ArticleBMC bioinformatics2019
FGMP: assessing fungal genome completeness.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- The Iceman's microbiome: unveiling millennia of microbial diversity and continuity.Microbiome · 2026Article
- Holistic genome assembly and analysis of theIMA fungus · 2026Article
- Dispensable genome and segmental duplications drive the genome plasticity inFrontiers in fungal biology · 2025Article
- Solving genomic puzzles: computational methods for metagenomic binning.Briefings in bioinformatics · 2024Review
- UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi.Nucleic acids research · 2023Article
- VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes.BMC bioinformatics · 2022Article
- Whole genome resequencing and comparative genome analysis of three Puccinia striiformis f. sp. tritici pathotypes prevalent in India.PloS one · 2022Article
- Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes.Genome biology and evolution · 2021Article
- Genomic insights into the host specific adaptation of the Pneumocystis genus.Communications biology · 2021Article
- Genome Assembly and Analyses of the MacrofungusBioMed research international · 2021Article
- Proteinaceous effector discovery and characterization in filamentous plant pathogens.Molecular plant pathology · 2020Review
- Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC.Genome biology · 2020Article
- What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen.Genome biology and evolution · 2020Article
- DOGMA: a web server for proteome and transcriptome quality assessment.Nucleic acids research · 2019Article
- Patterns of Conservation and Diversification in the Fungal Polarization Network.Genome biology and evolution · 2018Article
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2 authors.
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Abstract
backgroundInexpensive high-throughput DNA sequencing has democratized access to genetic information for most organisms so that research utilizing a genome or transcriptome of an organism is not limited to model systems. However, the quality of the assemblies of sampled genomes can vary greatly which hampers utility for comparisons and meaningful interpretation. The uncertainty of the completeness of a given genome sequence can limit feasibility of asserting patterns of high rates of gene loss reported in many lineages.
resultsWe propose a computational framework and sequence resource for assessing completeness of fungal genomes called FGMP (Fungal Genome Mapping Project). Our approach is based on evolutionary conserved sets of proteins and DNA elements and is applicable to various types of genomic data. We present a comparison of FGMP and state-of-the-art methods for genome completeness assessment utilizing 246 genome assemblies of fungi. We discuss genome assembly improvements/degradations in 57 cases where assemblies have been updated, as recorded by NCBI assembly archive.
conclusionFGMP is an accurate tool for quantifying level of completion from fungal genomic data. It is particularly useful for non-model organisms without reference genomes and can be used directly on unassembled reads, which can help reducing genome sequencing costs.
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