DNA repeats lead to the accelerated loss of gene order in bacteria
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The negative association between the number of repeats and genome stability has been observed and statistically confirmed in γ-proteobacteria, where genomes with more repeats undergo accelerated rearrangement rates, while genomes lacking repeats are more stable.
“The negative association between the number of repeats and genome stability has been observed and statistically confirmed in γ-proteobacteria, where the genomes contained more repeats undergoing accelerated rearrangement rates, while genomes lacking repeats were more stable.50”
From Whole genomic DNA sequencing and comparative genomic analysis of<i>Arthrospira platensis</i>: high genome plasticity and genetic diversity (2016) · cites this paper as [50]
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Genomics of Actinobacteria : Tracing the Evolutionary History of an Ancient Phylum
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“Because few rearrangements are observed at these short evolutionary distances (Rocha, 2003), genes outside conserved blocks of synteny are highly likely to be xenologues or false orthologues.”
BackgroundSelf-citationComparative and Evolutionary Analysis of the Bacterial Homologous Recombination Systems
Rocha, E. P. C., Cornet, E., & Michel, B. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010015 · Cited by 341 · see citing works
“], and among bacteria, the rate of chromosome rearrangements correlates with the number of repeated sequences in the genomes [”
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The organization of the bacterial genome.
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“Therefore, there is a negative association between genome stability and repeat density (91), which is particularly striking if these repeats are transposable elements (103).”
BackgroundSelf-citationThe replication-related organization of bacterial genomes
Rocha, E. P. C. (2004) · Microbiology · doi:10.1099/mic.0.26974-0 · Cited by 279 · see citing works
“On the other hand, rearrangement rates accelerate with the number of repeated elements in bacterial chromosomes (Rocha, 2003), which are maintained by either selfish systems (e.g. insertion sequences) or selection for elements capable of generating genetic diversity (e.g. for antigenic variation).”
BackgroundSelf-citationRickettsial evolution in the light of comparative genomics
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“Chromosomes containing a higher repeat density have higher rates of rearrangements leading to accelerated loss of gene order (Rocha, 2003).”
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“Inversions have been shown to occur through intramolecular recombination between repeat elements (Palmer, Nugent, and Herbon 1987; Ogihara et al. 1988; Achaz et al. 2003; Rocha 2003; Pombert et al. 2006).”
BackgroundDynamics of Genome Rearrangement in Bacterial Populations
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“The frequency of observed rearrangement in modern genomes correlates with the presence of repeats induced by mobile genetic elements [26,33].”
BackgroundCauses of Insertion Sequences Abundance in Prokaryotic Genomes
Touchon, M., & Rocha, E. P. C. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm014 · Cited by 241 · see citing works
“For example, many of these repeats are less than 15 bp, but there is a significant chance to find by chance alone 2 copies of a 15 bp generic repeat within a 2 kb DNA sequence (Rocha 2003a).”
BackgroundSelf-citationHigh Variability of Mitochondrial Gene Order among Fungi
Aguileta, G., de Vienne, D. M., Ross, O. N., Hood, M. E., Giraud, T., Petit, E., & Gabaldón, T. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu028 · Cited by 239 · see citing works
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“Chromosomes containing a higher repeat density have higher rates of rearrangements leading to accelerated loss of gene order [57].”
BackgroundCouturier, E., & Rocha, E. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05046.x · Cited by 220 · see citing works
“Recently, one of us proposed a method to quantify the intrinsic genome stability of genomes (Rocha, 2006), departing from a previously published analysis (Rocha, 2003).”
MethodSelf-citationGenesis, effects and fates of repeats in prokaryotic genomes
Treangen, T. J., Abraham, A., Touchon, M., & Rocha, E. P. C. (2009) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2009.00169.x · Cited by 172 · see citing works
Self-citationHow essential are nonessential genes?
Fang, G., Rocha, E., & Danchin, A. (2005) · Molecular biology and evolution · doi:10.1093/molbev/msi211 · Cited by 158 · see citing works
Self-citationTowards a prokaryotic genomic taxonomy
Coenye, T., Gevers, D., de Peer, Y. V., Vandamme, P. A. R., & Swings, J. (2005) · FEMS Microbiology Reviews · doi:10.1016/j.fmrre.2004.11.004 · Cited by 122 · see citing works
Persistence drives gene clustering in bacterial genomes
Fang, G., Rocha, E. P., & Danchin, A. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-4 · Cited by 112 · see citing works
Self-citationInference and analysis of the relative stability of bacterial chromosomes.
Rocha, E. (2006) · Molecular biology and evolution · doi:10.1093/molbev/msj052 · Cited by 94 · see citing works
“Hence, the number of orthologues involved in the comparisons is always very large.”
BackgroundMethodInfluentialSelf-citationVentura, M., Canchaya, C. A., Fitzgerald, G. F., Gupta, R. S., & van Sinderen, D. (2006) · Antonie van Leeuwenhoek · doi:10.1007/s10482-006-9122-6 · Cited by 111 · see citing works
“Genomes displaying an elevated repeat density have higher rates of reorganizations leading to accelerated loss of gene order as a result of homologous recombination (Rocha 2003).”
BackgroundOrder and disorder in bacterial genomes
Rocha, E. P. (2004) · Current Opinion in Microbiology · doi:10.1016/j.mib.2004.08.006 · Cited by 104 · see citing works
Self-citationHighly variable rates of genome rearrangements between hemiascomycetous yeast lineages
Fischer, G., Rocha, E. P. C., Brunet, F., Vergassola, M., & Dujon, B. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020032 · Cited by 101 · see citing works
“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-citationThe Temporal Dynamics of Slightly Deleterious Mutations in Escherichia coli and Shigella spp.
Balbi, K. J., Rocha, E. P. C., & Feil, E. J. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn252 · Cited by 76 · see citing works
“At the extreme are those ancient partnerships that have reached a ‘‘point of no return,’’ where mutual reliance between eukaryotic host and prokaryotic symbiont confines both to long-term coevolution.”
BackgroundMethodSelf-citationTandem repeat markers as novel diagnostic tools for high resolution fingerprinting of Wolbachia
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“Slipped-strand mispairing has previously been identified as a source for generation of repeat copies in general [63-65] and in E.”
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Complete mitochondrial genome of the medicinal fungus Ophiocordyceps sinensis
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Plastid Genome Assembly Using Long‐read data
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“The relationship is also supported by findings in bacterial genomes where repeated sequences lead to gene order rearrangements (Rocha, 2003).”
BackgroundGroEL dependency affects codon usage—support for a critical role of misfolding in gene evolution
Warnecke, T., & Hurst, L. D. (2010) · Molecular Systems Biology · doi:10.1038/msb.2009.94 · Cited by 53 · see citing works
“We obtained the alignments of nine E. coli/Shigella strains from Eduardo Rocha through Edward Feil (personal communication; see Rocha (2003) for details on orthologue identification and alignment).”
MethodJi, B., Zhang, S., Arnoux, P., Rouy, Z., Alberto, F., Philippe, N., Murat, D., Zhang, W., Rioux, J.-B., Ginet, N., et al. (2013) · Environmental Microbiology · doi:10.1111/1462-2920.12180 · Cited by 48 · see citing works
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“The factors responsible for the difference in mutation rates are not clear, but mutation rates may be promoted by factors such as short repeat units, high copy number arrays and repeat sequence homogeneity (Rocha, 2003).”
BackgroundXu, T., Qin, S., Hu, Y., Song, Z., Ying, J., Li, P., Dong, W., Zhao, F., Yang, H., & Bao, Q. (2016) · DNA Research · doi:10.1093/dnares/dsw023 · Cited by 37 · see citing works
“The negative association between the number of repeats and genome stability has been observed and statistically confirmed in c-proteobacteria, where the genomes contained more repeats undergoing accelerated rearrangement rates, while genomes lacking repeats were more stable.(50) Based on these molecular evidences, pre…”
BackgroundFonseca, P. L. C., Badotti, F., De-Paula, R. B., Araújo, D. S., Bortolini, D. E., Del‐Bem, L., Azevedo, V., Brenig, B., Aguiar, E. R. G. R., & Goés‐Neto, A. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00765 · Cited by 30 · see citing works
“Differences in genome ordering can be attributed due to non-homologous recombination processes, plasmid sequence integration or presence of transposable elements, such as IGI sequences and HEGs (Gordenin et al., 1993; Lavrov et al., 2002; Rocha, 2003; Repar and Warnecke, 2017).”
BackgroundComparative Genomics in Prokaryotes
Gregory, T. R., & DeSalle, R. (2005) · Elsevier eBooks · doi:10.1016/b978-012301463-4/50012-7 · Cited by 30 · see citing works
An Integrative Method for Accurate Comparative Genome Mapping
Swidan, F., Rocha, E. P. C., Shmoish, M., & Pinter, R. Y. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020075 · Cited by 29 · see citing works
“Finally, repeats, a major element of genome disruptions caused by homologous recombination [26], are by themselves recombination hotspots [25, 27 ].”
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“Horizontal gene transfer (HGT), transposition and intragenomic recombination are known to be important sources of evolutionary novelties, being responsible for bacterial huge metabolic diversity and adaptive potential, which are remarkable among free-living bacteria (Casjens, 1998; Rocha, 2008).”
BackgroundElevated Rate of Genome Rearrangements in Radiation-Resistant Bacteria
Repar, J., Supek, F., Klanjšček, T., Warnecke, T., Zahradka, K., & Zahradka, D. (2017) · Genetics · doi:10.1534/genetics.116.196154 · Cited by 19 · see citing works
“Achaz, G., E. Coissac, P. Netter, and E. P. C. Rocha, 2003 Associations between inverted repeats and the structural evolution of bacterial genomes.”
BackgroundGenetic and molecular characterization of multicomponent resistance of Pseudomonas against allicin
Borlinghaus, J., Bolger, A., Schier, C., Vogel, A., Usadel, B., Gruhlke, M. C. H., & Slusarenko, A. J. (2020) · Life Science Alliance · doi:10.26508/lsa.202000670 · Cited by 18 · see citing works
“It is unusual for multiple copies of genes to be maintained in bacteria without a clear selective advantage because of the genomic instability that arises through homologous recombination leading to genome rearrangements and loss of essential interim sequences (Rocha, 2003).”
Genomic Diversity and Chromosomal Rearrangements in Neisseria gonorrhoeae and Neisseria meningitidis
Shaskolskiy, B. L., Kravtsov, D., Kandinov, I., Dementieva, E., & Gryadunov, D. A. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms232415644 · Cited by 14 · see citing works
“The frequency of observed genomic rearrangements correlates with the number of mobile genetic elements and the state of repair/recombination systems in genomes [5,6].”
BackgroundShort and long-term genome stability analysis of prokaryotic genomes
Brilli, M., Lió, P., Lacroix, V., & Sagot, M. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-309 · Cited by 13 · see citing works
“[41] found an abundance of mobile genetic elements in the genome of Bifidobacterium longum ATCC15697 relative to other sequenced bifidobacteria, a feature positively affecting rearrangement frequencies [42].”
Repeated DNA sequences as an engine of biological diversification
Grechko, V. V. (2011) · Molecular Biology · doi:10.1134/s0026893311050050 · Cited by 12 · see citing works
“The network occurs, to a certain extent, in all eukaryotes [22] and prokaryotes (see [23] and refer ences therein).”
BackgroundPalindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii
Suyama, M., Lathe, W. C., & Peer Bork, B. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.08.051 · Cited by 9 · see citing works
“genomes, it has been concluded that there is a strong correlation between repeat density and gene order conservation, indicating that the repetitive elements are involved in genome rearrangements [32].”
BackgroundRahi, Y. J., Turco, S., Taratufolo, M. C., Tatì, M., Cerboneschi, M., Tegli, S., Valentini, F., D'ONGHIA, A. M., Iacobellis, N. S., Balestra, G. M., et al. (2020) · Journal of Plant Pathology · doi:10.1007/s42161-020-00589-0 · Cited by 8 · see citing works
For absent friends: life without recombination in mutualistic γ-proteobacteria
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Plastid Genome Assembly Using Long-read Data (ptGAUL)Preprint
Zhou, W., Armijos, C. E., Lee, C., Lu, R., Wang, J., Ruhlman, T. A., Jansen, R. K., Jones, A. M., & Jones, C. D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.19.517194 · Cited by 6 · see citing works
“The relationship is also supported by findings in bacterial genomes where repeated sequences lead to gene order rearrangements (Rocha, 2003).”
BackgroundAmoros, J., Namias, A., Durand, T., Alout, H., Martinez, J., Weill, M., & Sicard, M. (2026) · Genetics · doi:10.1093/genetics/iyag135 · Cited by 5 · see citing works
“The presence of highly conserved regions near cid pairs (especially in a palindromic manner) increases the probability of recombination (homologous or gene conversion) be-tween genomic regions flanked by these repetitions (Rocha 2003; Vos 2009; Paulsson et al. 2017).”
Shaskolskiy, B. L., Kandinov, I., Gryadunov, D. A., & Kravtsov, D. (2024) · Molecular Biology · doi:10.1134/s0026893324700535 · Cited by 5 · see citing works
Analyzing stochastic transcription to elucidate the nucleoid's organization
Riva, A., Carpentier, A.-S., Barloy-Hubler, F., Cheron, A., & Hénaut, A. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-125 · Cited by 4 · see citing works
“The conclusions are that gene order is not conserved and rearrangements frequent, not only when comparing different bacterial species [ 20 ] but also different variants of the same bacterial strain [21].”
BackgroundHighly variable rates of genome rearrangements between Hemiascomycetous yeast lineages
Fischer, G., Rocha, E. P. C., Brunet, F., Vergassola, M., & Dujon, B. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0020032.eor · Cited by 4 · see citing works
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“Recombination between 108 homologous segments in genomes leads to chromosomal instability (Hughes, 1999; Rocha, 109 2004), and among bacteria, the rate of chromosomal rearrangements correlates with the 110 number of repeated sequences in genomes (Rocha, 2003).”
BackgroundThe evolution of mitochondrial genome structure and function in insects
Stewart, J. B. (2005) · Summit (Simon Fraser University) · Cited by 3 · see citing works
On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem
Swidan, F., Ziv-Ukelson, M., & Pinter, R. Y. (2006) · Journal of Computational Biology · doi:10.1089/cmb.2006.13.1397 · Cited by 3 · see citing works
“Several studies indicate a strong association between repeats and recombination events (Rocha, 2003a, 2003b, 2004; Achaz et al., 2003; Rocha et al., 1999).”
On the evolution of chromosomal regions with high gene strand bias in bacteria
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Signal metrics analysis of oscillatory patterns in bacterial multi-omic networks
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“Moreover, even if the maintenance of the gene order is not well understood [29], this research could give new clues to its meaning, underlining its dynamical relations with the proteomic layer under the evolutionary pressure [36].”
Comparison of Genomes As 2-Level Pattern Analysis
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“This is consistent with the results in bacteria; the higher the repetition density is, the higher the rearrangement rate, ultimately leading to an accelerated loss of gene order (Rocha 2003).”
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Genome Projects on Model Organisms
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Dynamique des génomes du genre Streptomyces
Lorenzi, J.-N. (2020) · doi:10.70675/e7c5bbaaz782ez4c4az8e20z316346c872ad
- Authors
- Rocha, E. P. C.
- Affiliations
- Institut Pasteur (FR)
- Corresponding author
- Rocha, Eduardo P.C.
- ORCID
- Rocha, Eduardo P.C.
- Venue
- Trends in Genetics
- Publisher
- Elsevier BV
- Published
- 2003-11
- Volume
- 19
- Issue
- 11
- Pages
- 600-603
- ISSN
- 0168-9525 (ISSN-L)
- OpenAlex
- W1965467702
- Cited by
- 59
- References
- 28
- Citations by year
- 2026: 2 · 2024: 2 · 2023: 2 · 2022: 2 · 2020: 5 · 2018: 2 · 2017: 2 · 2016: 1 · 2015: 2 · 2014: 1 · 2013: 3 · 2012: 1
- FWCI
- 0.68
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Trends in Genetics (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- repetitive DNA, chromosomal rearrangements, horizontal gene transfer, Gammaproteobacteria
- MeSH terms
- Models, Genetic, Repetitive Sequences, Nucleic Acid, Evolution, Molecular, Gammaproteobacteria, Gene Order
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 ›
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