ArticleGenome biology and evolution2010
Evolutionary rates and gene dispensability associate with replication timing in the archaeon Sulfolobus islandicus.
Article in Genome biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 33 citations in OpenAlex.
- On the origins and variation of nucleotide skews of archaeal genomes.Frontiers in microbiology · 2026Article
- Article
- Chromosome organization affects genome evolution in Sulfolobus archaea.Nature microbiology · 2022Article
- Spatial Patterns of Gene Expression in Bacterial Genomes.Journal of molecular evolution · 2020Article
- Clustered Core- and Pan-Genome Content on Rhodobacteraceae Chromosomes.Genome biology and evolution · 2019Article
- Germline Structural Variations Are Preferential Sites of DNA Replication Timing Plasticity during Development.Genome biology and evolution · 2019Article
- Periodic Variation of Mutation Rates in Bacterial Genomes Associated with Replication Timing.mBio · 2018Article
- How a Genetically Stable Extremophile Evolves: Modes of Genome Diversification in the Archaeon Sulfolobus acidocaldarius.Journal of bacteriology · 2017Article
- Non-Random Inversion Landscapes in Prokaryotic Genomes Are Shaped by Heterogeneous Selection Pressures.Molecular biology and evolution · 2017Article
- The properties of spontaneous mutations in the opportunistic pathogen Pseudomonas aeruginosa.BMC genomics · 2016Article
- Coevolution of the Organization and Structure of Prokaryotic Genomes.Cold Spring Harbor perspectives in biology · 2016Review
- Determinants of the rate of protein sequence evolution.Nature reviews. Genetics · 2015Review
- Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition.Genome research · 2014Article
- A Brief Review: The Z-curve Theory and its Application in Genome Analysis.Current genomics · 2014Article
- Recombination shapes genome architecture in an organism from the archaeal domain.Genome biology and evolution · 2014Article
- Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon.Open biology · 2013Article
- Differential relationship of DNA replication timing to different forms of human mutation and variation.American journal of human genetics · 2012Article
- Sequencing and analysis of the gastrula transcriptome of the brittle star Ophiocoma wendtii.EvoDevo · 2012Article
- Mutation rates across budding yeast chromosome VI are correlated with replication timing.Genome biology and evolution · 2011Article
- Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities.Genome biology · 2011Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In bacterial chromosomes, the position of a gene relative to the single origin of replication generally reflects its replication timing, how often it is expressed, and consequently, its rate of evolution. However, because some archaeal genomes contain multiple origins of replication, bias in gene dosage caused by delayed replication should be minimized and hence the substitution rate of genes should associate less with chromosome position. To test this hypothesis, six archaeal genomes from the genus Sulfolobus containing three origins of replication were selected, conserved orthologs were identified, and the evolutionary rates (dN and dS) of these orthologs were quantified. Ortholog families were grouped by their consensus position and designated by their proximity to one of the three origins (O1, O2, O3). Conserved orthologs were concentrated near the origins and most variation in genome content occurred distant from the origins. Linear regressions of both synonymous and nonsynonymous substitution rates on distance from replication origins were significantly positive, the rates being greatest in the region furthest from any of the origins and slowest among genes near the origins. Genes near O1 also evolved faster than those near O2 and O3, which suggest that this origin may fire later in the cell cycle. Increased evolutionary rates and gene dispensability are strongly associated with reduced gene expression caused in part by reduced gene dosage during the cell cycle. Therefore, in this genus of Archaea as well as in many Bacteria, evolutionary rates and variation in genome content associate with replication timing.
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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.