Biology subjects

Molligan, J.

Publications and source records attributed to Molligan, J..

8 recordsLinked to original sources

bioRxiv2026

Recurrent plant-pathogen Enterobacterales offer complementary digestive functions in a polyphagous insect pest, Empaosca fabae

Nutritional homeostasis in many leafhoppers (Cicadellidae) is largely attributed to ancient obligate symbionts, yet the facultative bacteria these insects carry and if whether they contribute to digestion, remains poorly understood. This question is especially relevant in mesophyll cell-rupture feeders of the subfamily Typhlocybinae, which are reported to lack classical obligate associations. The potato leafhopper, Empoasca fabae, is a polyphagous, migratory Typhlocybine that feeds on more than 200 plant species. Metagenomic analysis of field-collected E. fabae recovered four complete metagenome-assembled genomes corresponding to the opportunistic plant-pathogenic Enterobacterales Enterobacter mori, Kosakonia cowanii, Pantoea agglomerans, and Pantoea ananatis, each highly similar to its type strain. Species-specific PCR across a five-year window showed that E. mori and K. cowanii were detected in every field sample and persistent in an inbred colony, demonstrating likely recurrent and maintained associations, whereas the two Pantoea species were detected intermittently. All four genomes encoded broad carbohydrate-processing repertoires, including sucrose phosphotransferase systems, glycolysis, and aromatic amino acid biosynthesis, suggesting a capacity to synthesize aromatic amino acids-essential for the host. Among 614 glycoside hydrolases, two putatively secreted GH5-25 cellulases were further examined, with recombinant K. cowanii KcGH5-1 hydrolyzing carboxymethyl cellulose at acidic pH, signifying a functional bacterial endoglucanase. These results identify recurrent plant-pathogenic Enterobacterales as carriers of complementary digestive functions, and as candidate contributors to the exceptional dietary breadth of a major migratory agricultural pest.

microbiology↗

bioRxiv2026

A horizontally acquired and recurrently expanded glycoside hydrolase subfamily across leafhoppers

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 {beta}-glucans and {beta}-mannans in vitro, despite GH5-40 enzymes being classically characterized as endo-{beta}-1,4-mannanases.

evolutionary biology↗

bioRxiv2026

Chromosome-level Genome Assembly of the Potato Leafhopper Empoasca fabae (Hemiptera: Cicadellidae)

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. SIGNIFICANCELeafhoppers (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.

genomics↗

bioRxiv2026

Genome-resolved metagenomics reveals conserved, flexible and emerging symbioses across global leafhoppers

BackgroundLeafhoppers are among the most important insect vectors of plant pathogens worldwide and depend on microbial symbionts to exploit nutrient-poor phloem diets. However, most studies of leafhopper-associated microbiota have focused on a limited number of taxa or marker-gene surveys, leaving the genomic diversity, ecological organization, and functional potential of these microbial communities poorly understood. Here, we generated the Global Leafhopper Microbiome Catalog by integrating genome-resolved metagenomics from 171 leafhopper species across 11 subfamilies and 13 countries, including the first microbiomes characterized from Arctic leafhoppers. ResultsDe novo assembly and genome reconstruction generated 337 high-quality non-redundant microbial genomes and 18.6 million non-redundant genes, substantially expanding the known microbial diversity associated with Cicadellidae, including several previously undescribed bacterial lineages. Comparative analyses revealed a recurrent modular microbiome architecture composed of: (i) a conserved core of obligate nutritional symbionts, dominated by Candidatus Karelsulcia and Candidatus Nasuia; (ii) a heterogeneous layer of secondary symbionts, including Wolbachia, Arsenophonus, Rickettsia, and Diplorickettsia; and (iii) a dynamic pool of environmentally acquired bacteria. While obligate symbionts remained highly conserved across divergent hosts, secondary and environmental taxa varied substantially among species and regions, suggesting repeated acquisition shaped by ecological filtering rather than host phylogeny alone. Comparative analyses between the specialist corn leafhopper Dalbulus maidis and the more polyphagous aster leafhopper Macrosteles quadrilineatus further showed that closely related vectors can maintain conserved ancestral symbionts while harboring markedly distinct accessory microbiomes. Arctic populations contained unique microbial assemblages enriched in functions associated with cold tolerance, oxidative stress, and reproductive manipulation. In addition, we identified numerous plant-associated bacteria, including phytoplasmas, spiroplasmas, Pantoea, and Erwinia, alongside taxa with predicted nutritional and plant growth-promoting functions. ConclusionsOur findings reveal that leafhopper microbiomes are structured through the interaction of ancient obligate symbioses and flexible environmentally responsive microbial layers. This work establishes a genome-resolved framework for understanding microbiome evolution in insect vectors and highlights the potential role of microbial community structure in host adaptation, pathogen ecology, and sustainable pest management.

microbiology↗

bioRxiv2025

'Candidatus Phytoplasma zeae': community-driven delineation of the maize bushy stunt phytoplasma, a Dalbulus-transmitted corn pathogen confined to the Americas

A novel phytoplasma species, Candidatus Phytoplasma zeae, is proposed based on ecological distinctiveness, vector specificity, whole-genome comparisons, and community consensus. This phytoplasma is associated with maize bushy stunt (MBS) disease in corn (Zea mays) and is transmitted exclusively by Dalbulus maidis and D. elimatus, two leafhopper species endemic to the Americas, and has been reported in Brazil, Colombia, Mexico, Peru, and several U.S. states. Here we sequenced and assembled the genome of MBS phytoplasma strains from Brazil, and U.S. to describe and propose this new species. Although the 16S rRNA gene sequence of the proposed reference strain, MBSP-BRRS, shares >99% identity with that of Ca. Phytoplasma asteris, key nucleotide polymorphisms distinguish Ca. P. zeae from other 16SrI-related phytoplasma species. Average nucleotide identity (ANI) and average amino acid identity (AAI) values between Ca. P. zeae and Ca. P. asteris are 97.70-98.00% and 96.65-96.88%, respectively, both near the established species delineation thresholds. Comparative genomic analyses revealed unique gene clusters in Ca. P. zeae associated with amino acid transport, defense mechanisms, and protein turnover, which may contribute to its specialization in corn. The ecological profile of Ca. P. zeae, including its narrow host range and restricted geographic distribution, supports its recognition as a novel species under Rule c of the IRPCM guidelines. The designation Candidatus Phytoplasma zeae is therefore proposed by members of the research community who have studied this pathogen for over a decade, with the MBSP-BrazilRS strain serving as the reference.

microbiology↗

bioRxiv2025

Diverse strains of aster yellows phytoplasma are associated with the potato leafhopper (Empoasca fabae) in Eastern Canada

Phytoplasmas are cell wall-less bacteria that are transmitted by phloem-feeding insects. In Canada, insect vectors of this pathogen are leafhoppers (Hemiptera: Cicadellidae), and they can contribute to significant economic losses. As climate change alters the composition and movement of insect communities, migratory species such as the potato leafhopper (Empoasca fabae, Harris 1841), one of the most abundant leafhoppers in Quebec, may play an emerging role in phytoplasma diseases. Although E. fabae is not currently confirmed to act as a vector, its frequent presence and abundance in fields, along with its potential to acquire phytoplasmas, deserve further investigation. In this study, we tested DNA from E. fabae collected in strawberry fields for the presence of Candidatus Phytoplasma using PCR, as well as inbred colonies for their ability to transmit this pathogen. The amplicons amplified from positive samples were cloned and sequenced to identify phytoplasma groups and subgroups. Our findings confirmed the presence of multiple Aster Yellows (16SrI-related) phytoplasma strains in E. fabae, based on phylogenetic analysis, restriction fragment length polymorphism (RFLP) profiling, and single-nucleotide polymorphism (SNP) profiles. However, the transmission assays did not show vector competence. We propose that although this leafhopper species hosts multiple, possibly new, phytoplasma subgroups, its capacity to transmit the disease remains limited and likely depends on high population density. Overall, these findings emphasize the importance of monitoring common pests like E. fabae as indicators of phytoplasma diversity in Eastern Canadian agricultural systems.

microbiology↗

bioRxiv2025

Uncovering diversity and climatic drivers of leafhopper-parasitoid dynamics in Canada

As climate change reshapes northern agroecosystems, leafhoppers (Hemiptera: Cicadellidae) are shifting their distributions, with implications for pest outbreaks and crop health. In Eastern Canada, we monitored strawberry farms from 2023 to 2024, collecting over 82,000 leafhoppers from 64 genera. Migratory species, Empoasca fabae and Macrosteles quadrilineatus, dominated captures, with sharp abundance increases above 16{degrees}C and 14{degrees}C, respectively, while local species declined under higher rainfall. A major finding was the first Canadian record of the corn pest Dalbulus maidis, a vector of multiple pathogens, likely introduced through long-distance dispersal. Insecticide applications generally failed to reduce leafhopper numbers, highlighting the limitations of current chemical control. Parasitism rates by Gonatopus wasps (Dryinidae), averaged ~3% but peaked in late summer at over 20%, primarily in M. quadrilineatus. Warmer temperatures and seasonal progression increased both parasitism probability and rates. Genomic analyses revealed at least three Gonatopus lineages, including the first complete mitochondrial genome for the genus from the New World, and confirmed multiple host species. We also recorded the first Canadian occurrence of G. clavipes. Our results demonstrate that parasitoids are active, climate-responsive, and capable of targeting dominant pest species. Together, these findings provide the first ecological and genomic baseline for leafhopper-parasitoid interactions in Canada. They point to the potential of conserving and enhancing native parasitoid populations as a foundation for climate-resilient, pesticide-free pest management strategies.

ecology↗

bioRxiv2024

De novo assembly and annotation of the Empoasca fabae mitochondrial genome

This study presents the assembly and annotation of the full-length mitochondrial genome for the leafhopper species Empoasca fabae Harris, 1841. The mitogenome was obtained from a contig-level assembly with the identified mitochondrial genome being 14,873 bp in length. The base composition was A (38.8%), T (39.1%), C (11.7%), and G (10.4%). The mitogenome comprised 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and showed a unique, non-AT-rich D-loop region. Nearly all PCGs being with an ATN start codon, while two begin with TCG and GTG. Phylogenetic analysis confirmed the placement of E. fabae within the subfamily Typhlocybinae, clustering with other species in the Empoasca genus.

genomics↗