Genome plasticity in Candida albicans is driven by long repeat sequences
Open accessAbstract
Genome rearrangements resulting in copy number variation (CNV) and loss of heterozygosity (LOH) are frequently observed during the somatic evolution of cancer and promote rapid adaptation of fungi to novel environments. In the human fungal pathogen Candida albicans, CNV and LOH confer increased virulence and antifungal drug resistance, yet the mechanisms driving these rearrangements are not completely understood. Here, we unveil an extensive array of long repeat sequences (65–6499 bp) that are associated with CNV, LOH, and chromosomal inversions. Many of these long repeat sequences are uncharacterized and encompass one or more coding sequences that are actively transcribed. Repeats associated with genome rearrangements are predominantly inverted and separated by up to ~1.6 Mb, an extraordinary distance for homology-based DNA repair/recombination in yeast. These repeat sequences are a significant source of genome plasticity across diverse strain backgrounds including clinical, environmental, and experimentally evolved isolates, and represent previously uncharacterized variation in the reference genome.
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Genome changes such as whole-chromosome aneuploidy and shorter amplifications can raise resistance.
“Copy number variations, including whole-chromosome aneuploidy and shorter-range amplifications, are genome changes that can increase resistance32,43–49.”
From Drug resistance and tolerance in fungi. (2020) · cites this paper as [49]
The Introduction (page not provided) says that amplification of a chromosome arm confers fluconazole resistance, and the Results report increased resistance with another segmental amplification. The paper also associates aneuploidy broadly with resistant isolates, but the passages do not establish that whole-chromosome aneuploidy itself increases resistance. (LLM, conf=0.82)
Experimental — accuracy not yet measuredMutations in Tac1 increase efflux activity.
“For example, mutations in Tac1, a positive transcriptional regulator of efflux pump genes, increases efflux activity49.”
From Drug resistance and tolerance in fungi. (2020) · cites this paper as [49]
The Introduction identifies Tac1 as a transcriptional activator of drug efflux pumps. It attributes fluconazole resistance to amplification of TAC1 and ERG11, but does not say that mutations in Tac1 increase efflux activity. (LLM, conf=0.84)
Experimental — accuracy not yet measuredThe copy number breakpoints of all segmental aneuploidies occurred at long repeat sequences.
“The copy number breakpoints of all segmental aneuploidies occurred at long repeat sequences as described previously (Todd et al. 2019; Todd and Selmecki 2020).”
From Antifungal Drug Concentration Impacts the Spectrum of Adaptive Mutations in <i>Candida albicans</i> (2023) · cites this paper as Todd et al. 2019
The segmental chromosome LOH events frequently occurred at long inverted repeat sequences similar to copy number breakpoints previously implicated in FLC adaptation.
“The segmental chromosome LOH events frequently occurred at long inverted repeat sequences similar to the copy number breakpoints previously implicated in FLC adaptation (Todd et al. 2019).”
From Antifungal Drug Concentration Impacts the Spectrum of Adaptive Mutations in <i>Candida albicans</i> (2023) · cites this paper as Todd et al. 2019
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Cites
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548 · see citing works
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works
Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1754 · Cited by 15,390 · see citing works
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEMPreprint
Li, H. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1303.3997 · Cited by 9,540 · see citing works
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049 · see citing works
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254 · see citing works
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEMPreprint
Li, H. (2014) · arXiv (Cornell University) · doi:10.6084/m9.figshare.963153.v1 · Cited by 5,150 · see citing works
Jacob, H. (1988) · Bioelectrochemistry and Bioenergetics · doi:10.1016/0302-4598(88)80052-7 · Cited by 4,911 · see citing works
REPuter: the manifold applications of repeat analysis on a genomic scale
Kurtz, S. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.22.4633 · Cited by 2,637 · see citing works
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 · see citing works
Elevated recombination rates in transcriptionally active DNA
Thomas, B. J., & Rothstein, R. J. (1989) · Cell · doi:10.1016/0092-8674(89)90584-9 · Cited by 1,633 · see citing works
THE STABILITY OF BROKEN ENDS OF CHROMOSOMES IN ZEA MAYS
McClintock, B. (1941) · Genetics · doi:10.1093/genetics/26.2.234 · Cited by 1,610 · see citing works
Evolution of pathogenicity and sexual reproduction in eight Candida genomes
Butler, G., Rasmussen, M. D., Lin, M. F., Santos, M. A. S., Sakthikumar, S., Munro, C. A., Rheinbay, E., Grabherr, M., Forche, A., Reedy, J. L., et al. (2009) · Nature · doi:10.1038/nature08064 · Cited by 1,065 · see citing works
Self-citationEffects of Aneuploidy on Cellular Physiology and Cell Division in Haploid Yeast
Torres, E. M., Sokolsky, T., Tucker, C. M., Chan, L. Y., Boselli, M., Dunham, M. J., & Amon, A. (2007) · Science · doi:10.1126/science.1142210 · Cited by 935 · see citing works
Repeat instability: mechanisms of dynamic mutations
Pearson, C. E., Edamura, K. N., & Cleary, J. D. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1689 · Cited by 924 · see citing works
Hastings, P. J., Ira, G., & Lupski, J. R. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000327 · Cited by 818 · see citing works
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 768 · see citing works
R loops: new modulators of genome dynamics and function
Santos-Pereira, J. M., & Aguilera, A. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3961 · Cited by 752 · see citing works
Aneuploidy and Isochromosome Formation in Drug-Resistant <i>Candida albicans</i>
Selmecki, A., Forche, A., & Berman, J. (2006) · Science · doi:10.1126/science.1128242 · Cited by 733 · see citing works
Self-citationSources of DNA Double-Strand Breaks and Models of Recombinational DNA RepairPreprint
Mehta, A., & Haber, J. E. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016428 · Cited by 728 · see citing works
A Recently Evolved Transcriptional Network Controls Biofilm Development in Candida albicans
Nobile, C. J., Fox, E. P., Nett, J. E., Sorrells, T. R., Mitrovich, Q. M., Hernday, A. D., Tuch, B. B., Andes, D. R., & Johnson, A. D. (2012) · Cell · doi:10.1016/j.cell.2011.10.048 · Cited by 711 · see citing works
Repeat instability : mechanisms of dynamic mutations
Pearson, C. E. (2005) · Medical Entomology and Zoology · Cited by 711 · see citing works
Intragenic tandem repeats generate functional variability
Verstrepen, K. J., Jansen, A., Lewitter, F., & Fink, G. R. (2005) · Nature Genetics · doi:10.1038/ng1618 · Cited by 616 · see citing works
Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast
Pavelka, N., Rancati, G., Zhu, J., Bradford, W. D., Saraf, A., Florens, L., Sanderson, B. W., Hattem, G. L., & Li, R. (2010) · Nature · doi:10.1038/nature09529 · Cited by 577 · see citing works
Dunham, M. J., Badrane, H., Ferea, T., Adams, J., Brown, P. O., Rosenzweig, F., & Botstein, D. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.242624799 · Cited by 564 · see citing works
The Behavior in Successive Nuclear Divisions of a Chromosome Broken at Meiosis
McClintock, B. (1939) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.25.8.405 · Cited by 559 · see citing works
Aguilera, A., & García-Muse, T. (2013) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133232 · Cited by 476 · see citing works
Regulation of Single-Strand Annealing and its Role in Genome Maintenance
Bhargava, R., Onyango, D. O., & Stark, J. M. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.06.007 · Cited by 475 · see citing works
Skrzypek, M. S., Binkley, J., Binkley, G., Miyasato, S. R., Simison, M., & Sherlock, G. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw924 · Cited by 455 · see citing works
Polyploidy can drive rapid adaptation in yeast
Selmecki, A. M., Maruvka, Y. E., Richmond, P. A., Guillet, M., Noam Shoresh, F., Sorenson, A. L., De, S., Kishony, R., Franziska Michor, A., Dowell, R. D., et al. (2015) · Nature · doi:10.1038/nature14187 · Cited by 444 · see citing works
Self-citationInduction of Mating in Candida albicans by Construction of MTL a and MTL α Strains
Magee, B. B., & Magee, P. T. (2000) · Science · doi:10.1126/science.289.5477.310 · Cited by 443 · see citing works
The evolution of drug resistance in clinical isolates of Candida albicans.
Ford, C. B., Funt, J. M., Abbey, D., Issi, L., Guiducci, C., Martinez, D. A., Delorey, T., Li, B. Y., White, T. C., Cuomo, C., et al. (2015) · eLife · doi:10.7554/elife.00662 · Cited by 348 · see citing works
Bennett, R. J., & Johnson, A. D. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg235 · Cited by 343 · see citing works
A Human-Curated Annotation of the Candida albicans Genome
Braun, B. R., van het Hoog, M., d'Enfert, C., Martchenko, M., Dungan, J., Kuo, A., Inglis, D. O., Uhl, M. A., Hogues, H., Berriman, M., et al. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010001 · Cited by 342 · see citing works
Forche, A., Alby, K., Schaefer, D., Johnson, A. D., Berman, J., & Bennett, R. J. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060110 · Cited by 338 · see citing works
Self-citationThe Fusion of Broken Ends of Chromosomes Following Nuclear Fusion
McClintock, B. (1942) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.28.11.458 · Cited by 330 · see citing works
Selmecki, A., Gerami‐Nejad, M., Paulson, C., Forche, A., & Berman, J. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06176.x · Cited by 325 · see citing works
Self-citationGenetic and phenotypic intra-species variation in <i>Candida albicans</i>
Hirakawa, M. P., Martinez, D. A., Sakthikumar, S., Anderson, M. Z., Berlin, A., Gujja, S., Zeng, Q., Zisson, E., Wang, J. M., Greenberg, J. M., et al. (2015) · Genome Research · doi:10.1101/gr.174623.114 · Cited by 320 · see citing works
Selmecki, A. M., Dulmage, K., Cowen, L. E., Anderson, J. B., & Berman, J. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000705 · Cited by 319 · see citing works
Self-citationThe ‘obligate diploid’ Candida albicans forms mating-competent haploids
Hickman, M. A., Zeng, G., Forche, A., Hirakawa, M. P., Abbey, D., Harrison, B. D., Wang, Y.-M., Su, C.-H., Bennett, R. J., Wang, Y., et al. (2013) · Nature · doi:10.1038/nature11865 · Cited by 284 · see citing works
Self-citationMechanisms of Gene Duplication and AmplificationPreprint
Reams, A. B., & Roth, J. R. (2015) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016592 · Cited by 266 · see citing works
Zhao, X., Oh, S.-H., Cheng, G., Green, C. B., Nuessen, J. A., Yeater, K., Leng, R. P., Brown, A. J. P., & Hoyer, L. L. (2004) · Microbiology · doi:10.1099/mic.0.26943-0 · Cited by 254 · see citing works
Genomic Plasticity of the Human Fungal Pathogen Candida albicans
Selmecki, A., Forche, A., & Berman, J. (2010) · Eukaryotic Cell · doi:10.1128/ec.00060-10 · Cited by 247 · see citing works
Self-citationIn Candida albicans, White-Opaque Switchers Are Homozygous for Mating Type
Lockhart, S. R., Pujol, C., Daniels, K. J., Miller, M. G., Johnson, A. D., Pfaller, M. A., & Soll, D. R. (2002) · Genetics · doi:10.1093/genetics/162.2.737 · Cited by 235 · see citing works
Stress Alters Rates and Types of Loss of Heterozygosity in Candida albicans
Forche, A., Abbey, D., Pisithkul, T., Weinzierl, M. A., Ringstrom, T., Bruck, D., Petersen, K., & Berman, J. (2011) · mBio · doi:10.1128/mbio.00129-11 · Cited by 234 · see citing works
Self-citationBreak-Induced Replication: The Where, The Why, and The How
Kramara, J., Osia, B., & Malkova, A. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.04.002 · Cited by 234 · see citing works
Break-Induced DNA ReplicationPreprint
Anand, R., Lovett, S. T., & Haber, J. E. (2013) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a010397 · Cited by 223 · see citing works
Kunkel, T. A. (1993) · Nature · doi:10.1038/365207a0 · Cited by 222 · see citing works
Hoyer, L. L., & Cota, E. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00280 · Cited by 216 · see citing works
Bruno, V. M., Wang, Z., Marjani, S. L., Euskirchen, G. M., Martin, J. V., Sherlock, G. J., & Snyder, M. P. (2010) · Genome Research · doi:10.1101/gr.109553.110 · Cited by 210 · see citing works
Gene flow contributes to diversification of the major fungal pathogen Candida albicans
Ropars, J., Maufrais, C., Diogo, D., Marcet-Houben, M., Perin, A., Sertour, N., Mosca, K., Permal, E., Laval, G., Bouchier, C., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04787-4 · Cited by 197 · see citing works
Mouse model of oropharyngeal candidiasis
Solis, N. V., & Filler, S. G. (2012) · Nature Protocols · doi:10.1038/nprot.2012.011 · Cited by 195 · see citing works
Centromeric DNA sequences in the pathogenic yeast Candida albicans are all different and unique
Sanyal, K., Baum, M. P., & Carbon, J. A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404318101 · Cited by 181 · see citing works
Break-induced replication: functions and molecular mechanism
Malkova, A., & Ira, G. (2013) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2013.05.007 · Cited by 180 · see citing works
Polyploid titan cells produce haploid and aneuploid progeny to promote stress adaptation
Gerstein, A. C., Fu, M. S., Mukaremera, L., Li, Z., Ormerod, K. L., Fraser, J. A., Berman, J., & Nielsen, K. (2015) · mBio · doi:10.1128/mbio.01340-15 · Cited by 167 · see citing works
Long Interspersed Element–1 (LINE-1): Passenger or Driver in Human Neoplasms?
Rodić, N., & Burns, K. H. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003402 · Cited by 165 · see citing works
Neocentromeres Form Efficiently at Multiple Possible Loci in Candida albicans
Ketel, C. S., Wang, H. S. W., McClellan, M., Bouchonville, K. J., Selmecki, A. M., Lahav, T., Gerami‐Nejad, M., & Berman, J. G. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000400 · Cited by 164 · see citing works
Self-citationSelmecki, A., Bergmann, S., & Berman, J. (2005) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.04492.x · Cited by 157 · see citing works
Self-citationCroll, D., Zala, M., & McDonald, B. A. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003567 · Cited by 155 · see citing works
Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen
Ene, I. V., Farrer, R. A., Hirakawa, M. P., Agwamba, K., Cuomo, C. A., & Bennett, R. J. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1806002115 · Cited by 155 · see citing works
Hoyer, L. L., Scherer, S., Shatzman, A. R., & Livi, G. P. (1995) · Molecular Microbiology · doi:10.1111/j.1365-2958.1995.tb02219.x · Cited by 150 · see citing works
Evolution in<i>Candida albicans</i>Populations During a Single Passage Through a Mouse Host
Forche, A., Magee, P. T., Selmecki, A., Berman, J., & May, G. (2009) · Genetics · doi:10.1534/genetics.109.103325 · Cited by 147 · see citing works
Self-citationPrevalence 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 147 · see citing works
Abbey, D. A., Funt, J., Lurie-Weinberger, M. N., Thompson, D. A., Regev, A., Myers, C. L., & Berman, J. (2014) · Genome Medicine · doi:10.1186/s13073-014-0100-8 · Cited by 147 · see citing works
Lobachev, K. S., Shor, B. M., Tran, H. T., Taylor, W., Keen, J. D., Resnick, M. A., & Gordenin, D. A. (1998) · Genetics · doi:10.1093/genetics/148.4.1507 · Cited by 144 · see citing works
Mutations Arising During Repair of Chromosome Breaks
Malkova, A., & Haber, J. E. (2012) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155547 · Cited by 141 · see citing works
Gresham, D., Usaite, R., Germann, S. M., Lisby, M., Botstein, D., & Regenberg, B. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1014023107 · Cited by 140 · see citing works
Rustchenko, E. P., Curran, T. M., & Sherman, F. (1993) · Journal of Bacteriology · doi:10.1128/jb.175.22.7189-7199.1993 · Cited by 137 · see citing works
Stukenbrock, E. H., Jørgensen, F. G., Zala, M., Hansen, T. T., McDonald, B. A., & Schierup, M. H. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001189 · Cited by 137 · see citing works
Variations of Candida albicans electrophoretic karyotypes
Rustchenko-Bulgac, E. P. (1991) · Journal of Bacteriology · doi:10.1128/jb.173.20.6586-6596.1991 · Cited by 132 · see citing works
Dosage compensation can buffer copy-number variation in wild yeast
Hose, J., Yong, C. M., Sardi, M. I., Wang, Z., Newton, M. A., & Gasch, A. P. (2015) · eLife · doi:10.7554/elife.05462 · Cited by 131 · see citing works
GC content elevates mutation and recombination rates in the yeast Saccharomyces cerevisiae
Kiktev, D. A., Sheng, Z., Lobachev, K. S., & Petes, T. D. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1807334115 · Cited by 124 · see citing works
Environmental change drives accelerated adaptation through stimulated copy number variation
Hull, R. M., Cruz, C., Jack, C. V., & Houseley, J. M. (2017) · PLoS Biology · doi:10.1371/journal.pbio.2001333 · Cited by 123 · see citing works
Single-cell copy number variant detection reveals the dynamics and diversity of adaptation
Lauer, S. L., Avecilla, G., Spealman, P., Sethia, G., Brandt, N. J., Levy, S. F., & Gresham, D. (2018) · PLoS Biology · doi:10.1371/journal.pbio.3000069 · Cited by 121 · see citing works
Regulations of sugar transporters: insights from yeast
Horák, J. (2013) · Current Genetics · doi:10.1007/s00294-013-0388-8 · Cited by 113 · see citing works
Whole-genome sequencing of a laboratory-evolved yeast strain
Araya, C. L., Payen, C., Dunham, M. J., & Fields, S. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-88 · Cited by 113 · see citing works
Gene amplification in yeast: CUP1 copy number regulates copper resistance
Fogel, S., Welch, J. W., Cathala, G., et al. (1983) · Current Genetics · doi:10.1007/bf00445874 · Cited by 112 · see citing works
Analysis of the serologic response to systemic Candida albicans infection in a murine model
Pitarch, A., Diez‐Orejas, R., Molero, G., Pardo, M., Sánchez, M., Gil, C., & Nombela, C. (2001) · PROTEOMICS · doi:10.1002/1615-9861(200104)1:4 · Cited by 105 · see citing works
VanHulle, K., Lemoine, F. J., Narayanan, V., Downing, B., Hull, K., McCullough, C., Bellinger, M., Lobachev, K. S., Petes, T. D., & Malkova, A. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01740-06 · Cited by 103 · see citing works
Highly 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
Richard, G., Dujon, B., & Haber, J. E. (1999) · Molecular and General Genetics MGG · doi:10.1007/s004380050031 · Cited by 101 · see citing works
Forche, A., Cromie, G., Gerstein, A. C., Solis, N. V., Pisithkul, T., Srifa, W., Jeffery, E., Abbey, D., Filler, S. G., Dudley, A. M., et al. (2018) · Genetics · doi:10.1534/genetics.118.301019 · Cited by 94 · see citing works
Self-citationThe Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects
Sunshine, A. B., Payen, C., Ong, G. T., Liachko, I., Tan, K. M., & Dunham, M. J. (2015) · PLoS Biology · doi:10.1371/journal.pbio.1002155 · Cited by 93 · see citing works
Wickes, B. L., Staudinger, J. L., Magee, B. B., et al. (1991) · Infection and Immunity · doi:10.1128/iai.59.7.2480-2484.1991 · Cited by 88 · see citing works
Fine-Resolution Physical Mapping of Genomic Diversity in Candida albicansPreprint
Chibana, H., Beckerman, J. L., & Magee, P. T. (2000) · Genome Research · doi:10.1101/gr.148600 · Cited by 88 · see citing works
Epigenetically-Inherited Centromere and Neocentromere DNA Replicates Earliest in S-Phase
Koren, A., Tsai, H.-J., Tirosh, I., Burrack, L. S., Barkai, N., & Berman, J. G. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001068 · Cited by 86 · see citing works
Aneuploid Chromosomes Are Highly Unstable during DNA Transformation of Candida albicans
Bouchonville, K. J., Forche, A., Tang, K. E. S., Selmecki, A. M., & Berman, J. G. (2009) · Eukaryotic Cell · doi:10.1128/ec.00209-09 · Cited by 85 · see citing works
Self-citationAneuploidy underlies a multicellular phenotypic switch
Tan, Z., Hays, M., Cromie, G. A., Jeffery, E. W., Scott, A. C., Ahyong, V., Sirr, A., Skupin, A., & Dudley, A. M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1301047110 · Cited by 84 · see citing works
Homologous recombination as a mechanism for genome rearrangements: environmental and genetic effects
Bishop, A. J. R. (2000) · Human Molecular Genetics · doi:10.1093/hmg/9.16.2427 · Cited by 84 · see citing works
Multiple LTR-Retrotransposon Families in the Asexual Yeast Candida albicansPreprint
Goodwin, T. J. D., & Poulter, R. T. M. (2000) · Genome Research · doi:10.1101/gr.10.2.174 · Cited by 80 · see citing works
Zhang, N.-X., Harrex, A., Holland, B., Fenton, L., Cannon, R., & Schmid, J. (2003) · Genome Research · doi:10.1101/gr.1024903 · Cited by 79 · see citing works
Achaz, G., Coissac, É., Viari, A., et al. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026410 · Cited by 75 · see citing works
Marcet-Houben, M., Marceddu, G., & Gabaldón, T. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-295 · Cited by 75 · see citing works
Payen, C., Rienzi, S. C. D., Ong, G. T., Pogachar, J. L., Sanchez, J. C., Sunshine, A. B., Raghuraman, M. K., Brewer, B. J., & Dunham, M. J. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.113.009365 · Cited by 75 · see citing works
Variance of ploidy in Candida albicans
Suzuki, T., Nishibayashi, S., Kuroiwa, T., Kanbe, T., & Tanaka, K. (1982) · Journal of Bacteriology · doi:10.1128/jb.152.2.893-896.1982 · Cited by 74 · see citing works
Transcription and Recombination: When RNA Meets DNAPreprint
Aguilera, A., & Gaillard, H. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016543 · Cited by 73 · see citing works
Chibana, H., Iwaguchi, S., Homma, M., Chindamporn, A., Nakagawa, Y., & Tanaka, K. (1994) · Journal of Bacteriology · doi:10.1128/jb.176.13.3851-3858.1994 · Cited by 61 · see citing works
Adamo, G. M., Lotti, M., Tamás, M. J., & Brocca, S. (2012) · Microbiology · doi:10.1099/mic.0.058024-0 · Cited by 60 · see citing works
Wang, J. M., Bennett, R. J., & Anderson, M. Z. (2018) · mBio · doi:10.1128/mbio.01205-18 · Cited by 59 · see citing works
Brewer, B. J., Payen, C., Raghuraman, M. K., & Dunham, M. J. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002016 · Cited by 55 · see citing works
The Influence of Polyploidy on the Evolution of Yeast Grown in a Sub-Optimal Carbon Source
Scott, A. L., Richmond, P. A., Dowell, R. D., & Selmecki, A. M. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx205 · Cited by 50 · see citing works
Self-citationOrigin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification
Brewer, B. J., Payen, C., Rienzi, S. C. D., Higgins, M. M., Ong, G. T., Dunham, M. J., & Raghuraman, M. K. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005699 · Cited by 47 · see citing works
Candida albicans repetitive elements display epigenetic diversity and plasticity
Freire-Benéitez, V., Price, R. J., Tarrant, D., Berman, J. G., & Buscaino, A. (2016) · Scientific Reports · doi:10.1038/srep22989 · Cited by 47 · see citing works
Flow Cytometry Analysis of Fungal Ploidy
Todd, R. T., Braverman, A. L., & Selmecki, A. M. (2018) · Current Protocols in Microbiology · doi:10.1002/cpmc.58 · Cited by 44 · see citing works
Self-citationChindamporn, A., Nakagawa, Y., Mizuguchi, I., Chibana, H., Doi, M., & Tanaka, K. (1998) · Microbiology · doi:10.1099/00221287-144-4-849 · Cited by 42 · see citing works
Genome Architecture and Its Roles in Human Copy Number Variation
Chen, L., Zhou, W., Zhang, L., & Zhang, F. (2014) · Genomics & Informatics · doi:10.5808/gi.2014.12.4.136 · Cited by 41 · see citing works
Burrack, L. S., Hutton, H. F., Matter, K. J., Clancey, S. A., Liachko, I., Plemmons, A. E., Saha, A., Power, E. A., Turman, B. J., Thevandavakkam, M. A., et al. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006317 · Cited by 40 · see citing works
Functional divergence of gene duplicates through ectopic recombination
Christiaens, J. F., Mulders, S. E. V., Duitama, J., et al. (2012) · EMBO Reports · doi:10.1038/embor.2012.157 · Cited by 39 · see citing works
Anderson, M. Z., Baller, J. A., Dulmage, K., Wigen, L., & Berman, J. G. (2012) · Eukaryotic Cell · doi:10.1128/ec.00230-12 · Cited by 38 · see citing works
Extensive Local Gene Duplication and Functional Divergence among Paralogs in Atlantic Salmon
Warren, I. A., Ciborowski, K. L., Casadei, E., Hazlerigg, D. G., Martín, S., Jordan, W. C., & Sumner, S. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu131 · Cited by 36 · see citing works
Effect of the Major Repeat Sequence on Mitotic Recombination in Candida albicans
Lephart, P., & Magee, P. T. (2006) · Genetics · doi:10.1534/genetics.106.063271 · Cited by 36 · see citing works
Exciting Developments in the Immunology of Fungal Infections
Brown, G. D., & Netea, M. G. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.04.010 · Cited by 35 · see citing works
Functional diversification accompanies gene family expansion of MED2 homologs in Candida albicans
Dunn, M. J., Kinney, G. M., Washington, P. M., Berman, J. G., & Anderson, M. Z. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007326 · Cited by 34 · see citing works
Mount, H. O., Revie, N. M., Todd, R. T., Anstett, K., Collins, C., Costanzo, M., Boone, C., Robbins, N., Selmecki, A., & Cowen, L. E. (2018) · PLOS Genetics · doi:10.1371/journal.pgen.1007319 · Cited by 34 · see citing works
Self-citationThe distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome
Strawbridge, E. M., Benson, G., Gelfand, Y., & Benham, C. J. (2010) · Current Genetics · doi:10.1007/s00294-010-0302-6 · Cited by 30 · see citing works
Ramakrishnan, S., Kockler, Z. W., Evans, R. J., Downing, B., & Malkova, A. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007543 · Cited by 28 · see citing works
Higashimoto, K., Maeda, T., Okada, J., Ohtsuka, Y., Sasaki, K., Hirose, A., Nomiyama, M., Takayanagi, T., Fukuzawa, R., Yatsuki, H., et al. (2013) · European Journal of Human Genetics · doi:10.1038/ejhg.2013.45 · Cited by 25 · see citing works
Tsai, H.-J., Baller, J. A., Liachko, I., Koren, A., Burrack, L. S., Hickman, M. A., Thevandavakkam, M. A., Rusché, L. N., & Berman, J. G. (2014) · mBio · doi:10.1128/mbio.01703-14 · Cited by 21 · see citing works
Coding fungal tandem repeats as generators of fungal diversity
Levdansky, E., Sharon, H., & Osherov, N. (2008) · Fungal Biology Reviews · doi:10.1016/j.fbr.2008.08.001 · Cited by 20 · see citing works
Chu, W., Rikkerink, E. H. A., & Magee, P. T. (1992) · Journal of Bacteriology · doi:10.1128/jb.174.9.2951-2957.1992 · Cited by 15 · see citing works
Goodwin, T. J. D., & Poulter, R. T. M. (1998) · Gene · doi:10.1016/s0378-1119(98)00362-x · Cited by 11 · see citing works
Impact of Genetic Background on Allele Selection in a Highly Mutable Candida albicans Gene, PNG2
Zhang, N., Cannon, R. D., Holland, B. R., Patchett, M. L., & Schmid, J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009614 · Cited by 11 · see citing works
Biological Roles of Protein-Coding Tandem Repeats in the Yeast Candida Albicans
Wilkins, M., Zhang, N., & Schmid, J. (2018) · Journal of Fungi · doi:10.3390/jof4030078 · Cited by 8 · see citing works
Sundstrom, P. (2002) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.1004386.154857 · Cited by 1 · see citing works
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Drug resistance and tolerance in fungi.
Berman, J., & Krysan, D. J. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0322-2 · Cited by 654 · see citing works
Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs
Todd, R. T., & Selmecki, A. (2020) · eLife · doi:10.7554/elife.58349 · Cited by 138 · see citing works
Self-citationThe Dynamic Fungal Genome: Polyploidy, Aneuploidy and Copy Number Variation in Response to Stress
Vande Zande, P., Zhou, X., & Selmecki, A. (2023) · Annual Review of Microbiology · doi:10.1146/annurev-micro-041320-112443 · Cited by 70 · see citing works
Self-citationA Double-Edged Sword: Aneuploidy is a Prevalent Strategy in Fungal Adaptation
Tsai, H.-J., & Nelliat, A. (2019) · Genes · doi:10.3390/genes10100787 · Cited by 60 · see citing works
Chen, L., Zhang, L., Xie, Y., Wang, Y., Tian, X., Fang, W., Xue, X., & Wang, L. (2023) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2023.115007 · Cited by 63 · see citing works
Antifungal Drug Concentration Impacts the Spectrum of Adaptive Mutations in <i>Candida albicans</i>
Todd, R. T., Soisangwan, N., Peters, S., Kemp, B., Crooks, T., Gerstein, A., & Selmecki, A. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad009 · Cited by 53 · see citing works
Self-citationFan, X., Dai, R.-C., Zhang, S., Geng, Y.-Y., Kang, M., Guo, D.-W., Mei, Y.-N., Pan, Y.-H., Sun, Z.-Y., Xu, Y.-C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43380-2 · Cited by 55 · see citing works
Mba, I. E., Nweze, E. I., Eze, E. A., & Anyaegbunam, Z. K. G. (2022) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2022.105256 · Cited by 46 · see citing works
Mitotic Recombination and Adaptive Genomic Changes in Human Pathogenic Fungi
Gusa, A., & Jinks-Robertson, S. (2019) · Genes · doi:10.3390/genes10110901 · Cited by 38 · see citing works
Kukurudz, R. J., Chapel, M., Wonitowy, Q., Adamu Bukari, A.-R., Sidney, B., Sierhuis, R., & Gerstein, A. C. (2022) · G3 · doi:10.1093/g3journal/jkac156 · Cited by 35 · see citing works
Ksiezopolska, E., Schikora-Tamarit, M. À., Carlos Nunez-Rodriguez, J., & Gabaldón, T. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1416509 · Cited by 15 · see citing works
- Authors
- Todd, R. T., Wikoff, T. D., Forche, A., & Selmecki, A.
- Affiliations
- Creighton University (US)
- Bowdoin College (US)
- Corresponding author
- Selmecki, Anna
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2019-06-07
- Volume
- 8
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC6591007
- OpenAlex
- W2948541340
- Cited by
- 118
- References
- 126
- Citations by year
- 2026: 11 · 2025: 11 · 2024: 27 · 2023: 16 · 2022: 23 · 2021: 12 · 2020: 10 · 2019: 8
- FWCI
- 4.39
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Bowdoin - Digital Commons (Bowdoin College) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Nebraska LB692 New Initiatives Grants (LB692 NE Tobacco Settlement Biomedical Research Development New Initiative Grant)
- Nebraska's Established Program to Stimulate Competitive Research (EPSCoR First Award)
- Nebraska Department of Health and Human Services (LB506-2017-55)
- Creighton University (CURAS Faculty Faculty Research Fund)
- National Center for Research Resources (P20RR018788 sub award)
- National Institutes of Health (R15 AI090633)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Health Sciences › Medicine › Infectious Diseases › Antifungal resistance and susceptibility
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- Candida albicans, genome plasticity, copy number variation, loss of heterozygosity, chromosomal inversions, genome rearrangement, homologous recombination, antifungal resistance, virulence, somatic evolution
- MeSH terms
- Adaptation, Biological, Candida albicans, Chromosome Inversion, Recombination, Genetic, Repetitive Sequences, Nucleic Acid, Gene Rearrangement, Genome, Fungal, Loss of Heterozygosity, DNA Copy Number Variations
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