ArticleJournal of molecular evolution2006
Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota.
Article in Journal of molecular evolution, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 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
42 citing papers in PubMed, 71 citations in OpenAlex.
- Article
- Orphan geneHorticulture research · 2024Article
- Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora.PLoS genetics · 2023Article
- Role of Brassica orphan gene BrLFM on leafy head formation in Chinese cabbage (Brassica rapa).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Taxonomically Restricted Genes in Bacillus may Form Clusters of Homologs and Can be Traced to a Large Reservoir of Noncoding Sequences.Genome biology and evolution · 2023Article
- Article
- Strong evidence for the adaptive walk model of gene evolution in Drosophila and Arabidopsis.PLoS biology · 2022Article
- Defining characteristics and conservation of poorly annotated genes in Caenorhabditis elegans using WormCat 2.0.Genetics · 2022Article
- Factors That Affect the Rates of Adaptive and Nonadaptive Evolution at the Gene Level in Humans and Chimpanzees.Genome biology and evolution · 2022Article
- Research Advances and Prospects of Orphan Genes in Plants.Frontiers in plant science · 2022Review
- Molecular Insights into the Genetic Variability of ORF Virus in a Mediterranean Region (Sardinia, Italy).Life (Basel, Switzerland) · 2021Article
- Many, but not all, lineage-specific genes can be explained by homology detection failure.PLoS biology · 2020Article
- Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis).BMC genomics · 2015Article
- Gene age predicts the strength of purifying selection acting on gene expression variation in humans.American journal of human genetics · 2014Article
- Uncovering adaptive evolution in the human lineage.BMC genomics · 2014Article
- How old is my gene?Trends in genetics : TIG · 2013Review
- Development in Aspergillus.Studies in mycology · 2013Article
- Emergence of novel domains in proteins.BMC evolutionary biology · 2013Article
- Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish.BMC genomics · 2013Article
- The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.PLoS genetics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The evolutionary origin of "orphan" genes, genes that lack sequence similarity to any known gene, remains a mystery. One suggestion has been that most orphan genes evolve rapidly so that similarity to other genes cannot be traced after a certain evolutionary distance. This can be tested by examining the divergence rates of genes with different degrees of lineage specificity. Here the lineage specificity (LS) of a gene describes the phylogenetic distribution of that gene's orthologues in related species. Highly lineage-specific genes will be distributed in fewer species in a phylogeny. In this study, we have used the complete genomes of seven ascomycotan fungi and two animals to define several levels of LS, such as Eukaryotes-core, Ascomycota-core, Euascomycetes-specific, Hemiascomycetes-specific, Aspergillus-specific, and Saccharomyces-specific. We compare the rates of gene evolution in groups of higher LS to those in groups with lower LS. Molecular evolutionary analyses indicate an increase in nonsynonymous nucleotide substitution rates in genes with higher LS. Several analyses suggest that LS is correlated with the evolutionary rate of the gene. This correlation is stronger than those of a number of other factors that have been proposed as predictors of a gene's evolutionary rate, including the expression level of genes, gene essentiality or dispensability, and the number of protein-protein interactions. The accelerated evolutionary rates of genes with higher LS may reflect the influence of selection and adaptive divergence during the emergence of orphan genes. These analyses suggest that accelerated rates of gene evolution may be responsible for the emergence of apparently orphan genes.
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.