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1 1 2 3 4 5 Parasexual Ploidy Reduction Drives Genetics: Early Online, published on May 18, 2015 as 10.1534/genetics.115.178020 1 2 3 4 5 6 Parasexual ploidy reduction drives population heterogeneity through random and 7 transient aneuploidy 8 Meleah A. Hickman*1, Carsten Paulson*, Aimee Dudley§ and Judith Berman*† 9 10 11 12 13 *Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, 14 MN 55455 15 §Pacific Northwest Diabetes Research Institute, Seattle, WA 98122 16 †Department of Molecular Microbiology and Biotechnology, George Wise Faculty of 17 Life Sciences Tel Aviv University, Ramat Aviv, Israel 69978, Corresponding Author: 18 [email protected] or [email protected] 19 20 1Current Address: Department of Biology, Emory University, Atlanta, GA 30322 21 1 Copyright 2015. 22 Abstract 23 The opportunistic pathogen Candida albicans has a large repertoire of mechanisms to generate 24 genetic and phenotypic diversity despite the lack of meiosis in its lifecycle. Its parasexual cycle 25 enables shifts in ploidy, which in turn, facilitate recombination, aneuploidy and homozygosis of 26 whole chromosomes to fuel rapid adaptation. Here we show that the tetraploid state potentiates 27 ploidy variation and drives population heterogeneity. In tetraploids, the rate of losing a single 28 heterozygous marker (LOH) is elevated ~30-fold higher than the rate in diploid cells. 29 Furthermore, isolates recovered after selection for LOH of one, two or three markers were 30 highly aneuploid, with a broad range of karyotypes including strains with a combination of di-, tri- 31 and tetra-somic chromosomes. We followed the ploidy trajectories for these tetraploid- and 32 aneuploid-derived isolates, using a combination of flow cytometry and ddRAD-sequencing. 33 Isolates derived from either tetraploid or aneuploid isolates predominately resolved to a stable 34 euploid state. The majority of isolates reduced to the conventional diploid state, however stable 35 triploid and tetraploid states were observed in ~30% of the isolates. Notably, aneuploid isolates 36 were more transient than tetraploid isolates, resolving to a euploid state within a few passages. 37 Furthermore, the likelihood that a particular isolate will resolve to the same ploidy state in 38 replicate evolution experiments is only ~50%, supporting the idea that the chromosome loss 39 process of the parasexual cycle is random and does not follow trajectories involving specific 40 combinations of chromosomes. Together, our results indicate that tetraploid progenitors can 41 produce populations of progeny cells with a high degree of genomic diversity, from altered 42 ploidy to homozygosis, providing an excellent source of genetic variation upon which selection 43 can act. 44 45 2 46 Introduction 47 Shifts in ploidy between haploid, diploid and/or polyploid states are mediated by both 48 sexual and asexual mechanisms and promote genetic variation within a population of cells. 49 Such transitions not only yield altered whole genome ploidy states, but also facilitate increased 50 frequencies of recombination, aneuploidy and whole chromosome homozygosis that appear to 51 be common features of mitotic divisions in eukaryotic pathogens, including parasites and fungi 52 (CALO et al. 2013). Importantly, these genome changes have the potential to fuel rapid 53 adaptation in microbial populations (SELMECKI et al. 2006; RANCATI et al. 2008; YONA et al. 54 2012) . Similar non-meiotic ploidy shifts occur in somatic mammalian cells such as hepatocytes, 55 and it is thought that some of the aneuploidies and ploidy shifts may provide cells with a 56 selective advantage (BERMAN and HADANY 2012; DUNCAN et al. 2012; DUNCAN 2013). Unusual 57 ploidy states also are a common feature of tumor cell populations, where mitotic collapse 58 (GORDON et al. 2012) and/or telomere defects (DAVOLI and DE LANGE 2012) yield tetraploids that 59 ultimately produce aneuploid progeny cells, some of which outcompete the surrounding cells. 60 Understanding how non-meiotic ploidy reduction occurs in tetraploid and aneuploid cells will 61 provide important insights into these unconventional, but not uncommon, processes. 62 Candida albicans, the most prevalent opportunistic fungal pathogen of humans, has long 63 been considered an asexual, highly heterozygous, obligate diploid organism, but this idea has 64 been challenged by the discovery of haploid (HICKMAN et al. 2013) and tetraploid isolates 65 (SUZUKI et al. 1986; LEGRAND et al. 2004) produced in vitro and/or in vivo. Tetraploid cells can 66 arise through cell cycle defects when exposed to fluconazole and subsequently undergo 67 unequal mitotic divisions with multiple spindles that give rise to aneuploid progeny (HARRISON et 68 al. 2014). Tetraploids can also arise through a diploid-tetraploid parasexual cycle (HULL et al. 69 2000; MAGEE and MAGEE 2000; BENNETT and JOHNSON 2003; FORCHE et al. 2008; SONG and 70 PETES 2012). This parasexual cycle involves mating between diploid cells followed by ploidy 71 reduction, or ‘concerted chromosome loss’ processes, in which loss of markers on one 3 72 chromosome is frequently accompanied by loss of markers on other chromosomes as well, 73 frequently resulting in diploid or near-diploid progeny (BENNETT and JOHNSON 2003). These 74 near-diploid parasexual progeny diverge from the parental type by whole chromosome 75 aneuploidy and by loss of heterozygosity (FORCHE et al. 2008), both of which provide population 76 heterogeneity upon which natural selection can act (BERMAN and HADANY 2012). 77 Completion of the parasexual cycle is thought to be non-meiotic: C. albicans has lost 78 multiple genes required for meiosis in related yeasts, including the transcriptional regulators 79 IME1 and SUM1 and several spore assembly genes (WONG et al. 2003; BUTLER et al. 2009). 80 Furthermore, no obvious ascospores have been detected (VAN DER WALT 1967). Other fungal 81 species also undergo non-meiotic ploidy reduction and parasexual cycles, including the closely 82 related C. tropicalis (SEERVAI et al. 2013) and more distantly related Aspergillus species 83 (PONTECORVO 1956) as well as the rice blast fungus, Magnaporthe grisea (ZEIGLER et al. 1997). 84 In slime molds (e.g. Dictyostelium), ploidy shifts occur through transient aneuploidy (SINHA and 85 ASHWORTH 1969). Non-meiotic ploidy reduction is not restricted to organisms with 86 unconventional life cycles: S. cerevisiae, which has a conventional sexual cycle, can also 87 undergo non-meiotic ploidy reductions, e.g., in mutant backgrounds deficient for DNA repair 88 (SONG and PETES 2012) or for chromosome cohesion (ALABRUDZINSKA et al. 2011) or when 89 polyploid cells are passaged for several hundred generations (GERSTEIN et al. 2006). 90 In S. cerevisiae, tetraploid and triploid cells are less stable than diploid cells (MAYER and 91 AGUILERA 1990; PAVELKA et al. 2010), triploids that undergo meiosis generate aneuploid 92 progeny (ST CHARLES et al. 2012) and tetraploids are prone to chromosome missegregation 93 events due to increased monopolar attachments (STORCHOVA et al. 2006), which may result in 94 aneuploid derivatives. Cells carrying aneuploidies can delay the cell cycle and decrease growth 95 rates (TORRES et al. 2007), especially when cells are propagated in laboratory conditions that 96 optimize rapid population growth. In particular, cells with high degrees of aneuploidy (with 97 genome contents between 1.5N and 2N) are more unstable than cells carrying a small number 4 98 of aneuploidies (i.e. with genome contents close to 1N) (ZHU et al. 2012). This phenomenon is 99 similar to observations in mammalian cells where highly aneuploid genomes are far less viable 100 than those with small numbers of extra chromosomes (WEAVER and CLEVELAND 2006). 101 In C. albicans, the stability of unconventional ploidy states (i.e. tetraploid and aneuploid) 102 and the process by which ploidy reduction occurs are not well understood. C. albicans can 103 tolerate and maintain chromosomal aneuploidy and large tracts of allele homozygosity 104 (LEGRAND et al. 2004; SELMECKI et al. 2005; ARBOUR et al. 2009; BOUCHONVILLE et al. 2009; 105 SELMECKI et al. 2010; ABBEY et al. 2011; ANDALUZ et al. 2011). In addition, exposure to external 106 stress conditions promotes genome instability and increases the rates and types of LOH (loss of 107 heterozygosity) in diploid cells (FORCHE et al. 2011). Specifically, chromosome loss events are 108 observed more frequently following exposure to fluconazole (FORCHE et al. 2011) or heat shock 109 (HILTON et al. 1985; BOUCHONVILLE et al. 2009) in diploid cells. Furthermore, elevated 110 temperatures and prolonged growth (7-10 days) on glucose-rich or on sorbose media results in 111 ~diploid progeny from tetraploid parents (BENNETT and JOHNSON 2003). However, it remains 112 unclear how rapidly tetraploid cells lose chromosomes to return to a diploid state or whether 113 other ploidy states can be maintained. 114 Here we found that the C. albicans tetraploid genome undergoes higher levels of LOH 115 than the diploid genome. Tetraploid cells underwent detectable ploidy changes over both short 116 and extended times of experimental evolution. Selection for marker loss in tetraploid cells 117 enriched for the rare cells that lose chromosomes, and these resulting aneuploids were 118 intermediates in the chromosome loss phase of the parasexual cycle. By determining the 119 chromosomal copy number of these isolates, we revealed a very broad range of ploidy states 120 and karyotypes, including some
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