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.
Clubroot disease, caused by the obligate biotrophic pathogen Plasmodiophora brassicae, is a major threat to canola (Brassica napus) production worldwide. Clubroot-resistant (CR) cultivars remain the most effective disease-management strategy, but the genetic basis of resistance in commercial canola remains poorly understood because many resistance sources are proprietary and associated genotypic information is rarely accessible. Although nucleotide-binding leucine-rich repeat (NLR) immune receptors account for most cloned CR genes, no pan-NLRome has incorporated CR lines used in commercial canola breeding. Here, we combined whole-genome sequencing and resistance gene enrichment sequencing (RenSeq) to assemble and annotate the NLR repertoires of five homozygous CR inbred lines (IH1–IH5) used for commercial breeding and displaying contrasting resistance profiles against predominant Canadian P. brassicae pathotypes. We integrated these NLRomes with the susceptible cultivar Westar to construct a comparative pan-NLRome for canola. Across the five CR lines, total NLR content was highly conserved, ranging from 504 to 517 genes, with TIR-NLRs representing the predominant class. C-JID-containing TIR-NLRs accounted for more than 30% of each NLR repertoire, and integrated-domain analysis identified conserved and genotype-specific NLR-IDs, including previously unreported domains in IH4. Pan-NLRome analysis resolved 366 NLR orthogroups (OGs), 60.7% of which were core, and identified resistant-line-enriched OGs absent from Westar as candidate CR-associated loci. Unexpectedly, a homolog of the functionally characterized CR gene, CRa, was detected in five CR lines. Moreover, a homolog of another CR gene, Crr1a, was detected in both resistant and susceptible lines, indicating that the presence/absence of a gene alone does not predict resistance. Instead, structural variation affecting LRR and C-JID regions suggests that allele-level diversity within conserved NLR loci contributes to CR-associated variation, with implications for allele-specific marker development and durable CR deployment.
Jiaxu Wu, Soham Mukhopadhyay, Muhammad Asim Javed et al.· bioRxiv· 0 citations
The potato leafhopper, Empoasca fabae (Harris, 1841), is a highly polyphagous, migratory insect pest of eastern North America that feeds on more than 200 herbaceous and woody plant species, causing substantial losses to forage and field crops. Despite its agricultural and ecological importance, no genome has been available for this species. Here, we present the first chromosome-level genome assembly of E. fabae, generated from Oxford Nanopore long reads, Illumina short reads, and Omni-C proximity-ligation data. The final assembly spans 908 Mb across 132 scaffolds, with 99.8% of the assembly captured in ten chromosome-length scaffolds (nine autosomes and an X chromosome) with a scaffold N50 of 96.2 Mb. The assembly is highly complete, recovering 92.4% of conserved hemipteran single-copy orthologs, and is composed of 47.6% repetitive sequence, dominated by long terminal repeat retrotransposons and unclassified elements. Read-depth comparison between male and female individuals supports assignment of a single sex-linked chromosome, consistent with an XO sex-determination system. BRAKER3 gene annotation predicted 31,406 protein-coding genes after retaining the longest isoform per locus. Comparative genome analysis against the two closest related Typhlocybinae species with genomes available, Matsumurasca onukii and Hebata decipiens, revealed extensive chromosome-scale collinearity, while defining a shared core gene repertoire. This reference genome provides a foundation for comparative and population genomic studies and for investigating genetic traits in this economically important crop pest species. SIGNIFICANCE Leafhoppers (Cicadellidae) are among the most diverse families of plant-feeding insects, but chromosome-level genomes remain scarce, particularly for mesophyll-feeding members of the subfamily Typhlocybinae. The potato leafhopper, Empoasca fabae, is an unusually polyphagous crop and migratory pest of major importance across North America. Here, we provide the first chromosome-level genome assembly for this species. This chromosomal reference reveals broad synteny with two related Typhlocybinae relatives. This assembly will serve as a critical resource, enabling further comparative genomics, population genomics, and functional studies of host-plant adaptation in a significant agricultural crop pest species.
Joshua Molligan, Florent Sylvestre, E. Pérez-López· bioRxiv· 0 citations