Gabriel Silva Profile

Quantitative comparison of fungal genome assembly strategies using short and long-reads from simulated and empirical sequencing data

[Silva, G. A. A.], Folorunso, T. R., Eckhardt, L. G., Willoughby, J. R.,

Jun 8, 2026 • bioRxiv

fungal genome assembly long-read sequencing short-read polishing assembly benchmarking bioinformatics

DOI

https://doi.org/10.64898/2026.06.03.729889

Abstract

High-quality fungal reference genomes are essential for comparative, functional, and evolutionary studies, yet fungal genome features such as repeats, structural rearrangements, accessory chromosomes, and intron-rich genes can complicate genome assembly and the selection of cost-effective sequencing strategies. Here, we benchmark fungal genome assembly performance using simulated and empirical short- and long-read datasets to evaluate how sequencing depth, assembler choice, and genome characteristics influence contiguity, completeness, accuracy, and computational requirements. Using simulated reads from complete fungal genomes spanning diverse sizes and compositions, we evaluated short-read, long-read, hybrid, and polished long-read assemblies across sequencing depths from 10X to 100X. Key trends were validated using empirical sequencing data from 10 fungal isolates assembled with multiple strategies, including different Flye assembler parameter sensitivity and short-read polishing. Across datasets, long reads produced the largest improvements in contiguity, with most gains achieved at ∼20-40X coverage and diminishing returns beyond moderate depth. Short-read polishing substantially improved base-level accuracy at relatively low cost, with ∼10-20X coverage often sufficient to approach maximal error reduction. Hybrid assemblers showed strong algorithmic variability, with trade-offs between contiguity, error rates, and computational demand. Genome architecture also influenced outcomes, as larger and more feature-dense genomes benefited more from long-read data while GC content had limited impact. Overall, our results suggest that moderate long-read coverage (∼30-40X) combined with modest short-read polishing (∼10-20X), particularly using Flye plus Polypolish, provides a strong balance of contiguity, completeness, accuracy, and resource efficiency for generating high-quality fungal genome assemblies.

Citation

Silva, G. A. A., Folorunso, T. R., Eckhardt, L. G., & Willoughby, J. R. (2026). Quantitative comparison of fungal genome assembly strategies using short and long-reads from simulated and empirical sequencing data. BioRxiv. https://doi.org/10.64898/2026.06.03.729889

Persistent genetic connectivity in caribou may buffer against inbreeding effects

Miranda Paez, A., Sattler, R., [Amorim De Albuquerque Silva, G.], Lamka, G., Demma, D., Willoughby, J. R.,

Mar 11, 2026 • PeerJ

caribou genetic connectivity inbreeding population genomics conservation genetics

Biology, Detection, and Management of Lecanosticta acicola - Emerging Challenges for the Management of Brown Spot Needle Blight in Pine Forests

[Silva, G.], Folorunso, T. R., Paez, A. M., Lamka, G. F., Singh, S., King, J., Henderson, L., Persyn, M., Mwema, T., Lindow, T., Amiri, N., Eckhardt, L., Narine, L., Willoughby, J. R.,

Jan 8, 2026 • Forest Pathology

Lecanosticta acicola brown spot needle blight forest pathology pathogen detection disease management

DOI

https://doi.org/10.1111/efp.70061

Abstract

Brown spot needle blight (BSNB), caused by the fungus Lecanosticta acicola, is a widely distributed foliar disease of pines that causes needle necrosis, premature defoliation, and growth loss in both natural forests and commercial plantations. Although L. acicola has been reported from more than 50 pine species worldwide, recent large-scale outbreaks on native loblolly (Pinus taeda) and eastern white pine (P. strobus) in North America highlight emerging management challenges within the pathogen's presumed native range. Here, we synthesise current knowledge of L. acicola taxonomy, biology, pathogenicity, and global distribution, with particular emphasis on how recent North American epidemics fit into the broader invasion history and what they reveal about host–pathogen–environment interactions. We review how taxonomic instability and cryptic diversity complicate species delimitation and surveillance, and evaluate diagnostic and monitoring approaches spanning field sampling, microscopy, culture-based isolation, spore trapping, species-specific PCR and LAMP assays, and the emerging roles of environmental DNA and remote sensing. We then assess control and management options, including fungicides where permitted, silvicultural and hygiene practices, and resistance breeding in pine improvement programs, and place these in the context of projected climate-driven range expansion and ecosystem impacts. Finally, we highlight key research and policy priorities, including coordinated long-term monitoring, genomics-informed resistance screening, and international collaboration and data standards, that are needed to support integrated management strategies and mitigate the growing threat of BSNB to pine-dominated forests in North America and globally.

Citation

Silva, G., Folorunso, T. R., Paez, A. M., Lamka, G. F., Singh, S., King, J., Henderson, L., Persyn, M., Mwema, T., Lindow, T., Amiri, N., Eckhardt, L., Narine, L., & Willoughby, J. R. (2026). Biology, detection, and management of lecanosticta acicola: Emerging challenges for the management of brown spot needle blight in pine forests. Forest Pathology, 56(1), e70061. https://doi.org/10.1111/efp.70061

Optimized protocol for culturing and extracting DNA from fungal isolates associated with brown spot needle blight in pine trees

Folorunso, T. R., [Silva, G.], Girón, M. E., Lindow, T., Persyn, M., Eckhardt, L., Willoughby, J. R.,

Dec 15, 2025 • PLOS ONE

fungal isolates DNA extraction brown spot needle blight pine trees forest pathology

Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history

[Silva, G. A. A.], Harder, A. M., Kirksey, K. B., Mathur, S., Willoughby, J. R.,

Oct 31, 2024 • PLoS Computational Biology

runs of homozygosity population genomics demographic history analysis parameters conservation genomics

DOI

https://doi.org/10.1371/journal.pcbi.1012566

Abstract

Wild populations are increasingly threatened by human-mediated climate change and land use changes. As populations decline, the probability of inbreeding increases, along with the potential for negative effects on individual fitness. Detecting and characterizing runs of homozygosity (ROHs) is a popular strategy for assessing the extent of individual inbreeding present in a population and can also shed light on the genetic mechanisms contributing to inbreeding depression. Here, we analyze simulated and empirical datasets to demonstrate the downstream effects of program selection and long-term demographic history on ROH inference, leading to context-dependent biases in the results. Through a sensitivity analysis we evaluate how various parameter values impact ROH-calling results, highlighting its utility as a tool for parameter exploration. Our results indicate that ROH inferences are sensitive to factors such as sequencing depth and ROH length distribution, with bias direction and magnitude varying with demographic history and the programs used. Estimation biases are particularly pronounced at lower sequencing depths, potentially leading to either underestimation or overestimation of inbreeding. These results are particularly important for the management of endangered species, as underestimating inbreeding signals in the genome can substantially undermine conservation initiatives. We also found that small true ROHs can be incorrectly lumped together and called as longer ROHs, leading to erroneous inference of recent inbreeding. To address these challenges, we suggest using a combination of ROH detection tools and ROH length-specific inferences, along with sensitivity analysis, to generate robust and context-appropriate population inferences regarding inbreeding history. We outline these recommendations for ROH estimation at multiple levels of sequencing effort, which are typical of conservation genomics studies.

Citation

Silva, G. A. A., Harder, A. M., Kirksey, K. B., Mathur, S., & Willoughby, J. R. (2024). Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history. PLOS Computational Biology, 20(10), e1012566. https://doi.org/10.1371/journal.pcbi.1012566

Genomic characterization of Aeromonas veronii provides insights into taxonomic assignment and reveals widespread virulence and resistance genes throughout the world

J. C. D. S. Maia, [G. A. D. A. Silva], L. S. D. B. Cunha, G. V. Gouveia, A. Góes-Neto, B. Brenig, F. A. Araújo, F. Aburjaile, R. T. J. Ramos, S. C. Soares, V. A. D. C. Azevedo, M. M. D. Costa, J. J. D. S. Gouveia,

Jun 11, 2023 • Antibiotics

Aeromonas veronii comparative genomics virulence antibiotic resistance taxonomy

Publications

Quantitative comparison of fungal genome assembly strategies using short and long-reads from simulated and empirical sequencing data

DOI

Abstract

Citation

Persistent genetic connectivity in caribou may buffer against inbreeding effects

DOI

Abstract

Citation

Biology, Detection, and Management of Lecanosticta acicola - Emerging Challenges for the Management of Brown Spot Needle Blight in Pine Forests

DOI

Abstract

Citation

Optimized protocol for culturing and extracting DNA from fungal isolates associated with brown spot needle blight in pine trees

DOI

Abstract

Citation

Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history

DOI

Abstract

Citation

Genomic characterization of Aeromonas veronii provides insights into taxonomic assignment and reveals widespread virulence and resistance genes throughout the world

DOI

Abstract

Citation