Biology subjects

Martin, F. N.

Publications and source records attributed to Martin, F. N..

5 recordsLinked to original sources

bioRxiv2025

PAQman: reference-free ensemble evaluation of long-read eukaryotic genome assemblies

Advances in long-read sequencing have made it easier and more cost effective to generate high-quality genome assemblies. However, assessing assembly quality remains a challenge, as existing tools often focus on a few metrics and/or require a reference assembly for comparison. Furthermore, the number of available metrics and associated tools for genome evaluation have expanded in recent years, making it more difficult for researchers to easily use and develop comprehensive pipelines. To address this, we developed the Post-Assembly Quality manager (PAQman), a tool that lowers the barrier to entry for assembly quality assessment by measuring seven reference-free features of genome quality within a single framework: Contiguity, Gene content, Completeness, Accuracy, Correctness, Coverage, and Telomerality. PAQman integrates multiple commonly used tools alongside custom scripts, requiring users to provide only a query genome assembly and its underlying long-read data, while providing a streamlined and consistent framework for quality assessment across datasets. Impact StatementPAQman is an ensemble-based tool for comprehensive, reference-free evaluation of genome assemblies derived from long-read sequencing data. The simultaneous integration of seven quality features enables users to easily assess assembly quality within a standardized, reproducible framework across diverse organisms, while lowering the barrier to entry for biologists analyzing their data.

bioinformatics↗

bioRxiv2024

Population genomics of Macrophomina spp. reveals cryptic host specialization and evidence for meiotic recombination

Knowledge of the factors structuring populations of pathogenic fungi is fundamental to disease management efforts and basic biology. High-quality short-read sequence data were obtained for 463 Macrophomina spp. isolates collected from 91 host plant species and soil in 23 countries. Analyses revealed high diversity, admixture, and equal mating type ratios suggesting on-going recombination. Although most tested isolates could asymptomatically colonize strawberry, only isolates from a single phylogroup caused disease. In addition to strawberry, evidence for host specialization was discovered for soybean, demonstrating this broad host range pathogen contains phylogroups with cryptic specialization. Geography x isolate genotype associations were weak, suggesting these species were frequently trafficked between regions. Re-analysis using genomic data supported current species boundaries, and new molecular markers were designed to specifically identify each species. Contrary to expectations, M. phaseolina should be considered a species with both specialist and generalist populations for which meiosis can increase genetic diversity.

genomics↗

bioRxiv2022

DNA-based detection of Aphanomyces cochlioides in soil and sugar beet plants

Aphanomyces cochlioides, the causal agent of seedling damping-off and Aphanomyces root rot (ARR) of sugar beet, causes yield losses in major sugar beet growing regions. Currently, a 4-week soil bioassay and a 2-day culture-based assay are used to diagnose presence of A. cochlioides. However, these assays can be time-consuming and lack sensitivity. In this study we developed a sensitive, specific, and rapid assay to detect and quantify DNA of A. cochlioides. We developed a TaqMan qPCR assay targeting a region of the mitochondrial genome of A. cochlioides representing a unique gene order for Aphanomyces with genus-specific primers and a species-specific probe. The qPCR assay detected A. cochlioides in 12 naturally infested field soil samples with disease severity index (DSI) values of 48-100, in sugar beet seedlings 5-7 days after planting, and with as little as 1 fg of pure A. cochlioides DNA. Adult sugar beet roots with ARR symptoms were sampled to further validate this qPCR assay. Aphanomyces cochlioides was detected in 95% of these samples using this qPCR assay, while only 23% of the same samples were positive using a culture-based assay. This shows the improved sensitivity of this qPCR assay for disease diagnosis and could provide growers with ARR risk of a field, which would help them make informed disease management decisions. However, further research is required to translate the results of this study to growers fields to quantify A. cochlioides with a high degree of accuracy.

plant biology↗

bioRxiv2021

A new oomycete metabarcoding method using the rps10 gene

Oomycetes are a group of eukaryotes related to brown algae and diatoms, many of which cause diseases in plants and animals. Improved methods are needed for rapid and accurate characterization of oomycete communities using DNA metabarcoding. We have identified the mitochondrial 40S ribosomal protein S10 gene (rps10) as a locus useful for oomycete metabarcoding and provide primers predicted to amplify all oomycetes based on available reference sequences from a wide range of taxa. We evaluated its utility relative to a popular barcode, the internal transcribed spacer 1 (ITS1), by sequencing environmental samples and a mock community using Illumina MiSeq. Amplified sequence variants (ASVs) and operational taxonomic units (OTUs) were identified per community. Both the sequence and predicted taxonomy of ASVs and OTUs were compared to the known composition of the mock community. Both rps10 and ITS yielded ASVs with sequences matching 21 of the 24 species in the mock community and matching all 24 when allowing for a 1 bp difference. Taxonomic classifications of ASVs included 23 members of the mock community for rps10 and 17 for ITS1. Sequencing results for the environmental samples suggest the proposed rps10 locus results in substantially less amplification of non-target organisms than the ITS1 method. The amplified rps10 region also has higher taxonomic resolution than ITS1, allowing for greater discrimination of closely related species. We present a new website with a searchable rps10 reference database for species identification and all protocols needed for oomycete metabarcoding. The rps10 barcode and methods described herein provide an effective tool for metabarcoding oomycetes using short-read sequencing. Interpretive summaryOomycetes are a group of eukaryotes related to brown algae and diatoms, many of which cause diseases in plants and animals. Improved methods are needed to rapidly characterize the diversity of oomycete species found in environmental samples. We have identified the mitochondrial 40S ribosomal protein S10 gene (rps10) as being useful for oomycete community sequencing. We evaluated its utility relative to a popular barcode, the internal transcribed spacer 1 (ITS1), by sequencing environmental samples and a community we synthesized in the laboratory. The amplified rps10 region is predicted to have a higher taxonomic resolution than ITS1, allowing for greater discrimination of closely related species. We present a new website with a searchable rps10 reference database for species identification and all protocols needed for oomycete community sequencing. The rps10 barcode and methods described herein provide an effective tool for characterizing oomycetes using environmental DNA sequencing.

microbiology↗

bioRxiv2021

A reference genome sequence resource for the sugar beet root rot pathogen Aphanomyces cochlioides

Aphanomyces cochlioides, the causal agent of damping-off and root rot of sugar beet (Beta vulgaris L.), is a soil-dwelling oomycete responsible for yield losses in all major sugar beet growing regions. Currently, genomic resources for A. cochlioides are limited. Here we report a de novo genome assembly using a combination of long-read MinION (Oxford Nanopore Technologies) and short-read Illumina sequence data for A. cochlioides isolate 103-1, from Breckenridge, MN. The assembled genome was 76.3 Mb, with a contig N50 of 2.6 Mb. The reference assembly was annotated and was composed of 32.1% repetitive elements and 20,274 gene models. This high-quality genome assembly of A. cochlioides will be a valuable resource for understanding genetic variation, virulence factors, and comparative genomics of this important sugar beet pathogen.

genomics↗