The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
Highly Variable Rates of Genome Rearrangements between Hemiascomycetous Yeast Lineages
Open accessAbstract
Hemiascomycete yeasts cover an evolutionary span comparable to that of the entire phylum of chordates. Since this group currently contains the largest number of complete genome sequences it presents unique opportunities to understand the evolution of genome organization in eukaryotes. We inferred rates of genome instability on all branches of a phylogenetic tree for 11 species and calculated species-specific rates of genome rearrangements. We characterized all inversion events that occurred within synteny blocks between six representatives of the different lineages. We show that the rates of macro- and microrearrangements of gene order are correlated within individual lineages but are highly variable across different lineages. The most unstable genomes correspond to the pathogenic yeasts Candida albicans and Candida glabrata. Chromosomal maps have been intensively shuffled by numerous interchromosomal rearrangements, even between species that have retained a very high physical fraction of their genomes within small synteny blocks. Despite this intensive reshuffling of gene positions, essential genes, which cluster in low recombination regions in the genome of Saccharomyces cerevisiae, tend to remain syntenic during evolution. This work reveals that the high plasticity of eukaryotic genomes results from rearrangement rates that vary between lineages but also at different evolutionary times of a given lineage.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“The C. glabrata genome displays robust synteny with the genome of the non-pathogenic yeast Saccharomyces cerevisiae, and synteny blocks were found to be present in 88% of the genome of these two yeasts [17,22].”
From Candida glabrata: A Lot More Than Meets the Eye (2019) · cites this paper as [22]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
PHYLIP-Phylogeny inference package (Version 3.2)
Felsenstein, J. (1989) · Cladistics · Cited by 17,682
Nonlinear programming: theory and algorithms
(1993) · Computers & Operations Research · doi:10.1016/0305-0548(93)90042-h · Cited by 5,803
Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M., et al. (1996) · Science · doi:10.1126/science.274.5287.546 · Cited by 4,423
Self-citationTREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
Schmidt, H. A., Strimmer, K., Vingron, M., & von Haeseler, A. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.3.502 · Cited by 2,512
Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., et al. (2004) · Nature · doi:10.1038/nature03025 · Cited by 1,966
Self-citation[5] Rapid and sensitive sequence comparison with FASTP and FASTA
Pearson, W. R. (1990) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(90)83007-v · Cited by 1,934
Molecular evidence for an ancient duplication of the entire yeast genome
Wolfe, K. H., & Shields, D. C. (1997) · Nature · doi:10.1038/42711 · Cited by 1,785
Sequencing and comparison of yeast species to identify genes and regulatory elements
Kellis, M., Patterson, N. J., Endrizzi, M. G., Birren, B. W., & Lander, E. S. (2003) · Nature · doi:10.1038/nature01644 · Cited by 1,751
Dujon, B., Sherman, D., Fischer, G., Durrens, P., Casaregola, S., Lafontaine, I., de Montigny, J., Marck, C., Neuvéglise, C., Talla, E., et al. (2004) · Nature · doi:10.1038/nature02579 · Cited by 1,623
Self-citationProof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
Kellis, M., Birren, B. W., & Lander, E. S. (2004) · Nature · doi:10.1038/nature02424 · Cited by 1,500
Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting
Cliften, P. F., Sudarsanam, P., Desikan, A., Fulton, L. A., Fulton, B., Majors, J. E., Waterston, R., Cohen, B. A., & Johnston, M. (2003) · Science · doi:10.1126/science.1084337 · Cited by 813
The diploid genome sequence of Candida albicans
Jones, T., Federspiel, N. A., Chibana, H., Dungan, J. M., Kalman, S., Magee, B. B., Newport, G., Thorstenson, Y. R., Agabian, N. M., Magee, P. T., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401648101 · Cited by 784
The evolutionary dynamics of eukaryotic gene order
Hurst, L. D., Pál, C., & Lercher, M. J. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1319 · Cited by 730
The Ashbya gossypii Genome as a Tool for Mapping the Ancient Saccharomyces cerevisiae Genome
Dietrich, F. S., Voegeli, S., Brachat, S., Lerch, A., Gates, K., Steiner, S., Mohr, C., Pöhlmann, R., Luedi, P. P., Choi, S., et al. (2004) · Science · doi:10.1126/science.1095781 · Cited by 633
Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps
Murphy, W. J., Larkin, D. M., der Wind, A. E.-V., Bourque, G., Tesler, G., Auvil, L. S., Beever, J. E., Chowdhary, B. P., Galibert, F., Gatzke, L., et al. (2005) · Science · doi:10.1126/science.1111387 · Cited by 603
Makałowski, W., & Boguski, M. S. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.16.9407 · Cited by 461
Pfaller, M. A., Jones, R. N., Doern, G. V., Sader, H. S., Messer, S. A., Houston, A., Coffman, S., Hollis, R. J., & The SENTRY Participant Group (2000) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.44.3.747-751.2000 · Cited by 378
Genome rearrangements in mammalian evolution: lessons from human and mouse genomes
Pevzner, P., & Tesler, G. (2003) · Genome Research · doi:10.1101/gr.757503 · Cited by 369
Chromosomal evolution in Saccharomyces
Fischer, G., James, S. A., Roberts, I. N., Oliver, S. G., & Louis, E. J. (2000) · Nature · doi:10.1038/35013058 · Cited by 304
Self-citationFunctional genomic analysis of the rates of protein evolution
Wall, D. P., Hirsh, A. E., Fraser, H. B., Kumm, J., Giaever, G. N., Eisen, M. B., & Feldman, M. W. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0501761102 · Cited by 265
Bourque, G., Zdobnov, E. M., Bork, P., Pevzner, P. A., & Tesler, G. (2005) · Genome Research · doi:10.1101/gr.3002305 · Cited by 162
Prevalence of small inversions in yeast gene order evolution
Seoighe, C., Federspiel, N. A., Jones, T., Hansen, N. F., Bivolarovic, V., Surzycki, R., Kuehn, R., Komp, C., Huizar, L., Davis, R. W., et al. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.240462997 · Cited by 149
Parametric genome rearrangement
Blanchette, M., Kunisawa, T., & Sankoff, D. (1996) · Gene · doi:10.1016/0378-1119(95)00878-0 · Cited by 147
Evidence for co-evolution of gene order and recombination rate
Pál, C., & Hurst, L. D. (2003) · Nature Genetics · doi:10.1038/ng1111 · Cited by 143
YEAST EVOLUTION AND COMPARATIVE GENOMICS
Liti, G., & Louis, E. J. (2005) · Annual Review of Microbiology · doi:10.1146/annurev.micro.59.030804.121400 · Cited by 130
Inference and analysis of the relative stability of bacterial chromosomes.
Rocha, E. (2006) · Molecular biology and evolution · doi:10.1093/molbev/msj052 · Cited by 94
Self-citationEvolution of Gene Order in the Genomes of Two Related Yeast SpeciesPreprint
Fischer, G., Neuvéglise, C., Durrens, P., Gaillardin, C. M., & Dujon, B. (2001) · Genome Research · doi:10.1101/gr.212701 · Cited by 92
Self-citationLlorente, B., Malpertuy, A., Neuvéglise, C., de Montigny, J., Aigle, M., Artiguenave, F., Blandin, G., Bolotin‐Fukuhara, M., Bon, E., Brottier, P., et al. (2000) · FEBS Letters · doi:10.1016/s0014-5793(00)02289-4 · Cited by 85
Self-citationDNA repeats lead to the accelerated loss of gene order in bacteria
Rocha, E. P. C. (2003) · Trends in Genetics · doi:10.1016/j.tig.2003.09.011 · Cited by 59 · cited 3×
“The GOC index was adapted from previous works [18,19] by allowing the presence of intervening genes between syntenic pairs of orthologs in order to recover most relations of GOC that would otherwise be lost due to the massive gene loss that occurred after the whole genome duplication event.”
Self-citationGenomic Exploration of the Hemiascomycetous Yeasts: 19. Ascomycetes‐specific genes
Malpertuy, A., Tekaia, F., Casarégola, S., Aigle, M., Artiguenave, F., Blandin, G., Bolotin‐Fukuhara, M., Bon, E., Brottier, P., de Montigny, J., et al. (2000) · FEBS Letters · doi:10.1016/s0014-5793(00)02290-0 · Cited by 58
Self-citationTaxonomic position of clinical isolates ofCandida famata
Nishikawa, A., Tomomatsu, H., Sugita, T., Ikeda, R., & Shinoda, T. (1996) · Medical Mycology · doi:10.1080/02681219680000731 · Cited by 37
Bone infection caused by debaryomyces hansenii in a normal host: a case report
Wong, B., Kiehn, T. E., Edwards, F. F., Bernard, E. M., Marcove, R. C., HARVEN, E. D., & Armstrong, D. (1982) · Journal of Clinical Microbiology · doi:10.1128/jcm.16.3.545-548.1982 · Cited by 34
Flagged first, then by citations
Cited by
Sorted by citations
Kubicek, C. P., Herrera‐Estrella, A., Seidl‐Seiboth, V., Martinez, D. A., Druzhinina, I. S., Thon, M. R., Zeilinger, S., Casas‐Flores, S., Horwitz, B. A., Mukherjee, P. K., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-4-r40 · Cited by 752
Hoffmann, A. A., & Rieseberg, L. H. (2008) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev.ecolsys.39.110707.173532 · Cited by 705
Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes
Richard, G., Kerrest, A., & Dujon, B. (2008) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00011-08 · Cited by 590
Self-citationGenome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis
Jeffries, T. W., Grigoriev, I. V., Grimwood, J., Laplaza, J. M., Aerts, A. L., Salamov, A. A., Schmutz, J., Lindquist, E., Dehal, P., Shapiro, H., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1290 · Cited by 492
Metadata
- Authors
- Fischer, G., Rocha, E. P. C., Brunet, F., Vergassola, M., & Dujon, B.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- École Normale Supérieure de Lyon (FR)
- Corresponding author
- Fischer, Gilles
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2006-03-10
- Volume
- 2
- Issue
- 3
- Pages
- e32
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC1391921
- OpenAlex
- W1982555149
- Cited by
- 101
- References
- 32
- Citations by year
- 2026: 1 · 2023: 6 · 2022: 1 · 2021: 3 · 2020: 2 · 2019: 4 · 2018: 7 · 2017: 7 · 2016: 6 · 2015: 1 · 2014: 5 · 2013: 3 · 2012: 5
- FWCI
- 6.63
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Association pour la Recherche sur le Cancer
- Institut Universitaire de France
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Immunology and Microbiology › Microbiology › Yeasts and Rust Fungi Studies
- Keywords
- genome rearrangement, hemiascomycetous yeasts, genomic instability, chromosomal inversions, synteny, interchromosomal rearrangements, Candida albicans, Candida glabrata, Saccharomyces cerevisiae, essential genes, gene order evolution, genome plasticity, recombination rate
- MeSH terms
- Candida albicans, Chromosome Mapping, Genes, Fungal, Phylogeny, Saccharomyces cerevisiae, Species Specificity, Models, Statistical, Chromosomes, Fungal, Genome, Bacterial, Genome, Fungal, Evolution, Molecular, Candida glabrata
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
