ArticlePloS one2009
Relationship between phylogenetic distribution and genomic features in Neurospora crassa.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed, 48 citations in OpenAlex.
- Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora.PLoS genetics · 2023Article
- The Lost and Found: Unraveling the Functions of Orphan Genes.Journal of developmental biology · 2023Review
- Architectural groups of a subtelomeric gene family evolve along distinct paths in Candida albicans.G3 (Bethesda, Md.) · 2022Article
- Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes.mBio · 2022Article
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- Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed.Nucleic acids research · 2021Article
- Transposon-mediated telomere destabilization: a driver of genome evolution in the blast fungus.Nucleic acids research · 2020Article
- Evolution and comparative genomics of the most common Trichoderma species.BMC genomics · 2019Article
- Functional diversification accompanies gene family expansion of MED2 homologs in Candida albicans.PLoS genetics · 2018Article
- Codon usage is an important determinant of gene expression levels largely through its effects on transcription.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Analysis of Magnaporthe oryzae Genome Reveals a Fungal Effector, Which Is Able to Induce Resistance Response in Transgenic Rice Line Containing Resistance Gene, Pi54.Frontiers in plant science · 2016Article
- Nonoptimal codon usage influences protein structure in intrinsically disordered regions.Molecular microbiology · 2015Article
- Article
- Discovering functions of unannotated genes from a transcriptome survey of wild fungal isolates.mBio · 2014Article
- Global gene expression and focused knockout analysis reveals genes associated with fungal fruiting body development in Neurospora crassa.Eukaryotic cell · 2014Article
- Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism.BMC genomics · 2013Article
- Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi.BMC evolutionary biology · 2012Article
- Intrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate intercellular connectivity.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Sex-specific gene expression during asexual development of Neurospora crassa.Fungal genetics and biology : FG & B · 2012Article
- Telomere-targeted retrotransposons in the rice blast fungus Magnaporthe oryzae: agents of telomere instability.Genetics · 2012Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
In the post-genome era, insufficient functional annotation of predicted genes greatly restricts the potential of mining genome data. We demonstrate that an evolutionary approach, which is independent of functional annotation, has great potential as a tool for genome analysis. We chose the genome of a model filamentous fungus Neurospora crassa as an example. Phylogenetic distribution of each predicted protein coding gene (PCG) in the N. crassa genome was used to classify genes into six mutually exclusive lineage specificity (LS) groups, i.e. Eukaryote/Prokaryote-core, Dikarya-core, Ascomycota-core, Pezizomycotina-specific, N. crassa-orphans and Others. Functional category analysis revealed that only approximately 23% of PCGs in the two most highly lineage-specific grouping, Pezizomycotina-specific and N. crassa-orphans, have functional annotation. In contrast, approximately 76% of PCGs in the remaining four LS groups have functional annotation. Analysis of chromosomal localization of N. crassa-orphan PCGs and genes encoding for secreted proteins showed enrichment in subtelomeric regions. The origin of N. crassa-orphans is not known. We found that 11% of N. crassa-orphans have paralogous N. crassa-orphan genes. Of the paralogous N. crassa-orphan gene pairs, 33% were tandemly located in the genome, implying a duplication origin of N. crassa-orphan PCGs in the past. LS grouping is thus a useful tool to explore and understand genome organization, evolution and gene function in fungi.
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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.