Biology subjects

Staton, M. E.

Publications and source records attributed to Staton, M. E..

8 recordsLinked to original sources

bioRxiv2026

Benchmarking SNP-Calling Accuracy Against Known Citrus Pedigrees Reveals Pangenome Advantages Over Linear References

BackgroundPangenomes are a promising new approach to genomics that can reduce reference bias in genotyping, but the reliability of such a data model remains unclear in tracking variation across species. To test the utility of graph-based pangenomes for interspecific breeding, we developed a Minigraph-Cactus super-pangenome representing four Citrus species derived from the founder lines of a citrus breeding program. To benchmark SNP calling accuracy using graph and linear-based approaches, we performed whole genome short read sequencing for two sets of pedigreed progeny: 30 F1 hybrids and 244 advanced hybrids from an F1 crossed with a parent not included in the pangenome. ResultsThe linear approach yielded more SNP calls than the graph-based approach, however, both methods exhibited similar Mendelian Inheritance Error Rates (MIER) in a tool-dependent manner. Reconstruction of parental haplotype blocks in the advanced hybrids revealed a striking improvement in performance in the pangenome graph-based calls, suggesting MIER is vulnerable to error when reference bias influences both parental and progeny genotype calls. Masking of regions diverged from the reference path improved MIER accuracy metrics and haplotype block reconstruction in both the linear and graph-based SNP calls. ConclusionsIn non-model systems, inheritance patterns observed from pedigreed hybrids provide a framework for benchmarking variant-calling accuracy using pangenomes. SNP miscalls originating from diverged regions can falsely satisfy MIER filters, thus we recommend haplotype blocks. The inherent structure of the pangenome graph has promising applications for removing regions of unreliable mapping quality, which cannot otherwise be reliably removed using traditional filtering metrics.

genomics↗

bioRxiv2025

Ragnarok: a flexible and RApid GeNe Annotation (ROcKs) pipeline deployed through Nextflow

MotivationHigh-quality genome assemblies and pangenomes are increasingly accessible and achievable due to advances in third-generation sequencing and assembly algorithms, but genome annotation remains a critical bottleneck. Existing gene annotation pipelines often require complex installations, multiple steps, long runtimes, and produce variable results, which impede quality and the downstream usage of the annotations. ResultsWe developed RAGNAROK (RApid GeNe Annotation ROcKs), a modular annotation pipeline built on Nextflow and Apptainer that integrates ab initio prediction, transcriptome and protein evidence, repeat annotation, functional assignment, and quality assessment into a single reproducible workflow. Moreover, RAGNAROK utilizes GPU acceleration and parallelization to produce high-quality gene annotations. We benchmarked against BRAKER3 across five diverse, reference-quality plant genomes and demonstrated that RAGNAROK achieved higher sensitivity, precision, and F1 scores at the exon, transcript, and gene levels. Furthermore, we demonstrated RAGNAROKs improvement in re-annotating a suite of five Rosaceae genomes that were previously annotated using MAKER. Overall, RAGNAROK produced more ideal mono:multi-exonic gene ratios, improved BUSCO completeness scores, and reduced missing gene content compared to other pipelines. Additionally, RAGNAROK consistently outperformed BRAKER3 in runtime, scaling efficiently from small to gigabase-scale genomes. RAGNAROK provides a flexible, rapid, scalable, and accurate solution for de novo and re-annotation of plant genomes. Its modular design and workflow scalability lay the foundation for future extensions to animal, fungal, and other eukaryotic genomes. Availability and ImplementationRAGNAROK is available as a GitHub repository at https://github.com/ryandkuster/ragnarok.

bioinformatics↗

bioRxiv2025

The telomere-to-telomere genome and lifestyle transcriptome profiling of Discula destructiva Redlin provide modern molecular and genomic context to a historical epidemic

Fungal pathogens have dramatically altered forests worldwide, yet the mechanisms underlying their virulence remain poorly understood. From the 1970s to the early 2000s, dogwood anthracnose, caused by Discula destructiva Redlin, devastated flowering and Pacific dogwoods (Cornus florida L. and C. nuttallii Aud., respectively). Despite the impacts of D. destructiva and other phytopathogens on forest ecosystems, genomic resources remain limited, hindering efforts to understand pathogenicity. The goal of this study was to evaluate the historical D. destructiva epidemic through a modern genomics lens by uncovering virulence- associated genes that likely contributed to its rapid spread across native dogwoods. We therefore utilized PacBio HiFi and Proximo Hi-C sequencing to assemble the first telomere-to-telomere, chromosome-scale genome for D. destructiva isolate AS111. The resulting 46.655 Mb assembly comprised eight chromosomes with an overall BUSCO completeness of 97.64%. We also identified 10,373 predicted gene models with an overall BUSCO completeness of 96.45%. To investigate gene expression across distinct life cycle phases, reproductive (sporulating) and vegetative (nonsporulating), we conducted RNA sequencing and identified 240 differentially expressed genes (padj < 0.05). GO enrichment revealed 162 upregulated genes during sporulation linked to plant cell wall degradation and sugar metabolism, whereas 78 downregulated genes were linked to electron carrier activity and redox balance. Among these 240 genes, 117 genes had predicted protein sequences that were also identified as a candidate virulence factor, including signal peptides, carbohydrate-active enzymes (CAZymes), and effectors, highlighting the role of sporulation-associated gene expression in D. destructiva virulence. Together, these findings suggest that the reproductive phase primes D. destructiva for host invasion and ecological persistence, which may influence its success as a forest pathogen. Author SummaryForest pathogens threaten ecosystems worldwide and cause extensive ecological and economic damage. Since the 1970s, native dogwood populations in North America have been devastated by dogwood anthracnose, caused by the exotic fungal pathogen Discula destructiva. Discula destructiva is just one of many destructive fungal pathogens in the order Diaporthales, which includes other noteworthy pathogens that cause chestnut blight (Cryphonectria parasitica) and butternut canker (Ophiognomonia clavigignenti-juglandacearum). Despite the widespread impact of fungal diseases, little is known about the genetic factors that drive their spread and severity. To help address this gap, we generated the first telomere-to-telomere, chromosome- scale genome assembly of D. destructiva and analyzed gene expression across distinct life cycle phases: reproductive (sporulating) and vegetative (nonsporulating) growth. Our findings revealed key sporulation-associated genes and virulence factors that may facilitate host infection and underscore the importance of sporulation in the pathogenicity of D. destructiva. These insights improve our understanding of the mechanisms that drive disease development, influence how fungal pathogens such as D. destructiva establish and persist in forest ecosystems, and provide a foundation for future comparative genomics among other devastating pathogens in Diaporthales.

genomics↗

bioRxiv2025

Chromosome-Scale Assemblies of Flowering Dogwood Cultivars Enable Identification of Candidate Genes Regulating Anthocyanin Biosynthesis in Leaves and Bracts

O_LIThe North American-native ornamental tree, flowering dogwood (Cornus florida L.), has a showy bract display that can range in color from white to pink to deep red. Although many trees have white bracts, there is consumer demand for novel pigmentation in the bracts combined with other traits of interest. Because the genetic basis of all traits in flowering dogwood is unknown, combining them using traditional breeding efforts is time, labor, and space-intensive. C_LIO_LIWe developed foundational genomic resources to establish marker-assisted selection within flowering dogwood breeding. We generated diploid, chromosome-scale, annotated genome assemblies for one pink-bracted and red-leafed tree and one white-bracted and green-leafed tree. Additionally, a phenotyping protocol for bract color and presence/absence diagnostic SNPs for bract and leaf color were established. C_LIO_LIWe leveraged these resources to evaluate linkage associations and differential gene expression related to anthocyanin biosynthesis to identify candidate genes regulating bract and leaf pigmentation. Within a 14Mb locus we identified 14 anthocyanin-related candidate genes. Two genes, with MYB (g19533) and RING finger (g19556) binding domains, had both differential gene expression and variants with the expected segregation pattern. C_LIO_LIThese resources will be valuable in combining pink-red bracts with other traits to advance flowering dogwood breeding. C_LI

genomics↗

bioRxiv2025

Reduced processing and toxin binding associated with resistance to Vip3Aa in a resistant strain of fall armyworm (Spodoptera frugiperda) from Louisiana

BackgroundTransgenic crops expressing Cry and Vip3Aa insecticidal proteins from the bacterium Bacillus thuringiensis are a primary tool for controlling fall armyworm (Spodoptera frugiperda) populations. The evolution of resistance to Cry proteins in the native range of the fall armyworm has increased reliance and intensified the selection of resistance to Vip3Aa. In this study, we identified mechanisms of resistance to Vip3Aa in the LA-RR strain of S. frugiperda originating from Louisiana (USA). ResultsMidgut epithelial damage in susceptible larvae was evidenced by a significant drop in midgut pH after feeding on either Vip3Aa protoxin or activated toxin. In contrast, this midgut pH drop was only detected for activated Vip3Aa toxin in LA-RR larvae. Midgut fluids from LA-RR larvae displayed delayed processing of Vip3Aa protoxin when compared to fluids from susceptible larvae, and this slower processing was associated with reduced activity and expression of trypsin and chymotrypsin enzyme genes in the LA-RR strain. In bioassays, LA-RR larvae were significantly more susceptible to Vip3Aa protoxin pre-processed by midgut fluids from susceptible than from LA-RR larvae. In addition, midgut brush border membrane vesicles from LA-RR larvae exhibited lower specific Vip3Aa toxin binding than vesicles from the susceptible strain. ConclusionThe results of this study support that both slower proteolytic processing and reduced specific binding are associated with resistance to Vip3Aa in an S. frugiperda strain from the Western hemisphere, the native range of this pest. This information increases our understanding of resistance to Vip3Aa and advances monitoring and fall armyworm management.

plant biology↗

bioRxiv2024

A haplotype-resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks

O_LIWhite oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. C_LIO_LIWe report the first haplotype-resolved chromosome-scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. In addition, we probe the genetic diversity of this widespread species and investigate its phylogenetic relationships with other oaks using whole-genome data. C_LIO_LIOur genome assembly comprises two haplotypes each consisting of 12 chromosomes. We found that the species has high genetic diversity, much of which predates the divergence of Q. alba from other oak species and likely impacts divergence time estimation in Quercus. Our phylogenetic results highlight phylogenetic discordance across the genus and suggest different relationships among North American oaks than have been reported previously. Despite a high preservation of chromosome synteny and genome size across the Quercus phylogeny, certain gene families have undergone rapid changes in size including resistance genes (R genes). C_LIO_LIThe white oak genome represents a major new resource for studying genome diversity and evolution in Quercus and forest trees more generally. Future research will continue to reveal the full scope of genomic diversity across the white oak clade. C_LI

genomics↗

bioRxiv2020

Integration of Transcriptome and Small RNA Sequencing to Decipher Molecular Interaction of Chenopodium quinoa Varieties with Cucumber Mosaic Virus

Saponins are secondary metabolites with antiviral properties. Low saponin (sweet) varieties of quinoa (Chenopodium quinoa) have been developed because seeds high in saponins taste bitter. The aim of this study was to elucidate the role of saponin in resistance of quinoa to Cucumber mosaic virus (CMV). Differential gene expression was studied in time-series study of CMV infection. High-throughput transcriptome sequence data were obtained from 36 samples (3 varieties x +/- CMV x 1 or 4 days after inoculation x 3 replicates). Translation, lipid, nitrogen, amino acid metabolism, and mono- and sesquiterpenoid biosynthesis genes were upregulated in CMV infections. In Red Head, (bitter), CMV-induced systemic symptoms were concurrent with downregulation of a key saponin biosynthesis gene, TSARL1, four days after inoculation. In local lesion responses (sweet and semi-sweet), TSARL1 levels remained up-regulated. Known microRNAs (miRNA) (81) from 11 miR families and 876 predicted novel miRNAs were identified. Differentially expressed miRNA and short interfering RNA clusters (24nt) induced by CMV infection are predicted to target genomic and intergenic regions enriched in repetitive elements. This is the first report of integrated RNASeq and sRNASeq data in quinoa-virus interactions and provides comprehensive understanding of involved genes, non-coding regions, and biological pathways in virus resistance.

plant biology↗

bioRxiv2019

The Chinese chestnut genome: a reference for species restoration

Forest tree species are increasingly subject to severe mortalities from exotic pests, diseases, and invasive organisms, accelerated by climate change. Forest health issues are threatening multiple species and ecosystem sustainability globally. While sources of resistance may be available in related species, or among surviving trees, introgression of resistance genes into threatened tree species in reasonable time frames requires genome-wide breeding tools. Asian species of chestnut (Castanea spp.) are being employed as donors of disease resistance genes to restore native chestnut species in North America and Europe. To aid in the restoration of threatened chestnut species, we present the assembly of a reference genome with chromosome-scale sequences for Chinese chestnut (C. mollissima), the disease-resistance donor for American chestnut restoration. We also demonstrate the value of the genome as a platform for research and species restoration, including new insights into the evolution of blight resistance in Asian chestnut species, the locations in the genome of ecologically important signatures of selection differentiating American chestnut from Chinese chestnut, the identification of candidate genes for disease resistance, and preliminary comparisons of genome organization with related species.

genomics↗