies were available. We then identified CESA genes from additional species, for which only short-read sequence data was available, by using BLAST searches and targeted gene assemblies. We validated this approach by comparing the assembled paralogs from the short-read data to the genes identified from whole genome assemblies in the eight reference species. This approach allowed us to identify paralogs directly from short-read data and greatly expand our sample set. Results from the combined empirical data support the hypothesis that CESA genes diversified within the moss lineage at least as early as the mesozoic period, during or possibly even prior to the onset of moss diversification, but also continue to diversify within modern species. In addition, we found evidence for purifying selection as the dominant force shaping these genes and observed that different lineages experienced different levels of evolutionary constraint. Lastly, our approach to assemble paralogs has the potential to allow researchers to improve analyses of gene duplication events.
Alyssa Hartmann, Corinna Breusing, Alexandra Walling et al.· Journal of Molecular Evoluti...· 0 citations
Divergence in cis-regulatory elements and subcellular targeting, in the absence of protein function modification, were potent drivers of metabolic evolution, providing a strategy for re-engineering valuable chemical diversity into cultivated crops.
Fungal biosynthetic gene clusters (BGCs) offer a genomic entry point for natural-product discovery, but predicted regions alone neither establish pathway activity nor identify metabolites. Armillaria is a useful model because chemically rich, forest-associated species span pathogenic and saprotrophic lifestyles. We analysed nine assemblies in a role-aware design: seven independent taxa with high completeness assessed using Benchmarking Universal Single-Copy Orthologs (BUSCO), an A. mellea BUSCO duplication-sensitivity sample and an A. solidipes intraspecific strain control for A. ostoyae. The analysis resolved a terpene-rich repertoire containing a shared but edge-robust gene cluster family (GCF) component alongside unevenly distributed candidate families. Targeted neighbourhood analysis recovered protoilludene synthase (PRO1) orthologs in all assemblies (92.2–100.0% amino-acid identity); the core neighbourhood was retained across the seven primary taxa, whereas flanking tailoring-associated genes varied. Notably, the A. gallica PRO1 ortholog lay 23,614 bp outside the nearest antiSMASH region. Thus, whole-region prediction can obscure pathway-centred conservation in basidiomycetes. The resulting framework prioritises reproducible candidates while reserving chemical identity, expression and ecological function for direct validation.
Hui-Jun Su, Ming Luo, Yu-Huan Miao et al.· Journal of Fungi· 0 citations
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.
Jian-Xin Shen, M. Qiao, Jiahao Hong et al.· IMA Fungus· 0 citations
A large-scale genome-wide analysis of the PP2C gene family using 402 representative plant genomes and integrated phylogenetic, duplication type, motif, expression, pangenome and selection-pressure analyses provides a comprehensive evolutionary framework for PP2C functional diversification and candidate resources for stress-resistance improvement in horticultural crops.
Quan-Long Liu, Jian-Bin Quan, Yuhua Cui et al.· Horticulture Research· 0 citations
The genus Talaromyces is an important source of structurally diverse secondary metabolites, yet the conservation and diversification of its biosynthetic potential remain incompletely understood at the genus level. Here, we performed comparative genomic and biosynthetic analyses of 24 Talaromyces species to characterize biosynthetic gene cluster (BGC) diversity, gene cluster family (GCF) distribution, and potential relevance to antifungal natural-product discovery. Genome mining identified 1550 BGCs, ranging from 41 to 81 per species, with polyketide synthase (PKS), nonribosomal peptide synthetase (NRPS), terpene, and hybrid PKS–NRPS pathways representing the major biosynthetic classes. The BGCs were grouped into 828 GCFs, of which 567 (68.5%) were species-specific, indicating extensive lineage-level diversification. In contrast, several metabolite-associated biosynthetic systems were conserved across multiple species. Notably, squalestatin S1-associated BGCs occurred in all 24 species but were distributed among 15 distinct GCFs, demonstrating conservation of predicted biosynthetic capacity despite substantial variation in cluster architecture. GCFs associated with characterized antifungal metabolites, including ilicicolin H, leucinostatins, zopfiellin, sordarin, and monorden/monocillins, were also identified. Moreover, 553 GCFs (66.8%) lacked close matches to characterized MIBiG clusters and were classified as chemically unresolved, highlighting a substantial unexplored biosynthetic repertoire. Overall, these findings reveal extensive diversification alongside selective conservation of secondary-metabolite pathways across Talaromyces and provide a genomic framework for prioritizing species and BGCs for antifungal natural-product discovery and biocontrol-oriented investigation. These genome-based predictions require metabolomic and functional validation to confirm metabolite production and biological activity.
B. Chellappan, Hashem Al-Sheikh· Journal of Fungi· 0 citations
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