ArticleApplied and environmental microbiology2012
Short-read sequencing for genomic analysis of the brown rot fungus Fibroporia radiculosa.
Article in Applied and environmental microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
17 citing papers in PubMed, 37 citations in OpenAlex.
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- Fungal-Metal Interactions: A Review of Toxicity and Homeostasis.Journal of fungi (Basel, Switzerland) · 2021Review
- Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont,G3 (Bethesda, Md.) · 2020Article
- Gene Expression Analysis of Three Putative Copper-Transporting ATPases in Copper-TolerantFrontiers in microbiology · 2020Article
- Degradative Capacity of Two Strains ofFrontiers in microbiology · 2020Article
- Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi.Mycology · 2018Article
- De Novo Sequencing of aThe Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · 2018Article
- Glyoxal oxidases: their nature and properties.World journal of microbiology & biotechnology · 2017Review
- Genomic and transcriptomic analyses of the medicinal fungus Antrodia cinnamomea for its metabolite biosynthesis and sexual development.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Gene expression analysis of copper tolerance and wood decay in the brown rot fungus Fibroporia radiculosa.Applied and environmental microbiology · 2013Article
- Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The feasibility of short-read sequencing for genomic analysis was demonstrated for Fibroporia radiculosa, a copper-tolerant fungus that causes brown rot decay of wood. The effect of read quality on genomic assembly was assessed by filtering Illumina GAIIx reads from a single run of a paired-end library (75-nucleotide read length and 300-bp fragment size) at three different stringency levels and then assembling each data set with Velvet. A simple approach was devised to determine which filter stringency was "best." Venn diagrams identified the regions containing reads that were used in an assembly but were of a low-enough quality to be removed by a filter. By plotting base quality histograms of reads in this region, we judged whether a filter was too stringent or not stringent enough. Our best assembly had a genome size of 33.6 Mb, an N50 of 65.8 kb for a k-mer of 51, and a maximum contig length of 347 kb. Using GeneMark, 9,262 genes were predicted. TargetP and SignalP analyses showed that among the 1,213 genes with secreted products, 986 had motifs for signal peptides and 227 had motifs for signal anchors. Blast2GO analysis provided functional annotation for 5,407 genes. We identified 29 genes with putative roles in copper tolerance and 73 genes for lignocellulose degradation. A search for homologs of these 102 genes showed that F. radiculosa exhibited more similarity to Postia placenta than Serpula lacrymans. Notable differences were found, however, and their involvements in copper tolerance and wood decay are discussed.
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Registered trials
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