Biology subjects

Perez-Lopez, E.

Publications and source records attributed to Perez-Lopez, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Mitochondrial genomes of leafhoppers and a parasitoid fly expand genomic resources for the Eastern Canadian Arctic

Arctic and Subarctic insect biodiversity remains poorly represented in molecular reference databases, limiting the identification of resident taxa and the detection of ecological changes associated with climate warming. Leafhoppers are particularly relevant to northern surveillance because they are sensitive to changes in vegetation and climate, and some species transmit phytoplasmas and other plant pathogens. We used Illumina sequencing to characterize mitochondrial genomes from pooled, morphologically identified leafhoppers collected through the Nunavik Sentinels community science program in Eeyou Istchee, Nunavik, and Nunatsiavut. Eight complete mitochondrial genomes were recovered, representing seven leafhopper lineages and one pipunculid fly. The genomes ranged from 15,475 to 18,051 bp, had mean sequencing depths of 1,003x-3,366x, and contained the 37 genes expected in insect mitochondria. Molecular analyses revealed a Sorhoanus-like lineage within a pool identified as Psammotettix alienus, demonstrating the capacity of untargeted sequencing to detect taxa overlooked during morphological sorting. A Tomosvaryella-like mitochondrial genome was also recovered from a pool composed of Diplocolenus abdominalis. This finding is consistent with the presence of parasitoid within a host but does not establish a direct host-parasitoid association. COI comparisons supported the higher level placement of the taxa but frequently failed to provide species-level resolution because of incomplete reference coverage, inconsistent nomenclature, and low divergence among closely related species. Phylogenetic analysis of the 13 mitochondrial protein-coding genes supported the expected tribal placements, but provided limited resolution for some deeper relationships, reinforcing the need to expand the availability of nuclear genomic data for leafhopper phylogenetics. These voucher-linked and geographically referenced mitogenomes expand the molecular representation of northern insects and provide foundational resources for monitoring leafhopper diversity, potential plant disease vectors, and their natural enemies in rapidly changing northern ecosystems.

genomics↗

bioRxiv2026

Global population genomics and pangenome of the clubroot pathogen link clonal expansion and effector diversification to resistance breakdown in canola

Clubroot disease, caused by the obligate biotrophic protist Plasmodiophora brassicae, threatens Brassica crops worldwide. Novel pathogen virulence frequently breaks resistance in agricultural crops, and yet explanations for isolate evolution remain unknown. We combined whole genome sequencing of 192 isolates from 24 countries with a pangenome analysis of 55 high-quality complete or nearly complete genome assemblies and performed functional effector analyses to investigate potential mechanisms of virulence emergence. Three major phylogenetic clusters were identified, including two highly clonal lineages with contrasting virulence profiles, and a genetically diverse population retaining signatures of recombination. Our findings support a model in which genome-wide purifying selection maintained core genome integrity, while effector genes evolved under less constraint. Despite a compact closed pangenome, we identified chromosome 17 as a major hotspot of single nucleotide and structural variations, transposable elements and expansion of ankyrin repeat effectors. Within the variable chromosome 17, PbAnk2 alleles from virulent and avirulent isolates encoded proteins with distinct predicted structures. PbAnk2 interacted with the Arabidopsis co-chaperone DJC31 in yeast two-hybrid and BiFC assays, whereas co-immunoprecipitation did not detect an interaction for the allele found in isolates that break CRa-mediated resistance, suggesting that allelic variation may alter PbAnk2's association with DJC31. These findings reveal the clonal expansion of virulent isolates and connect it to effector diversification that led to resistance breakdown and establish a genomic framework for pathogen surveillance and durable clubroot resistance.

genomics↗

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

RenSeq and whole genome sequencing uncover allelic diversity of clubroot resistance genes in commercial breeding canola lines

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.

plant 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

Is the winter survival area of Empoasca fabae continuously expanding?

O_LIEmpoasca fabae is a migratory pest that overwinters in the Southeastern United States (US) and damages crops throughout its summer range in North America. Its spring arrival has advanced by 9.7 days between 1951 and 2012, and increased damage is linked to warmer conditions that accelerate host and pest development. Yet whether this advance is also associated with a northward expansion of its winter survival area remains an open question. C_LIO_LIHere, we analyzed 126 years of minimum temperature data across the contiguous US to address this question. Using its winter survival threshold (-9{degrees}C), we calculated the annual winter survival area for E. fabae (temperature-only) and tested for time-series trends. We also mapped the potential overwintering area (temperature + winter hosts) under evergreen and pine-only forest scenarios. C_LIO_LIThe estimated winter survival area varies over 126 years, showing a nonlinear pattern. However, we found no significant trend, change-point year, or rate of change. This lack of significance was also observed when considering the 1951-2012 period. C_LIO_LIThe Southeastern US remained consistently suitable for winter survival, while the northern edge varied latitudinally, especially within the range of 35{degrees}-40{degrees}N, with no clear trend. C_LIO_LIPotential overwintering areas extend into Central Florida and the Texas Gulf Coastal Plain but exclude parts of Tennessee. In the pine-only scenario, the area in Mississippi and Alabama would be smaller. C_LIO_LIThe winter survival area for E. fabae has not continually expanded. The Southeastern US area remains suitable for over 126 years, whereas the northern range varies dynamically. C_LI GRAPHICAL ABSTRACT AND HIGHLIGHTS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/727670v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1062508org.highwire.dtl.DTLVardef@696e4borg.highwire.dtl.DTLVardef@1c7ff29org.highwire.dtl.DTLVardef@14109c5_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIThe winter survival zone (temperature only) of Empoasca fabae has not expanded continuously over the past 126 years. C_LIO_LIThe Southeastern United States remained suitable over this period, with the maximum northward extent of potential survival reaching 45{degrees}N and high variation within the range of 35{degrees}-40{degrees}N. C_LIO_LIUpdated potential overwintering zones (temperature + winter hosts) extend into Central Florida and the Texas Gulf Coastal Plain. C_LI

ecology↗

bioRxiv2026

Leafhoppers' pest status in Quebec from 1868 to 2025

O_LIOver the past decade, leafhoppers (Hemiptera: Cicadellidae) have gained increasing attention as pests and vectors of phytoplasma diseases in Quebec. C_LIO_LIDrawing on historical and modern reports spanning 1868 to 2025, we investigate whether leafhopper pest status has been changing in the province, focusing on two leafhopper groups: those that overwinter in Quebec (local species) and those that do not (migratory species). C_LIO_LILocal species have been reported as pests since at least 1886 and have been considered of secondary significance. Migratory species, first mentioned in 1908, have been listed more frequently as economically important. C_LIO_LIEmpoasca fabae and Macrosteles quadrilineatus were associated with 10 crops, accounting for 11-88% of adult specimens in reported crop assemblages. On the other hand, local species, such as Erythroneura ssp. and Zonocyba (= Typhlocyba) pomaria, were reported mainly on grapevines and apples, respectively. C_LIO_LIWe found that the first field reports of leafhoppers from 1997 to 2025 are advancing in crops where migratory species are most frequently reported (e.g., potato and strawberry), whereas in crops where local species appear to predominate, no significant association was found (e.g., apple and grapevine). C_LIO_LIOur findings indicate that recent changes in leafhopper pest status in Quebec are likely due to migratory species, a group that has historically been a significant component of the leafhopper assemblage on agricultural crops. In Quebec agriculture, what was once loin des yeux, loin du cur (out of sight, out of mind) appears to be shifting toward pres des yeux, pres du cur (now visible and therefore important). C_LI GRAPHICAL ABSTRACT AND HIGHLIGHTS O_FIG O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/727661v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1c58d5forg.highwire.dtl.DTLVardef@c45e02org.highwire.dtl.DTLVardef@1f801ceorg.highwire.dtl.DTLVardef@13eb7e3_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIThe pest status of leafhoppers has changed in Quebec over recent decades, but whether local or migratory species are driving this shift remains unknown. C_LIO_LILocal species have been recognized as pests since at least 1886, and migratory species since 1908. However, migratory species were more frequently reported in historical documents. C_LIO_LIMigratory species (Empoasca fabae and Macrosteles quadrilineatus) appear to be driving the recent status change, as evidenced by earlier first reports and presence across multiple crops. C_LI

ecology↗

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↗

bioRxiv2026

A clubroot pathogen PBS3-like effector manipulates hormonal crosstalk to alter root morphology during colonization

O_LISalicylic acid (SA) and auxin are key regulators of plant immunity and development. The clubroot pathogen Plasmodiophora brassicae encodes PbGH3, an effector related to the GH3 family involved in phytohormone homeostasis. Although PbGH3 was proposed to conjugate auxin in vitro, its biological function in planta has remained unclear. This study aimed to determine the in vivo role of PbGH3 during host colonization. C_LIO_LIWe generated Arabidopsis thaliana and Brassica napus lines overexpressing PbGH3 and characterized their developmental phenotypes, hormone profiles, gene expression, and susceptibility to infection. Structural modeling was performed to assess PbGH3 similarity to plant GH3 proteins, and functional complementation was tested using the Arabidopsis gh3.12 mutant. C_LIO_LIThe expression of PbGH3 in Arabidopsis induced auxin-related developmental phenotypes without detectable accumulation of auxin conjugates. Instead, PbGH3 structurally and functionally resembled GH3.12/PBS3 inducing increased conjugated SA levels, reduced jasmonic acid, suppressed PIN2 expression, and increased root hair number and infection. PbGH3 complemented SA-related defects in the gh3.12 mutant. C_LIO_LIPbGH3 functions as a modulator of SA metabolism rather than an auxin-conjugating enzyme, likely competing with host GH3.12/PBS3 to constrain effective SA accumulation. This reveals a novel strategy by which P. brassicae disrupts SA-auxin homeostasis to promote host colonization and ensure disease development. C_LI PLAIN LANGUAGE SUMMARYThis study shows that the clubroot pathogen uses a protein called PbGH3 to modify the plants salicylic acid balance. This alters root traits and increases susceptibility to infection. Arabidopsis and canola plants engineered to produce PbGH3 showed similar changes, revealing that the pathogen uses this protein to disrupt hormone regulation and create conditions that support its colonization.

plant biology↗

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↗

bioRxiv2025

Pectobacterium sinaloense sp. nov., a novel phytopathogenic species isolated from potato plants in Mexico

As part of a broader effort to survey and characterize the diversity of pectolytic bacteria affecting potato crops in Mexico, phytopathogenic strains were isolated from soft rot symptoms in potato plants in Sinaloa. Among them, an atypical Pectobacterium-like strain, LFLA-215T, could not be confidently assigned to any known species through biochemical or molecular methods. To clarify its taxonomic position and explore its genomic and functional features, whole-genome sequencing and comparative analyses were conducted, accompanied by biochemical, morphological and pathogenicity evaluations. The strain LFLA-215T is Gram-stain-negative, with peritrichous flagella, catalase-positive, and oxidase-negative. Phylogenetic analyses based on the 16S rRNA operon, dnaJ, and 923 core genes, confirmed that strain LFLA-215T belongs to the genus Pectobacterium. However, genomic similarity values with other Pectobacterium species, ranging from 87.73-93.53% (ANIb), 87.63-93.46% (ANIu), and 34.0-52.1% (isDDH), fell below species delineation thresholds. Pectobacterium colocasium LJ1T showed the closest relationship to LFLA-215T, whereas Pectobacterium parmentieri RNS 08-42-1AT was the most distantly related. Although LFLA-215T fulfilled Kochs postulates and demonstrated pathogenicity in potato plants, its virulence on tubers was comparatively lower than that of other known Pectobacterium strains, which could be related to the size and the reduction of the total number of genes when analyzed its complete genome reported here. Taken all together, our findings support the classification of strain LFLA-215T as a novel species within the genus Pectobacterium, for which the name Pectobacterium sinaloense sp. nov. is proposed, with LFLA-215T designated as the type strain.

microbiology↗

bioRxiv2025

Arabidopsis ecotype screening reveals novel sources of clubroot resistance and insights into resistance inheritance

Clubroot, caused by Plasmodiophora brassicae, poses a persistent threat to Brassicaceae crops, particularly in regions where resistant cultivars are under strong selection pressure. To identify new sources of resistance and better understand the underlying genetic mechanisms, we evaluated 60 Arabidopsis thaliana ecotypes against the highly virulent Canadian pathotype 3A. Using stringent phenotyping criteria, pathogen DNA quantification, and survival analysis, we identified eight resistant ecotypes, including two novel sources, Marce-1 and DraII-6. DraII-6 exhibited exceptionally low disease symptoms and a high survival rate. While the resistance gene RPB1/WeiTsing was present in most ecotypes, its expression in DraII-6 was significantly elevated at early infection stages, suggesting a potential role in pathogen suppression. However, genetic analysis of F1 and F2 progeny from a DraII-6 x Col-0 cross revealed a recessive resistance pattern, supporting the hypothesis that RPB1 alone may not be sufficient to confer resistance to clubroot in DraII-6. Our findings highlight the complexity of clubroot resistance and the need for further research into gene regulation and resistance networks beyond RPB1, particularly in the context of translating Arabidopsis-based insights to Brassica crops. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/649024v1_ufig1.gif" ALT="Figure 1"> View larger version (98K): org.highwire.dtl.DTLVardef@1e30ef3org.highwire.dtl.DTLVardef@1ea7aa4org.highwire.dtl.DTLVardef@119c0a3org.highwire.dtl.DTLVardef@1b62891_HPS_FORMAT_FIGEXP M_FIG C_FIG Natural variability of Arabidopsis thaliana ecotypes in response to the Canadian clubroot pathotype 3A. The abstract also celebrates the first author, Melaine Gonzalez-Garcia, who is submitting this manuscript just one week before welcoming her first child.

plant biology↗

bioRxiv2025

Seasonal Phenology of Empoasca fabae (Hemiptera: Cicadellidae) in Quebec, Canada

Climate change is reshaping insect population dynamics in North America, notably impacting the migratory pest Empoasca fabae (Harris) (Hemiptera: Cicadellidae). While its phenology is well studied in the United States, knowledge gaps exist regarding its dynamics in Eastern Canada, one of its northernmost migration areas. Our study integrates degree-day models, CLIMEX ecological niche modeling, and field-collected data from Quebec to assess E. fabae seasonal phenology and monthly climatic suitability. Our results indicate that E. fabae completes one to two generations in Quebec, with earlier emergence and higher generational potential in warmer southeastern regions compared to cooler northeastern regions. CLIMEX modeling showed that suitable climatic conditions for E. fabae growth begin in April, peak from May to September, and decline by November. First adult captures occurred from late May to early June, with population peaks in June-July and a decrease by September. Observed adult peaks occurred earlier than predicted by degree-day models, suggesting that additional environmental factors, such as wind patterns and host plant availability, influence early-season population dynamics. This study provides a comprehensive understanding of E. fabae phenology in Quebec and highlights the importance of incorporating climatic and ecological modeling to predict future population trends. Further research on diapause onset, late-season persistence, and migration patterns is needed to refine predictive models and inform pest management strategies in Quebec. Understanding these factors will be essential in mitigating potential economic impacts amid ongoing climate change.

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↗

bioRxiv2024

Structure-guided secretome analysis of gall-forming microbes offers insights into effector diversity and evolution

Phytopathogens secrete effector molecules to manipulate host immunity and metabolism. Recent advances in structural genomics have identified fungal effector families whose members adopt similar folds despite sequence divergence, highlighting their importance in virulence and immune evasion. To extend the scope of comparative structure-guided analysis to more evolutionarily distant phytopathogens with similar lifestyles, we used AlphaFold2 to predict the 3D structures of the secretome from selected plasmodiophorid, oomycete, and fungal gall-forming pathogens. Clustering protein folds based on structural homology revealed species-specific expansions and a low abundance of known orphan effector families. We identified novel sequence-unrelated but structurally similar (SUSS) effector clusters, rich in conserved motifs such as CCG and RAYH. We demonstrate that these motifs likely play a central role in maintaining the overall fold. We also identified a SUSS cluster adopting a nucleoside hydrolase-like fold conserved among various gall-forming microbes. Notably, ankyrin proteins (ANK) were significantly expanded in gall-forming plasmodiophorids, with most being highly expressed during clubroot disease, suggesting a role in pathogenicity. Subsequently, we screened ANK proteins against Arabidopsis immunity hubs using AlphaFold-Multimer and verified one of the positive results by Y2H and BiFC assays to show that the ankyrin effector PBTT_00818 targets host MPK3 and a zinc-binding dehydrogenase. These findings suggest a potential new mechanism in which ANK effectors target multiple host proteins involved in stress sensing, opening a novel avenue to study the role of ANK in host-pathogen interactions. Altogether, this study advances our understanding of secretome landscapes in gall-forming microbes and provides a valuable resource for broadening structural phylogenomic studies across diverse phytopathogens.

microbiology↗