The DOI matches its Crossref record; 75 of the 75 references it cites were found in a registry or an index.
Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes
Open accessAbstract
Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. While there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. We analyzed closely related prokaryote strains or species with small genomes (Helicobacter, Neisseria, Streptococcus, Sulfolobus), average-sized genomes (Bacillus, Enterobacteriaceae), and large genomes (Pseudomonas, Bradyrhizobiaceae) to untangle the effects of duplication and horizontal transfer. After removing the effects of transposable elements and phages, we show that the vast majority of expansions of protein families are due to transfer, even among large genomes. Transferred genes--xenologs--persist longer in prokaryotic lineages possibly due to a higher/longer adaptive role. On the other hand, duplicated genes--paralogs--are expressed more, and, when persistent, they evolve slower. This suggests that gene transfer and gene duplication have very different roles in shaping the evolution of biological systems: transfer allows the acquisition of new functions and duplication leads to higher gene dosage. Accordingly, we show that paralogs share most protein-protein interactions and genetic regulators, whereas xenologs share very few of them. Prokaryotes invented most of life's biochemical diversity. Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families.
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 source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Recent theoretical, comparative genomic and experimental research on microbial evolution clearly indicates that HGT is the principal factor in microbial adaptation and innovation (46, 65, 66, 80).”
From Origin and Evolution of the Universal Genetic Code (2017) · cites this paper as [80]
Experimental — accuracy not yet measuredIn the citing paper
“Given that HGT, even if limited by both physical and selective barriers, remained a key factor of microbial evolution [36,37,38,39,40], and apparently, a condition for long term survival of microbial populations [41,42]”
From Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code (2017) · cites this paper as [40]
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
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · cited 7×
“OrthoMCL defines putative orthologous relationships between a pair of genomes as BLASTP reciprocal better/best hits.”
MethodInfluentialMUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662 · cited 1×
“Protein alignments were generated using MUSCLE [73] and then back-translated to DNA.”
MethodOrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707 · cited 2×
“OrthoMCL defines putative orthologous relationships between a pair of genomes as BLASTP reciprocal better/best hits.”
MethodPAML: a program package for phylogenetic analysis by maximum likelihood
Yang, Z. (1997) · Computer applications in the biosciences · doi:10.1093/bioinformatics/13.5.555 · Cited by 5,377 · cited 1×
“Non-synonymous (dN) and synonymous (dS) substitution rates in paralogs (blue; dashed linear fit) and xenologs (red; solid linear fit) in all clades computed using Codeml from PAML [76] (model = 1, fix_omega = 0).”
MethodSharp, P. M., & Li, W.-H. (1987) · Nucleic Acids Research · doi:10.1093/nar/15.3.1281 · Cited by 3,992 · cited 1×
“We first tested if the two classes of protein families have different gene expression levels using the codon adaptation index (CAI; [44]).”
MethodLateral gene transfer and the nature of bacterial innovation
Ochman, H., Lawrence, J. G., & Groisman, E. A. (2000) · Nature · doi:10.1038/35012500 · Cited by 3,816 · cited 1×
“Horizontal gene transfer (HGT) results in the acquisition of radically new genetic information, liberating genomic evolutionary processes from tinkering exclusively with pre-existing genes”
BackgroundAn efficient algorithm for large-scale detection of protein families
Enright, A. J. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.7.1575 · Cited by 3,536 · cited 4×
“OrthoMCL defines putative orthologous relationships between a pair of genomes as BLASTP reciprocal better/best hits.”
MethodInfluentialISfinder: the reference centre for bacterial insertion sequences
Siguier, P. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj014 · Cited by 2,767 · cited 2×
“coli our databank contained all IS present in IS Finder [67].”
BackgroundTREE-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 · cited 1×
“Tree-Puzzle [74] was used to generate the matrix of distances by maximum likelihood with the HKY+C model and exact parameter estimates.”
MethodBIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
Gascuel, O. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025808 · Cited by 1,850 · cited 2×
“The trees were then computed from these distance matrices using BIONJ [75].”
MethodInfluentialThe Phaeodactylum genome reveals the evolutionary history of diatom genomes
Bowler, C., Allen, A. E., Badger, J. H., Grimwood, J., Jabbari, K., Kuo, A., Maheswari, U., Martens, C., Maumus, F., Otillar, R., et al. (2008) · Nature · doi:10.1038/nature07410 · Cited by 1,719
Bayesian Estimation of Ancestral Character States on Phylogenies
Pagel, M. D., Meade, A., & Barker, D. (2004) · Systematic Biology · doi:10.1080/10635150490522232 · Cited by 1,383 · cited 6×
“Using the BayesTraits ancestral state information [33], we calculated the age of expansions as the distance from the leaf node (genome currently containing the paralog or xenolog) to the ancestral node where the gene expansion event occurred (with respect to the root).”
MethodInfluentialHorizontal gene transfer in eukaryotic evolution
Keeling, P. J., & Palmer, J. D. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2386 · Cited by 1,355 · cited 1×
“in prokaryotes. Importantly, recent works have shown that extensive horizontal transfer also exists among eukaryotes”
BackgroundThe evolution of gene duplications: classifying and distinguishing between models
Innan, H., & Kondrashov, F. A. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2689 · Cited by 1,338
Turning a hobby into a job: How duplicated genes find new functions
Conant, G. C., & Wolfe, K. H. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2482 · Cited by 1,281 · cited 1×
“. Duplicated genes can thus be fixed because sub- or neo-functionalization processes render the two copies adaptive when selection for higher gene dosage ceases (reviewed in”
BackgroundComparative genomics: the bacterial pan-genome
Tettelin, H., Riley, D., Cattuto, C., & Medini, D. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.09.006 · Cited by 1,120 · cited 1×
“HGT occurs at very high rates leading to very large species pan-genomes [25].”
BackgroundProkaryotic Evolution in Light of Gene Transfer
Gogarten, J. P., Doolittle, W. F., & Lawrence, J. G. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004046 · Cited by 986
Derelle, É., Ferraz, C., Rombauts, S., Rouzé, P., Worden, A. Z., Robbens, S., Partensky, F., Degroeve, S., Echeynié, S., Cooke, R., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0604795103 · Cited by 893
Amelioration of Bacterial Genomes: Rates of Change and Exchange
Lawrence, J. G., & Ochman, H. (1997) · Journal of Molecular Evolution · doi:10.1007/pl00006158 · Cited by 865 · cited 1×
“We also tested if higher evolutionary rates in xenologs were caused by amelioration to the host GC content [47] (see Materials and Methods).”
BackgroundThe complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse
McLeod, M. P., Warren, R. M., Hsiao, W., Araki, N., Myhre, M., Fernandes, C., Miyazawa, D., Wong, W., Lillquist, A. L., Wang, D. Y. Q., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607048103 · Cited by 645
Feil, E. J., Holmes, E. C., Bessen, D. E., Chan, M., Day, N., Enright, M. C., Goldstein, R., Hood, D. W., Kalia, A., Moore, C. E., et al. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.98.1.182 · Cited by 522 · cited 1×
“Interestingly, both clades naturally transform conspecific DNA and are known to have extremely high rates of intra-species horizontal transfer [42,43].”
BackgroundGene regulatory network growth by duplication
Teichmann, S. A., & Babu, M. M. (2004) · Nature Genetics · doi:10.1038/ng1340 · Cited by 502 · cited 2×
“Furthermore, models aiming at explaining the patterns of biological networks are in general based on the preconception that protein families expand by gene duplication processes [20,21].”
BackgroundAdaptive evolution of bacterial metabolic networks by horizontal gene transfer
Pál, C., Papp, B., & Lercher, M. J. (2005) · Nature Genetics · doi:10.1038/ng1686 · Cited by 497 · cited 1×
“As such, expansions are a particular case of the processes leading to the horizontal transfer of genetic information that is known to shape metabolic [59], genetic [53] and interaction networks [60,61] in prokaryotes.”
BackgroundEvolution of sensory complexity recorded in a myxobacterial genome
Goldman, B. S., Nierman, W. C., Kaiser, D., Slater, S. C., Durkin, A. S., Eisen, J. A., Ronning, C. M., Barbazuk, W. B., Blanchard, M., Field, C., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607335103 · Cited by 449
Falush, D., Kraft, C., Taylor, N. S., Correa, P., Fox, J. G., Achtman, M., & Suerbaum, S. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.251396098 · Cited by 435 · cited 1×
“Interestingly, both clades naturally transform conspecific DNA and are known to have extremely high rates of intra-species horizontal transfer [42,43].”
BackgroundComplete genome sequence of the myxobacterium Sorangium cellulosum
Schneiker, S., Perlova, O., Kaiser, O., Gerth, K., Alici, A., Altmeyer, M. O., Bartels, D., Bekel, T., Beyer, S., Bode, E., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1354 · Cited by 425 · cited 1×
“Prokaryotes have highly variable gene repertoires, varying from just over 100 genes to nearly 10000 [1,2].”
BackgroundGenome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer
Sorek, R., Zhu, Y., Creevey, C. J., Francino, M. P., Bork, P., & Rubin, E. M. (2007) · Science · doi:10.1126/science.1147112 · Cited by 421 · cited 1×
“coli’s promiscuity to most transferred genes [55] and data highlighting the impact of transferred genes on the evolution of Salmonella [56].”
BackgroundModular networks and cumulative impact of lateral transfer in prokaryote genome evolution
Dagan, T., Artzy-Randrup, Y., & Martin, W. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800679105 · Cited by 409
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
Hu, P., Janga, S. C., Babu, M., Díaz-Mejía, J. J., Butland, G., Yang, W., Pogoutse, O., Guo, X., Phanse, S., Wong, P., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000096 · Cited by 387
Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene ContentPreprint
Snel, ., Bork, P., & Huynen, M. A. (2001) · Genome Research · doi:10.1101/gr.176501 · Cited by 359
Evolutionary Origins of Genomic Repertoires in Bacteria
Lerat, E., Daubin, V., Ochman, H., & Moran, N. A. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030130 · Cited by 338 · cited 2×
“prokaryote genome might have been affected by HGT [26–28], it has been estimated that HGT contributes at best to 25% of all expansions of protein families [26,29–32] (22% overall but 60% for large protein families in [23]).”
BackgroundMethodPhylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer eventsPreprint
Zhaxybayeva, O., Gogarten, J. P., Charlebois, R. L., Doolittle, W. F., & Papke, R. T. (2006) · Genome Research · doi:10.1101/gr.5322306 · Cited by 336
Fouts, D. E. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl732 · Cited by 333 · cited 1×
“We used Phage_finder to predict prophages [68].”
Gene amplification and adaptive evolution in bacteria.
Andersson, D., & Hughes, D. (2009) · Annual Review of Genetics · doi:10.1146/annurev-genet-102108-134805 · Cited by 308 · cited 3×
“Duplication processes in prokaryotes produce tandem, strictly identical copies of genes [8,38,39].”
BackgroundResultThe life and death of gene families
Demuth, J. P., & Hahn, M. W. (2009) · BioEssays · doi:10.1002/bies.080085 · Cited by 306
An Analysis of Determinants of Amino Acids Substitution Rates in Bacterial Proteins
Rocha, E. P. C., & Danchin, A. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh004 · Cited by 283
Self-citationMcCutcheon, J. P., McDonald, B. R., & Moran, N. A. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000565 · Cited by 275 · cited 1×
“Prokaryotes have highly variable gene repertoires, varying from just over 100 genes to nearly 10000 [1,2].”
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 · cited 1×
“We also removed IS and phage sequences, but not the corresponding cargo regions, because these elements constitute a large fraction of repeats in genomes [15], are known to be horizontally transferred and are in general quickly lost [34,35].”
MethodSelf-citationCho, N., Kim, H., Lee, J., Kim, S.-Y., Kim, J., Cha, S., Kim, S.-Y., Darby, A. C., Fuxelius, H., Yin, J., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0611553104 · Cited by 234
GENE AMPLIFICATION AND GENOMIC PLASTICITY IN PROKARYOTES
Romero, D., & Palacios, R. (1997) · Annual Review of Genetics · doi:10.1146/annurev.genet.31.1.91 · Cited by 234 · cited 2×
“Duplication processes in prokaryotes produce tandem, strictly identical copies of genes [8,38,39].”
BackgroundThe Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation
Alm, E. J., Huang, K. H., & Arkin, A. P. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020143 · Cited by 214 · cited 1×
“). There is ample evidence that intra-chromosomal gene duplication (IGD) has an adaptive role in bacteria”
BackgroundEvolution after gene duplication: models, mechanisms, sequences, systems, and organisms
Tellgren‐Roth, C., Rastogi, S., Arvestad, L., Dittmar, K., Light, S., Ekman, D. S., & Liberles, D. A. (2006) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.21124 · Cited by 211
The Balance of Driving Forces During Genome Evolution in ProkaryotesPreprint
Kunin, V., & Ouzounis, C. A. (2003) · Genome Research · doi:10.1101/gr.1092603 · Cited by 203 · cited 1×
“. Yet, while up to 96% of the genes in a given prokaryote genome might have been affected by HGT”
BackgroundAn adaptive radiation model for the origin of new gene functions
Francino, M. P. (2005) · Nature Genetics · doi:10.1038/ng1579 · Cited by 203 · cited 1×
“. They can take place by horizontal gene transfer, in which case homologs are called xenologs, or by intra-chromosomal duplication, in which case homologs are called paralogs. Genes are identical upon duplication and if there is no direct selection on multiple copies, the redundant extra copies are quickly lost. Yet,…”
BackgroundEvolution of protein complexes by duplication of homomeric interactions
Pereira‐Leal, J. B., Levy, E. D., Kamp, C., & Teichmann, S. A. (2007) · Genome biology · doi:10.1186/gb-2007-8-4-r51 · Cited by 192 · cited 6×
“As a result, PPI networks will evolve very differently in lineages affected by horizontal transfer relative to lineages with strictly vertical transmission of genetic information.”
BackgroundInfluentialGene duplication and biased functional retention of paralogs in bacterial genomes
Gevers, D., Vandepoele, K., Simillion, C., & de Peer, Y. V. (2004) · Trends in Microbiology · doi:10.1016/j.tim.2004.02.007 · Cited by 186
Genesis, 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 182 · cited 1×
“We also removed IS and phage sequences, but not the corresponding cargo regions, because these elements constitute a large fraction of repeats in genomes [15], are known to be horizontally transferred and are in general quickly lost [34,35].”
MethodSelf-citationLercher, M. J., & Pál, C. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm283 · Cited by 172 · cited 2×
“As such, expansions are a particular case of the processes leading to the horizontal transfer of genetic information that is known to shape metabolic [59], genetic [53] and interaction networks [60,61] in prokaryotes.”
BackgroundUnbiased Quantitation of Escherichia coli Membrane Proteome Using Phase Transfer Surfactants
Masuda, T., Saito, N., Tomita, M., & Ishihama, Y. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900240-mcp200 · Cited by 152 · cited 1×
“Similar results were found using proteomic data (emPAI) [45] (p,0.”
ResultHorizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli
Price, M. N., Dehal, P., & Arkin, A. P. (2008) · Genome biology · doi:10.1186/gb-2008-9-1-r4 · Cited by 149 · cited 1×
“This picture is in agreement with the frequently observed co-transfer of transcription factors and their target genes [52], and”
ResultExtensive repetitive DNA facilitates prokaryotic genome plasticity
Aras, R. A., Kang, J., Tschumi, A. I., Harasaki, Y., & Blaser, M. J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1735481100 · Cited by 138 · cited 9×
“It is well-established that such repeated elements often engage in gene conversion for antigenic variation both in Neisseria and in Helicobacter [40,41].”
BackgroundInfluentialGene duplications, robustness and evolutionary innovations
Wagner, A. (2008) · BioEssays · doi:10.1002/bies.20728 · Cited by 129
Multiple pathways of selected gene amplification during adaptive mutation
Kugelberg, E., Kofoid, E., Reams, A. B., Andersson, D. I., & Roth, J. R. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0608309103 · Cited by 129
Howell‐Adams, B., & Seifert, H. S. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.02067.x · Cited by 111 · cited 9×
“It is well-established that such repeated elements often engage in gene conversion for antigenic variation both in Neisseria and in Helicobacter [40,41].”
BackgroundInfluentialWagner, A. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj085 · Cited by 108 · cited 1×
“We also removed IS and phage sequences, but not the corresponding cargo regions, because these elements constitute a large fraction of repeats in genomes [15], are known to be horizontally transferred and are in general quickly lost [34,35].”
MethodOrigin and fate of repeats in bacteria
Achaz, G. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf391 · Cited by 106 · cited 2×
“Duplication processes in prokaryotes produce tandem, strictly identical copies of genes [8,38,39].”
BackgroundInference 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-citationSimilar compositional biases are caused by very different mutational effectsPreprint
Rocha, E. P. C., Touchon, M., & Feil, E. J. (2006) · Genome Research · doi:10.1101/gr.5525106 · Cited by 88 · cited 1×
“To limit false positives this list was further refined by combining information on the distribution of similarity of these putative orthologs with gene order conservation data (as in [71]).”
MethodSelf-citationComparative genomics of gene-family size in closely related bacteria
Pushker, R., Mira, Á., & Rodríguez‐Valera, F. (2004) · Genome biology · doi:10.1186/gb-2004-5-4-r27 · Cited by 84
Evolution by leaps: gene duplication in bacteria
Serres, M. H., Kerr, A. R. W., McCormack, T. J., & Riley, M. (2009) · Biology Direct · doi:10.1186/1745-6150-4-46 · Cited by 83
The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli
van Passel, M. W. J., Marri, P. R., & Ochman, H. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000059 · Cited by 77 · cited 1×
“This is in agreement with high rates of change but low rates of fixation of changes in gene repertoires [36,37].”
ResultComplexity, connectivity, and duplicability as barriers to lateral gene transfer
Wellner, A., Lurie-Weinberger, M. N., & Gophna, U. (2007) · Genome biology · doi:10.1186/gb-2007-8-8-r156 · Cited by 76 · cited 1×
“As such, expansions are a particular case of the processes leading to the horizontal transfer of genetic information that is known to shape metabolic [59], genetic [53] and interaction networks [60,61] in prokaryotes.”
BackgroundGenetic flux over time in the Salmonella lineage
Vernikos, G. S., Thomson, N. R., & Parkhill, J. (2007) · Genome biology · doi:10.1186/gb-2007-8-6-r100 · Cited by 74
The impact of long-distance horizontal gene transfer on prokaryotic genome size
Cordero, O. X., & Hogeweg, P. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907584106 · Cited by 72 · cited 1×
“This is concordant with the proposed role of horizontal transfer in the increase in size of the largest bacterial genomes [54].”
BackgroundConservation and topology of protein interaction networks under duplication-divergence evolution
Evlampiev, K., & Isambert, H. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804119105 · Cited by 58 · cited 7×
“As a result, PPI networks will evolve very differently in lineages affected by horizontal transfer relative to lineages with strictly vertical transmission of genetic information.”
BackgroundInfluentialDuplication is more common among laterally transferred genes than among indigenous genes
Hooper, S. D., & Berg, O. G. (2003) · Genome biology · doi:10.1186/gb-2003-4-8-r48 · Cited by 58 · cited 1×
“coli, where genes with the lowest CAI were found to be overrepresented among recent duplications [30], this discrepancy probably results from our explicit removal of IS and phages that have very low CAI because they are A+T rich and are lowly expressed under exponential growth.”
BackgroundDetecting laterally transferred genes: use of entropic clustering methods and genome position
Azad, R. K., & Lawrence, J. G. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm204 · Cited by 54 · cited 1×
“At these distances, gene order conservation is high [58], and positional information can significantly decrease classification errors [72].”
BackgroundLindroos, H. L., Pettersson, O. V., Mira, Á., Repsilber, D., Näslund, K., & Andersson, S. G. E. (2006) · Journal of Bacteriology · doi:10.1128/jb.00472-06 · Cited by 53
Evolutionary patterns in prokaryotic genomes
Rocha, E. P. C. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.09.007 · Cited by 46 · cited 1×
“This is in agreement with high rates of change but low rates of fixation of changes in gene repertoires [36,37].”
ResultSelf-citationNew insights into the regulatory networks of paralogous genes in bacteria
Martínez‐Núñez, M. A., Pérez‐Rueda, E., Gutiérrez-Ríos, R.-M., & Merino, E. (2009) · Microbiology · doi:10.1099/mic.0.033266-0 · Cited by 38
Parmley, J. L., & Hurst, L. D. (2007) · Journal of Molecular Evolution · doi:10.1007/s00239-006-0207-7 · Cited by 36
The Role of Domain Redundancy in Genetic Robustness Against Null Mutations
Pasek, S., Risler, J., & Brézellec, P. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.07.033 · Cited by 27 · cited 1×
“. Such variations in genome size are typically associated with expansions and contractions of protein families. Expansions of protein families are associated with the acquisition of novel functions, novel regulatory structures and system robustness”
BackgroundOn the need for widespread horizontal gene transfers under genome size constraint
Isambert, H., & Stein, R. R. (2009) · Biology Direct · doi:10.1186/1745-6150-4-28 · Cited by 26 · cited 1×
“It has been proposed that due to deletion biases in prokaryotes, gene duplications are not afforded with sufficient opportunity for neo- or sub-functionalization, reducing its role to transient gene amplification [57].”
BackgroundA Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats
Treangen, T. J., Darling, A. E., Achaz, G., Ragan, M. A., Messeguer, X., & Rocha, E. P. C. (2009) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2009.9 · Cited by 16 · cited 1×
“To remove small fragments of IS elements we searched for regions of homology with known IS in the genome using Repeatoire [69].”
MethodSelf-citationErosion of interaction networks in reduced and degraded genomes
Ochman, H., Liu, R., & Rocha, E. P. C. (2007) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.21147 · Cited by 13 · cited 1×
“As such, expansions are a particular case of the processes leading to the horizontal transfer of genetic information that is known to shape metabolic [59], genetic [53] and interaction networks [60,61] in prokaryotes.”
BackgroundSelf-citation
Flagged first, then by citations
Research works printed but not linked: 1
- G Vernikos, 2007, Genetic flux over time in the Salmonella lineage., Genome Biology, 8, R100, 10.1186/gb-2007-8-6-r100 · DOI
Cited by
Sorted by citations
Horizontal gene transfer: building the web of life
Soucy, S. M., Huang, J., & Gogarten, J. P. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3962 · Cited by 1,530
Transposable Elements, Epigenetics, and Genome Evolution
Fedoroff, N. V. (2012) · Science · doi:10.1126/science.338.6108.758 · Cited by 634
Antibiotic resistance in Pseudomonas aeruginosa – Mechanisms, epidemiology and evolution
Botelho, J., Grosso, F., & Peixe, L. M. S. V. (2019) · Drug Resistance Updates · doi:10.1016/j.drup.2019.07.002 · Cited by 590
Stecher, B., Denzler, R., Maier, L., Bernet, F., Sanders, M. J., Pickard, D. J., Barthel, M., Westendorf, A. M., Krogfelt, K. A., Walker, A. W., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1113246109 · Cited by 492
Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote
Schönknecht, G., Chen, W., Ternes, C. M., Barbier, G. G., Shrestha, R. P., Stanke, M., Bräutigam, A., Baker, B. J., Banfield, J. F., Garavito, R. M., et al. (2013) · Science · doi:10.1126/science.1231707 · Cited by 490
Metadata
- Authors
- Treangen, T. J., & Rocha, E. P. C.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Treangen, Todd J.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-01-27
- Volume
- 7
- Issue
- 1
- Pages
- e1001284
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC3029252
- OpenAlex
- W2022927779
- Cited by
- 509
- References
- 75
- Citations by year
- 2026: 18 · 2025: 34 · 2024: 36 · 2023: 26 · 2022: 29 · 2021: 32 · 2020: 52 · 2019: 27 · 2018: 33 · 2017: 31 · 2016: 38 · 2015: 29 · 2014: 34 · 2013: 33 · 2012: 28
- FWCI
- 15.99
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, other-oa)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Centre National de la Recherche Scientifique
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- horizontal gene transfer, gene duplication, protein family expansion, prokaryotes, paralogs, functional novelty, gene dosage, protein-protein interaction, regulatory genes, genome size, Helicobacter, Neisseria, Streptococcus, Sulfolobus, Bacillus, Enterobacteriaceae, Pseudomonas, Bradyrhizobiaceae
- MeSH terms
- Bacillus, Bacteria, Enterobacteriaceae, Multigene Family, Neisseria, Phylogeny, Pseudomonas, Streptococcus, Genome, Bacterial, Sulfolobus, Helicobacter, Evolution, Molecular, Computational Biology, Gene Duplication, Gene Transfer, Horizontal, Bradyrhizobiaceae
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
