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Article
Open AccessIntron losses and gains in the nematodes
The evolution of spliceosomal introns has been widely studied among various eukaryotic groups. Researchers nearly reached the consensuses on the pattern and the mechanisms of intron losses and gains across euk...
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Article
Open AccessA positive correlation between GC content and growth temperature in prokaryotes
GC pairs are generally more stable than AT pairs; GC-rich genomes were proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies consistently showed positive correlations between ...
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Article
Open AccessDesiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer
Although horizontal gene transfer (HGT) is a widely accepted force in the evolution of prokaryotic genomes, its role in the evolution of eukaryotic genomes remains hotly debated. Some bdelloid rotifers that ar...
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Article
Open AccessAerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have
Among the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines results in G to T mutations. Therefore, the mutations resulting from oxidat...
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Article
Open AccessEvaluation of the mechanisms of intron loss and gain in the social amoebae Dictyostelium
Spliceosomal introns are a common feature of eukaryotic genomes. To approach a comprehensive understanding of intron evolution on Earth, studies should look beyond repeatedly studied groups such as animals, pl...
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Open AccessImprecise intron losses are less frequent than precise intron losses but are not rare in plants
In this study, we identified 19 intron losses, including 11 precise intron losses (PILs), six imprecise intron losses (IILs), one de-exonization, and one exon deletion in tomato and potato, and 17 IILs in Arabido...
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Open AccessFrequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss
Although intron loss in evolution has been described, the mechanism involved is still unclear. Three models have been proposed, the reverse transcriptase (RT) model, genomic deletion model and double-strand-br...
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Article
Open AccessWhy eukaryotic cells use introns to enhance gene expression: Splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity
The costs and benefits of spliceosomal introns in eukaryotes have not been established. One recognized effect of intron splicing is its known enhancement of gene expression. However, the mechanism regulating s...
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Evaluation of Models of the Mechanisms Underlying Intron Loss and Gain in Aspergillus Fungi
Although intron loss and gain have been widely observed, their mechanisms are still to be determined. In four Aspergillus genomes, we found 204 cases of intron loss and 84 cases of intron gain. Using this data, w...
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Article
Low Contents of Carbon and Nitrogen in Highly Abundant Proteins: Evidence of Selection for the Economy of Atomic Composition
Proteins that assimilate particular elements were found to avoid using amino acids containing the element, which indicates that the metabolic constraints of amino acids may influence the evolution of proteins....
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Open AccessExon definition as a potential negative force against intron losses in evolution
Previous studies have indicated that the wide variation in intron density (the number of introns per gene) among different eukaryotes largely reflects varying degrees of intron loss during evolution. The most ...
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Article
Strand compositional asymmetries in vertebrate large genes
Both transcription-associated and replication-associated strand compositional asymmetries have recently been shown in vertebrate genomes. In this paper, we illustrate that transcription-associated strand compo...
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Open AccessEvidence against the energetic cost hypothesis for the short introns in highly expressed genes
In animals, the moss Physcomitrella patens and the pollen of Arabidopsis thaliana, highly expressed genes have shorter introns than weakly expressed genes. A popular explanation for this is selection for transcri...
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Open AccessProtecting exons from deleterious R-loops: a potential advantage of having introns
Accumulating evidence indicates that the nascent RNA can invade and pair with one strand of DNA, forming an R-loop structure that threatens the stability of the genome. In addition, the cost and benefit of int...
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Article
Relationship Between mRNA Stability and Length: An Old Question with a New Twist
The half-life of individual mRNA plays a central role in controlling the level of gene expression. However, the determinants of mRNA stability have not yet been well defined. Most previous studies suggest that...
