ArticleGenome biology2007
The determinants of gene order conservation in yeasts.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 68 citations in OpenAlex.
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- Unbiased anchors for reliable genome-wide synteny detection.Algorithms for molecular biology : AMB · 2025Article
- Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.Frontiers in bioinformatics · 2023Review
- Distinct chromosomal "niches" in the genome ofNAR genomics and bioinformatics · 2022Article
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- Recombination Rate Variation and Infrequent Sex Influence Genetic Diversity in Chlamydomonas reinhardtii.Genome biology and evolution · 2020Article
- Additional Layer of Regulation via Convergent Gene Orientation in Yeasts.Molecular biology and evolution · 2020Article
- Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype.Scientific reports · 2019Article
- Comparative Analysis ofInsects · 2019Article
- Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations.Bioinformatics (Oxford, England) · 2018Article
- Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus.Genome research · 2016Article
- Towards the bridging of molecular genetics data across Xenopus species.BMC genomics · 2016Article
- SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand.Genome biology and evolution · 2015Article
- Neighboring Genes Show Correlated Evolution in Gene Expression.Molecular biology and evolution · 2015Article
- Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints.PLoS computational biology · 2015Article
- DBC1/CCAR2 and CCAR1 Are Largely Disordered Proteins that Have Evolved from One Common Ancestor.BioMed research international · 2014Article
- Expression-based segmentation of the Drosophila genome.BMC genomics · 2013Article
- Physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Females and males contribute in opposite ways to the evolution of gene order in Drosophila.PloS one · 2013Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhy do some groups of physically linked genes stay linked over long evolutionary periods? Although several factors are associated with the formation of gene clusters in eukaryotic genomes, the particular contribution of each feature to clustering maintenance remains unclear.
resultsWe quantify the strength of the proposed factors in a yeast lineage. First we identify the magnitude of each variable to determine linkage conservation by using several comparator species at different distances to Saccharomyces cerevisiae. For adjacent gene pairs, in line with null simulations, intergenic distance acts as the strongest covariate. Which of the other covariates appear important depends on the comparator, although high co-expression is related to synteny conservation commonly, especially in the more distant comparisons, these being expected to reveal strong but relatively rare selection. We also analyze those pairs that are immediate neighbors through all the lineages considered. Current intergene distance is again the best predictor, followed by the local density of essential genes and co-regulation, with co-expression and recombination rate being the weakest predictors. The genome duplication seen in yeast leaves some mark on linkage conservation, as adjacent pairs resolved as single copy in all post-whole genome duplication species are more often found as adjacent in pre-duplication species.
conclusionCurrent intergene distance is consistently the strongest predictor of synteny conservation as expected under a simple null model. Other variables are of lesser importance and their relevance depends both on the species comparison in question and the fate of the duplicates following genome duplication.
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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.