The DOI matches its Crossref record; 26 of the 26 references it cites were found in a registry or an index.
Evolution of gene order conservation in prokaryotes
Open accessAbstract
BACKGROUND: As more complete genomes are sequenced, conservation of gene order between different organisms is emerging as an informative property of the genomes. Conservation of gene order has been used for predicting function and functional interactions of proteins, as well as for studying the evolutionary relationships between genomes. The reasons for the maintenance of gene order are still not well understood, as the organization of the prokaryote genome into operons and lateral gene transfer cannot possibly account for all the instances of conservation found. Comprehensive studies of gene order are one way of elucidating the nature of these maintaining forces. RESULTS: Gene order is extensively conserved between closely related species, but rapidly becomes less conserved among more distantly related organisms, probably in a cooperative fashion. This trend could be universal in prokaryotic genomes, as archaeal genomes are likely to behave similarly to bacterial genomes. Gene order conservation could therefore be used as a valid phylogenetic measure to study relationships between species. Even between very distant species, remnants of gene order conservation exist in the form of highly conserved clusters of genes. This suggests the existence of selective processes that maintain the organization of these regions. Because the clusters often span more than one operon, common regulation probably cannot be invoked as the cause of the maintenance of gene order. CONCLUSIONS: Gene order conservation is a genomic measure that can be useful for studying relationships between prokaryotes and the evolutionary forces shaping their genomes. Gene organization is extensively conserved in some genomic regions, and further studies are needed to elucidate the reason for this conservation.
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?
The cited source says what the claim attributes to it.
In the citing paper
“In conjunction with this, biological insight into genome locality (i.e., operonal or transcription unit structure) of related bacterial organisms can assist in clarifying the function of unknown JCVI-syn3A genes since genome architecture/gene locality is often significantly conserved in related organisms.47,48”
From Toward the Complete Functional Characterization of a Minimal Bacterial Proteome (2022) · cites this paper as [47]
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
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Phylogenetic Classification and the Universal Tree
Doolittle, W. F. (1999) · Science · doi:10.1126/science.284.5423.2124 · Cited by 1,888
Nelson, K. E., Clayton, R. A., Gill, S. R., Gwinn, M. L., Dodson, R. J., Haft, D. H., Hickey, E. K., Peterson, J. D., Nelson, W. C., Ketchum, K. A., et al. (1999) · Nature · doi:10.1038/20601 · Cited by 1,493
The use of gene clusters to infer functional coupling.
Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G., & Maltsev, N. (1999) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.96.6.2896 · Cited by 1,365
Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS
Shigenobu, S., Watanabe, H., Hattori, M., Sakaki, Y., & Ishikawa, H. (2000) · Nature · doi:10.1038/35024074 · Cited by 1,338
Conservation of gene order: a fingerprint of proteins that physically interact
Dandekar, T. (1998) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(98)01274-2 · Cited by 1,047
The genome sequence of the plant pathogen Xylella fastidiosa
Simpson, A. J. G., Reinach, F. C., Arruda, P., Abreu, F. A., Acencio, M. L., Alvarenga, R., Alves, L. M. C., Araya, J. E., Baía, G. S., Baptista, C. S., et al. (2000) · Nature · doi:10.1038/35018003 · Cited by 929
Genome phylogeny based on gene content
Snel, B., Bork, P., & Huynen, M. A. (1999) · Nature Genetics · doi:10.1038/5052 · Cited by 722
Selfish Operons: Horizontal Transfer May Drive the Evolution of Gene Clusters
Lawrence, J. G., & Roth, J. R. (1996) · Genetics · doi:10.1093/genetics/143.4.1843 · Cited by 689
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences.Preprint
Huynen, M., Snel, B., Lathe, W. C., & Bork, P. (2000) · Genome Research · doi:10.1101/gr.10.8.1204 · Cited by 525
Research works printed but not linked: 6
- Ayala JA, Garrido T, de Pedro MA, Vicente M: New Comprehensive Biochemistry, Vol 27: Bacterial Cell Wall. London; Elsevier Science:. 1994, 73-101.
- Andersson JO: Is Buchnera a bacterium or an organelle?. Curr Biol. 2000, 10: R866-R868. 10.1016/S0960-9822(00)00816-2. · DOI
- Roth JR, Benson N, Galitski T, Haack K, Lawrence JG, Miesel L: Rearrangements of the bacterial chromosome: formation and applications. In Escherichia coli and Salmonella typhimurium. Edited by Neidhardt FC, Curtiss R, Ingraham JL, Lin ECC, Brooks Low K, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE. Washington DC: ASM Press;. 1996
- Moran N, Munson MA, Baumann P, Ishikawa H: A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts. Proc R Soc Lond B. 1993, 253: 161-171. · DOI
- Tamames J, Ouzounis C, Casari G, Valencia A: EUCLID: Automatic classification of proteins in functional classes by their database annotations. Bioinformatics. 1996, 14: 542-543. 10.1093/bioinformatics/14.6.542. · DOI
- National Center for Biotechnological Information. [http://www.ncbi.nlm.nih.gov]
Cited by
Sorted by citations
Items 101–189 of 189
Completely sequenced genomes of pathogenic bacteria: A review
Guzmán, E., Romeu, A., & Garcı́a-Vallvé, S. (2008) · Enfermedades Infecciosas y Microbiología Clínica · doi:10.1157/13115544 · Cited by 16
Doddapaneni, H., Liao, H.-L., Lin, H., Bai, X.-J., Zhao, X.-L., Civerolo, E., Irey, M., Coletta-Filho, H., & Pietersen, G. (2008) · BMC Research Notes · doi:10.1186/1756-0500-1-72 · Cited by 14
“Studies of the comparative gene organization and gene order among related bacteria, can lead to improved understanding of the functional significance of gene arrangements among them [11,12].”
BackgroundA hybrid gene team model and its application to genome analysis.
Kim, S., Choi, J.-H., Saple, A., & Yang, J. (2006) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720006001850 · Cited by 14
Synteny-aware functional annotation of bacteriophage genomes with PhyntenyPreprint
Grigson, S., Bouras, G., Papudeshi, B., Mallawaarachchi, V., Roach, M., Decewicz, P., & Edwards, R. (2025) · bioRxiv · doi:10.1101/2025.07.28.667340 · Cited by 13
“While global gene order is less conserved in bacteria than in phages, functionally related genes in bacteria often cluster together in operons or other conserved neighborhoods, providing valuable context for functional inference 53 .”
Brandis, G., Cao, S., & Hughes, D. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz129 · Cited by 13
“So far, the underlying mechanism behind this selection is only poorly understood (Tamames 2001).”
BackgroundKhedkar, S., & Seshasayee, A. (2016) · G3: Genes, Genomes, Genetics · doi:10.1534/g3.116.028274 · Cited by 13
“Gene organization changes as species diverge (Tamames 2001).”
Short and long-term genome stability analysis of prokaryotic genomes
Brilli, M., Liò, P., Lacroix, V., & Sagot, M. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-309 · Cited by 13
“This suggests that the main selective pressure towards gene clustering could be the co-localization of the synthesis of interacting partners, as it has been previously proposed on a limited number of genomes [18,52,53].”
Mahmood, K., Konagurthu, A., Song, J., Buckle, A., Webb, G. I., & Whisstock, J. (2010) · Bioinform. · doi:10.1093/bioinformatics/btq339 · Cited by 13
Brandis, G. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab041 · Cited by 12
“Conservation on a higher order, operon synteny, is virtually absent in bacteria (Tamames 2001).”
BackgroundUniversal and idiosyncratic characteristic lengths in bacterial genomes
Junier, I., Frémont, P., & Rivoire, O. (2018) · Physical Biology · doi:10.1088/1478-3975/aab4ac · Cited by 12
Niu, Y.-L., Moghimyfiroozabad, S., Safaie, S., Yang, Y., Jonas, E., & Alavian, K. N. (2017) · Journal of Molecular Evolution · doi:10.1007/s00239-017-9819-3 · Cited by 12
“Gene order in transcription units is generally conserved among the phylogenetically close species, but this conservation is rapidly lost over a short period of evolutionary time (Tamames 2001).”
BackgroundInfluentialRangel-Chávez, C. P., Galán-Vásquez, E., & Martínez‐Antonio, A. (2017) · Molecular BioSystems · doi:10.1039/c6mb00789a · Cited by 15
Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency
Weng, F. C., Su, C.-H., Hsu, M.-T., Wang, T.-Y., Tsai, H.-K., & Wang, D. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-565 · Cited by 12
“Since gene order conservation is a genomic feature that is extensively conserved between closely related species [35,36], the trend should be universal in prokaryotic genomes [37].”
BackgroundEmerging trends in genomic and epigenomic regulation of plant specialised metabolism.
Conneely, L., Berkowitz, O., & Lewsey, M. G. (2022) · Phytochemistry · doi:10.1016/j.phytochem.2022.113427 · Cited by 11
Was the Last Bacterial Common Ancestor a Monoderm after All?
Léonard, R. R., Sauvage, E., Lupo, V., Perrin, A., Sirjacobs, D., Charlier, P., Kerff, F., & Baurain, D. (2022) · Genes · doi:10.3390/genes13020376 · Cited by 11
“This cluster is found in many bacteria and its composition and gene order are generally well conserved [19,20].”
BackgroundThairu, M., & Hansen, A. (2019) · FEMS Microbiology Letters · doi:10.1093/femsle/fnz049 · Cited by 11
A two-enzyme adaptive unit within bacterial folate metabolism
Schober, A., Mathis, A. D., Ingle, C., Park, J. O., Chen, L., Rabinowitz, J. D., Junier, I., Rivoire, O., & Reynolds, K. (2017) · bioRxiv · doi:10.1101/120006 · Cited by 11
Kumar, A., Manivelan, V., & Bansal, M. (2016) · FEMS Microbiology Letters · doi:10.1093/femsle/fnw207 · Cited by 11
From multiple pathogenicity islands to a unique organized pathogenicity archipelago
Bouyioukos, C., Reverchon, S., & Képès, F. (2016) · Scientific Reports · doi:10.1038/srep27978 · Cited by 13
Identification of conserved gene clusters in multiple genomes based on synteny and homology
Sarkar, A., Soueidan, H., & Nikolski, M. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-s9-s18 · Cited by 11
“Third, the authors relax the definition of conserved regions by allowing gaps [18,21-24].”
BackgroundDíaz, R., Vargas-Lagunas, C., Villalobos-López, M. Á., Peralta, H., Mora, Y., Encarnación‐Guevara, S., Girard, L., & Mora, J. (2010) · Journal of Bacteriology · doi:10.1128/jb.01010-10 · Cited by 9
“Conservation of a syntenic block could be favored by selective pressure because the arrangement allows the sequential or coordinated expression of genes that correctly integrate important metabolic functions (41, 64, 69).”
BackgroundGenome classification by gene distribution: An overlapping subspace clustering approach
Li, J., Halgamuge, S., & Tang, S.-L. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-116 · Cited by 11
“Such conservation may be caused by functional constraints, such as favoring lateral gene transfer [46] or allowing co-transcription and co-regulation of genes [43,46].”
BackgroundThe bacterial dcw gene cluster: an island in the genome?
Mingorance, J., & Tamames, J. (2004) · Kluwer Academic Publishers eBooks · doi:10.1007/0-306-48579-6_13 · Cited by 11
“coli genes have a genome organization highly conserved across the prokaryotes (Tamames, 2001).”
BackgroundSelf-citationDuca, S. D., Semenzato, G., Esposito, A., Liò, P., & Fani, R. (2023) · Genes · doi:10.3390/genes14040949 · Cited by 10
“According to Tamames [34], the maintenance of gene order can be due to (i) recent divergence of the species, (ii) horizontal gene transfer of a block of genes, or (iii) the importance of the integrity of the cluster to the fitness of the cell.”
BackgroundInfluentialA study on multi-omic oscillations in Escherichia coli metabolic networks
Bardozzo, F., Lió, P., & Tagliaferri, R. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2175-5 · Cited by 14
Vishnoi, A., Roy, R., Prasad, H. K., & Bhattacharya, A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0014159 · Cited by 13
“These may lead to discrepancies in phylogeny in both closely and distantly related genomes [14], for example, they fails to give a correct relationship when closely related genomes share less number of genes because of secondary loss due to adaptation in different ecological niche or due to duplication of genes [15].”
BackgroundPapaleo, M. C., Russo, E., Fondi, M., Emiliani, G., Frandi, A., Brilli, M., Pastorelli, R., & Fani, R. (2009) · Gene · doi:10.1016/j.gene.2009.08.002 · Cited by 10
“This idea is in agreement with the notion that genes coding for proteins that have to interact to form an active complex very often are clustered in conserved operons (Tamames, 2001).”
ResultReplication-Dependent Organization Constrains Positioning of Long DNA Repeats in Bacterial Genomes
Malhotra, N., & Seshasayee, A. S. N. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac102 · Cited by 8
Genome modularization reveals overlapped gene topology is necessary for efficient viral reproduction
Wright, B. W., Ruan, J.-F., Molloy, M., & Jaschke, P. R. (2020) · bioRxiv · doi:10.1101/2020.06.10.143693 · Cited by 9
“…Tsochatzidou, Malliarou et al., 2017) and as such, gene order tends to be evolutionarily conserved (Dandekar, Snel et al., 1998, Davila Lopez, Martinez Guerra et al., 2010, Herniou, Olszewski et al., 2003, Minot, Wu et al., 2012, Poyatos & Hurst, 2007, Singer, Lloyd et al., 2004, Tamames, 2001).”
BackgroundFLIM-MAP: Gene Context Based Identification of Functional Modules in Bacterial Metabolic Pathways
Bhatt, V., Mohapatra, A., Anand, S., Kuntal, B. K., & Mande, S. S. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02183 · Cited by 9
“It is now well established that bacterial metabolic pathways are encoded by co-regulated genes lying in juxtaposition (evolutionarily conserved gene clusters and/or operons) on the genome for improved efficiency (Overbeek et al., 1999; Tamames, 2001; Ballouz et al., 2010).”
Individual Gene Cluster Statistics in Noisy Maps
Raghupathy, N., & Durand, D. (2005) · Comparative Genomics · doi:10.1007/11554714_10 · Cited by 9
“The intuitive notion that gene clusters share similar, but not conserved, gene content has been translated into a number of different formal models for finding and testing clusters (Arabidopsis Genome Initiative, 2000; Bansal, 1999; Bergeron et al., 2002; Ponting et al., 2000; Calabrese et al., 2003; Goldberg et al.,…”
BackgroundConserved units of co-expression in bacterial genomes: an evolutionary insight into gene regulation
Junier, I., & Rivoire, O. (2014) · bioRxiv · doi:10.1101/012526 · Cited by 8
“…we apply here this approach to a systematic analysis of the conservation of relative distances between orthologous genes in different species, known as synteny properties (Lathe et al, 2000; Tamames, 2001; Rogozin et al, 2002; Snel et al, 2002; Rocha, 2005; Wright et al, 2007; Fang et al, 2008).”
MethodInfluentialLacroix, T., Loux, V., Gendrault, A., Hoebeke, M., & Gibrat, J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku867 · Cited by 8
Evolutionary trends in the prokaryotic community and prokaryotic community-phage systems
Lashin, S., Matushkin, Y., Suslov, V., & Kolchanov, N. (2011) · Russian Journal of Genetics · doi:10.1134/s1022795411110123 · Cited by 8
Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction
Wright, B. W., Ruan, J., Molloy, M. P., & Jaschke, P. R. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00323 · Cited by 13
Librado, P., & Rozas, J. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt158 · Cited by 7
“For each inferred cluster, we measured the conservation level as the branch length score (BLS), that is, the total divergence time (Tamura et al. 2004) since the cluster origin.”
MethodKról, J., Mazur, A., Marczak, M., & Skorupska, A. (2008) · Zeitschrift für Induktive Abstammungs- und Vererbungslehre · doi:10.1007/s00438-007-0299-9 · Cited by 7
“genome evolution and seem to be correlated with gene essentiality when speciWc functions are concerned (Tamames 2001; Guerrero et al. 2005).”
BackgroundCurrent trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes
Brilli, M., Fani, R., & Liò, P. (2007) · Briefings Bioinform. · doi:10.1093/bib/bbm051 · Cited by 7
“Genes of a metabolic pathway can be organized in operons; the evolutionary origin of operons and the selective forces promoting or demoting it are still a matter of debate [44–50], but one of the major benefits of an operon is the co-expression of component genes.”
BackgroundSchmidt, T., & Stoye, J. (2007) · doi:10.1007/978-1-59745-515-2_12 · Cited by 7
Transporter's evolution and carbohydrate metabolic clusters.
Plantinga, T. H., van der Does, C., & Driessen, A. (2004) · Trends in Microbiology · doi:10.1016/j.tim.2003.11.001 · Cited by 7
Daifuku, T., Yoshida, T., Kitamura, T., Kawaichi, S., Inoue, T., Nomura, K., Yoshida, Y., Kuno, S., & Sako, Y. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01089-13 · Cited by 6
“Genome synteny decreases with phylogenetic distance, although this relationship varies depending on the group examined (32, 33).”
BackgroundTheories of biological evolution from the viewpoint of the modern systemic biology
Lashin, S., Suslov, V., & Matushkin, Y. (2012) · Russian Journal of Genetics · doi:10.1134/s1022795412030064 · Cited by 6
Lashin, S., Matushkin, Y., Suslov, V., & Kolchanov, N. (2012) · Ecological Modelling · doi:10.1016/j.ecolmodel.2011.11.004 · Cited by 6
GO4genome: A Prokaryotic Phylogeny Based on Genome Organization
Merkl, R., & Wiezer, A. (2009) · Journal of Molecular Evolution · doi:10.1007/s00239-009-9233-6 · Cited by 6
Exploring genome architecture through GOV: a WWW-based gene order visualizer
Sakharkar, K. R., & Chow, V. (2004) · Bioinform. · doi:10.1093/bioinformatics/bth046 · Cited by 6
“As more and more genomes are being sequenced, gene order comparison is emerging as an informative property of the genomes which gives information not only on genome architecture but also on the functions and interactions of the proteins in genomes besides information on genome and organismal evolution ( Tamames, 2001…”
BackgroundVicente, M., Tamames, J., Valencia, A., & Mingorance, J. (2004) · Springer US · doi:10.1007/b113362 · Cited by 6
Self-citationRusu, I. (2013) · Theoretical Computer Science · doi:10.1016/j.tcs.2014.06.004 · Cited by 5
“Under the assumption that a set of genes occurring in neighboring locations within several genomes represent functionally related genes [11, 17, 21], common intervals and their subclasses are used to represent such conserved regions, thus helping for instance to detect clusters of functionally related genes [18, 22],…”
BackgroundModeling and comparing the organization of circular genomes
Shieh, G. S., Zheng, S.-R., Johnson, R. A., Chang, Y.-F., Shimizu, K., Wang, C.-C., & Tang, S.-L. (2011) · Bioinform. · doi:10.1093/bioinformatics/btr049 · Cited by 5
“Contact: gshieh@stat.sinica.edu.tw Supplementary information: Supplementary data are available at Bioinformatics online.”
InfluentialMotro, Y., Dunn, D., La, T., Phillips, N., Hampson, D., & Bellgard, M. (2008) · doi:10.4137/mbi.s762 · Cited by 5
“Three potential reasons for gene order conservation between species have been suggested (Tamames, 2001).”
BackgroundStochastic evolution and multifractal classification of prokaryotes
Berryman, M. J., Allison, A. G., & Abbott, D. (2003) · SPIE International Symposium on Fluctuations and Noise · doi:10.1117/12.484914 · Cited by 5
Gene order in Prokaryotes: conservation and implications
Gomez, M., Cases, I., & Valencia, A. (2004) · Kluwer Academic Publishers eBooks · doi:10.1007/0-306-48579-6_11 · Cited by 5
Luo, T., Zhang, Q., Pang, S., Qin, Y., Zhang, B., & Bian, X. (2025) · Genes · doi:10.3390/genes16050565 · Cited by 4
MALDI‐TOF‐MS Based on Ribosomal Protein Coding in S10‐spc‐alpha Operons for Proteotyping
Tamura, H. (2017) · doi:10.1002/9781118960226.ch12 · Cited by 4
Kanyó, I., & Molnár, L. (2016) · doi:10.1016/j.genrep.2016.09.004 · Cited by 4
Comparative genomic analysis by microbial COGs self-attraction rate.
Santoni, D., & Spica, V. R. (2009) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2009.01.035 · Cited by 4
“4 instrument to evaluate phylogenetic distances in prokaryotes (Tamames, 2001).”
BackgroundInfluentialRodríguez-Salinas, E., Remacle, C., & González‐Halphen, D. (2012) · Advances in botanical research · doi:10.1016/b978-0-12-394279-1.00008-9 · Cited by 2
Evolutionary Genomics of the Nitrogen-Fixing Symbiotic Bacteria
González, V., Lozano, L. F., Castillo-Ramírez, S., González, I., Bustos, P., Santamaría, R. I., Fernández, J. L., Acosta, J. L., & Dávila, G. (2008) · Soil biology · doi:10.1007/978-3-540-75575-3_7 · Cited by 4
“It has been shown that gene order is well correlated with the phylogenetic distance that separates the different clades (Tamames 2001).”
BackgroundIdentification and characterization of archaeal pseudomurein biosynthesis genes through pangenomics
Lupo, V., Roomans, C., Royen, E., Ongena, L., Jacquemin, O., Mullender, C., Kerff, F., & Baurain, D. (2025) · mSystems · doi:10.1128/msystems.01401-24 · Cited by 5
DeGenPrime provides robust primer design and optimization unlocking the biosphere
Fulghum, B., Tanker, S., & White, R. (2023) · bioRxiv · doi:10.1093/bioadv/vbae044 · Cited by 3
“In fact, as two species are more distantly related, the conserved regions tend to disappear (Tamames 2001).”
Backgroundde Paula, T. G., Zanella, B., de Moraes, L. N., Valente, J. S., Nascimento-Oliveira, J. I., Mareco, E. A., Fernandez, G., & Dal-Pai-Silva, M. (2021) · Comparative biochemistry and physiology. Part A, Molecular & integrative physiology · doi:10.1016/j.cbpa.2021.111120 · Cited by 3
Large and small rearrangements in the evolution of prokaryotic genomes
Markov, A., & Zakharov, I. A. (2006) · Russian Journal of Genetics · doi:10.1134/s1022795406110123 · Cited by 3
“As the number of prokaryotic genome sequences increased, different quantitative and qualitative methods of gene order comparisons were suggested and applied for the analysis of prokaryotic genomes [10–17].”
MethodNetSyn: prokaryotic genomic context exploration of protein families
Stam, M., Langlois, J., Chevalier, C., Mainguy, J., Reboul, G., Bastard, K., Médigue, C., & Vallenet, D. (2026) · bioRxiv · doi:10.1101/2023.02.15.528638 · Cited by 2
Rethinking metagenome-assembled genome completeness: are we truly recovering complete genomes?
Pellegrinetti, T., Molligan, J., Mendes, L. W., Pedrinho, A., & Pérez-López, E. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1884628 · Cited by 2
“…used markers, including ribosomal proteins, occur within conserved operonic regions or tightly linked genomic neighborhoods (Wang et al., 2000; Tamames, 2001), meaning that completeness estimates may disproportionately reflect recovery of specific conserved genome fractions while providing…”
Bardozzo, F., Lió, P., & Tagliaferri, R. (2020) · Bioinform. · doi:10.1093/bioinformatics/btaa966 · Cited by 2
“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].”
Caldini, C., Duca, S. D., Vassallo, A., Semenzato, G., Fani, R., Pavone, F., & Gardini, L. (2026) · Microorganisms · doi:10.3390/microorganisms14040772 · Cited by 1
Unraveling the Transcriptional Landscape within a Minimized Bacterium via Comparative AnalysisPreprint
Brier, T. A., Cournoyer, J. E., Gilbert, B. R., Glass, S. A., Gao, Y.-L., Yu, Y., Thornburg, Z. R., Goglin, K. C., John, G., Mamaghani, T., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.23.681674 · Cited by 1
“Genome sequence architecture or the arrangement of the genetic motifs along the chromosome is highly conserved across bacterial life (Tamames, 2001; Fondi et al., 2022).”
Ma, L., Zhang, T., Ye, S., Lin, W., Lv, Y., Liu, W.-M., Kong, F.-J., Liu, B.-H., Tang, Y., & Lin, X.-Y. (2025) · Plant Science · doi:10.1016/j.plantsci.2025.112691 · Cited by 1
Origin and Evolution of Pseudomurein Biosynthetic Gene ClustersPreprint
Lupo, V., Roomans, C., Royen, E., Ongena, L., Jacquemin, O., Kerff, F., & Baurain, D. (2022) · bioRxiv · doi:10.1101/2022.11.30.518518 · Cited by 1
“The order of the genes within this cluster is relatively well conserved across the different bacterial lineages (Tamames 2001; Mingorance and Tamames 2004; Real and Henriques 2006), even if some species lack one or more PG biosynthesis genes in their genome (Pilhofer et al.”
BackgroundDeng, X., Zhao, X., Liang, Y., Zhang, L., Jiang, J.-P., Zhao, G.-P., & Zhou, Y. (2019) · BMC Genomics · doi:10.1186/s12864-019-6234-8 · Cited by 1
Phylogenetic analysis of housekeeping Archaeal proteins and early stages of Archaea evolution
Gunbin, K. V., Suslov, V., & Afonnikov, D. (2013) · Paleontological journal · doi:10.1134/s0031030113090098 · Cited by 1
“…is limited by functional importance of particular genes 1 (Shestakov, 2007), which depends on the presence of duplicated gene copies (Shestakov, 2007, Tamames, 2001) and ecology of community, i.e., coexistence of species donors and acceptors of genes in space and time 2 (Shestakov, 2007).”
BackgroundMoreau, V. H. (2010) · doi:10.3844/ajbbsp.2010.35.39 · Cited by 1
“…between organisms and a phylogenetic distance matrix can be constructed from a set of DNA or protein sequences of homologous genes from such organisms (Tamames et al., 1997; Lathe et al., 2000; Huynen and Bork, 1998; Aravind, 2000; Tamames, 2001; Rogozin et al., 2004; Dandekar et al., 1998).”
BackgroundInfluentialMolecular evolution of the N-acetylglucosamine-6-phosphate deacetylase gene
Arunkumar, K., & Manoj, N. (2010) · doi:10.1145/1722024.1722076 · Cited by 1
“If the gene order is conserved between distantly related organisms then that might indicates selection pressure that keeps them together [9, 22].”
BackgroundProtein sequences of linked genes are highly conserved in two bacterial species
Theodosiou, T., & Iliopoulos, I. (2006) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2006.01093.x · Cited by 1
“The use of other approaches, including best reciprocal hits (Tamames, 2001; Pal & Hurst, 2003) and variable cut-off values do not significantly alter the main results presented here (not shown).”
MethodSingh, G. B., & Singh, H. (2005) · IEEE Engineering in Medicine and Biology Magazine · doi:10.1109/memb.2005.1436463 · Cited by 1
“Finally, the Conserved Gene Order-based methods utilize information about the gene neighbors in multiple organisms to predict protein function [ 4 ].”
MethodWhat Genomics Has Taught Us about Bacterial Cell Wall Biosynthesis
Dover, L. (2007) · doi:10.1128/9781555815530.ch13 · Cited by 1
Zhang, J.-W., Du, X.-Y., Tang, J.-B., Dong, X., Guo, X.-S., Li, M., & Xu, D.-M. (2026) · Microorganisms · doi:10.3390/microorganisms14081848
“Functionally coupled genes tend to co-localize in prokaryotic genomes, a principle established by comparative genomics [11–13].”
Unsupervised Whole-Genome Representation Learning Captures Bacterial PhenotypesPreprint
Dufault, C., & Moses, A. M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.01.646674
“Additionally, gene order in prokaryotic genomes has been found to have functional importance, with clusters of genes beyond operons being maintained over evolution (Tamames (2001)).”
Phylogenetic tree inference from local gene contentPreprint
Glazko, G., Gensheimer, M., & Mushegian, A. (2015) · bioRxiv · doi:10.1101/017699
“These observations suggest that (dis)similarity of gene order in two species can reflect the time since their divergence [13, 41, 42] and may therefore be useful for reconstruction of evolutionary events.”
BackgroundIdentifying gene clusters by discovering common intervals in indeterminate strings
Doerr, D., Stoye, J., Böcker, S., & Jahn, K. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-s6-s2 · Cited by 15
“Initial gene cluster models considered only completely conserved genomic segments that retain gene order and orientation [1,2].”
Extending common intervals searching from permutations to sequences
Rusu, I. (2013) · J. Discrete Algorithms · doi:10.1016/j.jda.2014.10.004
“One of the main assumptions in comparative genomics is that a set of genes occurring in neighboring locations within several genomes represent functionally related genes [9, 14, 18].”
BackgroundAnálise in silico de regiões promotoras de genes de Xylella fastidiosa
Tria, F. D. K. (2013) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/d.95.2013.tde-13082013-194053
Easy Identification of Generalized Common and Conserved Nested Intervals
de Montgolfier, F., Raffinot, M., & Rusu, I. (2013) · J. Comput. Biol. · doi:10.1089/cmb.2013.0146
“A very strong paradigm is that groups of genes that remain ‘‘close’’ during evolution work together (see, for instance, Galperin and Koonin, 2000, Lathe et al., 2000, Tamames, 2001).”
Estudos evolutivos do divisomo, um complexo multiprotéico responsável pela divisão bacteriana
de Souza, R. F. (2007) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.46.2007.tde-28032008-100032
(2019) · Elsevier eBooks · doi:10.1016/b978-0-12-813635-5.16001-x
Ciancio, A. (2016) · Springer eBooks · doi:10.1007/978-94-024-0884-3_9
Probabilistic Reconstruction and Comparative Systems Biology of Microbial Metabolism
Caviedes, G. P. (2013) · doi:10.7916/d80c534r
“2) made it possible to extend comparative analysis to complete genomes and the structures of several molecular networks[72-75].”
BackgroundSearching Biological Databases Using Biolinguistic Methods
Singh, G. B. (2006) · Applied mycology and biotechnology · doi:10.1016/s1874-5334(06)80017-1
(2005) · Geological Society London Memoirs · doi:10.1144/gsl.mem.2005.031.01.16
Metadata
- Authors
- Tamames, J.
- Affiliations
- Consejo Superior de Investigaciones Científicas (ES)
- Corresponding author
- Tamames, Javier
- ORCID
- Tamames, Javier
- Venue
- Genome Biology
- Published
- 2001-06-01
- Volume
- 2
- Issue
- 6
- Pages
- RESEARCH0020-RESEARCH0020
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC33396
- OpenAlex
- W1598176384
- Cited by
- 213
- References
- 29
- Citations by year
- 2026: 4 · 2025: 8 · 2024: 3 · 2023: 3 · 2022: 5 · 2021: 5 · 2020: 8 · 2019: 4 · 2018: 4 · 2017: 5 · 2016: 8 · 2015: 3 · 2014: 12 · 2013: 12 · 2012: 8
- FWCI
- 3.27
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genome biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, other-oa)
- Funders
- Centro Nacional de Biotecnología
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Keywords
- gene order conservation, prokaryotic genomes, genome organization, gene clusters, operon, horizontal gene transfer, archaeal genomes, genome evolution, gene expression regulation
- MeSH terms
- Phylogeny, Genome, Bacterial, Conserved Sequence, Evolution, Molecular, Genome, Archaeal, 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 ›
Are you an author, or do you see a problem with this page? Request a review
