ArticleGenome biology and evolution2016
OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes.
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
83 citing papers in PubMed, 164 citations in OpenAlex.
- A marine-derived fungal genome of Annulohypoxylon annulatoides reveals AT-rich isochores with putative regulatory functions.G3 (Bethesda, Md.) · 2026Article
- Clustering of inverted triplications in centromeric and subtelomeric chromosomal regions ofMicrobiology spectrum · 2026Article
- Regions of low gene expression promote maintenance and adaptation of horizontally acquired genes in yeasts.Communications biology · 2026Article
- Evolution of genomic architecture of the plant-pathogenic fungusMicrobial genomics · 2026Article
- EffectorFisher: association of disease phenotype with pangenomic protein-isoform profiles for improved prediction of fungal pathogenicity effectors.Scientific reports · 2026Article
- Conserved 'Late' Effector Genes From Leptosphaeria maculans Inducing Gene-For-Gene Quantitative Resistance in Brassica napus Semi-Winter Genotypes.Molecular plant pathology · 2026Article
- Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism.Genome biology and evolution · 2026Article
- Machine-learning-based analysis of host-depletedBioinformatics advances · 2026Article
- Harnessing Genomics ofPlants (Basel, Switzerland) · 2025Article
- Genomic organization, domain assortments, and nucleotide-binding domain diversity of NLR proteins in Sordariales fungi.PLoS genetics · 2025Article
- IMA GENOME - F20 A draft genome assembly ofIMA fungus · 2025Article
- Article
- Repeat-induced point mutations driving Parastagonospora nodorum genomic diversity are balanced by selection against non-synonymous mutations.Communications biology · 2024Article
- Population-level whole-genome sequencing ofMicrobial genomics · 2024Article
- Highly Repetitive Genome ofInternational journal of molecular sciences · 2024Article
- Genomic and Pathogenic Characterization ofGenes · 2024Article
- The massive 340 megabase genome of Anisogramma anomala, a biotrophic ascomycete that causes eastern filbert blight of hazelnut.BMC genomics · 2024Article
- Template-Based Modelling of the Structure of Fungal Effector Proteins.Molecular biotechnology · 2024Article
- Pan-genome survey ofFrontiers in microbiology · 2024Article
- Comparative genomics of the extremophileFrontiers in fungal biology · 2024Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a novel method to measure the local GC-content bias in genomes and a survey of published fungal species. The method, enacted as "OcculterCut" (https://sourceforge.net/projects/occultercut, last accessed April 30, 2016), identified species containing distinct AT-rich regions. In most fungal taxa, AT-rich regions are a signature of repeat-induced point mutation (RIP), which targets repetitive DNA and decreases GC-content though the conversion of cytosine to thymine bases. RIP has in turn been identified as a driver of fungal genome evolution, as RIP mutations can also occur in single-copy genes neighboring repeat-rich regions. Over time RIP perpetuates "two speeds" of gene evolution in the GC-equilibrated and AT-rich regions of fungal genomes. In this study, genomes showing evidence of this process are found to be common, particularly among the Pezizomycotina. Further analysis highlighted differences in amino acid composition and putative functions of genes from these regions, supporting the hypothesis that these regions play an important role in fungal evolution. OcculterCut can also be used to identify genes undergoing RIP-assisted diversifying selection, such as small, secreted effector proteins that mediate host-microbe disease interactions.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.