CGH signal ratios reflect the similarities or differences between reference and test genomes, and can detect the amplification, absence, or divergence of sequences. The CGH approach was applied to C. neoformans by first designing high-density tiling arrays of oligonucleotide probes with an average length and spacing of 50 base pairs (bp) and 44 bp, respectively, based on the genomes of strains JEC21 (serotype D) and H99 (serotype A; see Materials and methods, below). To establish a framework for identifying regions of difference in Cryptococcus genomes, CGH data collected with the tiling arrays was initially calibrated by comparing the Log2 ratios of the fluorescence intensity with the corresponding sequence identity for previously sequenced mating-type (MAT) regions of the test and reference genomes (Figure 1). The sequences of the approximately 100 kb MAT loci of representative serotype A (H99 and 125.91) and D (JEC21 and JEC20) strains were available for this analysis 1546. The sequences of the MATa and MATα alleles were obtained from GenBank and the sequence identities for the coding regions of 20 genes in each of these loci were plotted against the corresponding Log2 ratios for the hybridization signals of the probes in the genes. That is, the average of the normalized Log2 ratios from every eight probes (spanning about 400 bp) covering each of the 20 MAT genes were compared with the corresponding genomic sequences for the MATa versus MATα alleles. A correlation was found between sequence identity in the MAT regions and the Log2 ratios from hybridization signals for each of the comparisons (r² = 0.78 for the serotype A strains H99 and 125.91, and r² = 0.81 for the serotype D strains JEC21 and JEC20; Figure 1). The Log2 ratios for the hybridization signals ranged from 0.585 to -4.374, and from 0.971 to -4.382 in MAT regions of the serotype A and D strains, respectively. Based on these comparisons, Log2 ratios between -3.77 and 0.49 corresponded to sequence identities in the range of about 75% to 100% (Figure 1). We confirmed that these calibration values held true for randomly selected regions outside the MAT locus by comparing the identity between seven sequenced regions and hybridization probes (198 probes) against the Log2 ratio for those individual probes with the related strains NIH433 and NIH12 (described below, and data not shown).

In general, our observed correlations between the Log2 ratio and sequence identity are similar to CGH results for other organisms 53545556. For example, Log2 ratios between -4.0 and 0.5 corresponded to sequence identities (probe/target identity) between 81% and 100% in Campylobacter jejuni 56. Furthermore, CGH data for Chlamydia trachomatis showed a linear relationship between Log2 ratio and sequence identity between 75% and 99% 57. In general, a Log2 ratio of ±1.0 is used in many CGH experiments to identify divergent (or deleted) and duplicated genes, representing a conservative threshold for divergent gene detection 555658. For our analysis, the observed correlation between sequence identity and Log2 ratio allowed us to predict whether specific regions in the genomes were divergent, deleted, and/or amplified. The use of these data for whole genome comparisons for serotype A, D, and AD strains are described below.

Initially, we used CGH to compare the genomes of two serotype D progenitor strains, NIH433 (MATa) and NIH12 (MATα), with the genome of the derived strain JEC21 (MATα). JEC21 is commonly used in laboratory experiments and the genome of this strain has the best annotation of the sequenced cryptococcal genomes 46. The strain was obtained from a series of back crosses (starting with NIH433 and NIH12) and was the MATα representative of a congenic strain pair (with JEC20) used to examine the role of mating type in virulence 1759. NIH433 is an environmental isolate from pigeon droppings in Denmark, and NIH12 is a clinical isolate from a patient with osteomyelitis. The cross of NIH12 and NIH433 yielded two F₁ strains B3501 (MATα) and B3502 (MATa), and a cross of these strains yielded JEC20 (B-4476) 1759. JEC20 was subsequently used as the parent in a series of backcrosses to generate JEC21. Thus, approximately 50% of the overall genetic background of JEC21 should be derived from each of the NIH12 and NIH433 genomes.

Initially, we hybridized the JEC21 array with DNA from the MATa strain NIH433 to compare the genomes of strains of opposite mating type. As expected, CGH showed that the MATa locus was divergent from the MATα locus of JEC21 with Log2 ratios ranging from -5.27 to 1.24 for probes in the region. However, the analysis revealed an unexpected pattern of regions with either similar or divergent hybridization signals along 10 of the 14 chromosomes (Figure 2), in addition to the divergence observed at the MAT locus (Figures 1 and 3). Interestingly, each of these regions accounted for approximately 50% of the JEC21 genome, with regions of similarity accounting for about 8.73 Mb (50.6%) and divergent regions representing about 8.53 Mb (49.4%). Note that the JEC21 array did not contain the centromere sequences (or the rDNA cluster) and therefore covered about 17.3 Mb of the approximately 19 Mb genome 46 (Additional data file 1). These regions may represent the segments of the JEC21 genome originating from either NIH433 or NIH12, and the borders of the regions are likely to be sites of recombination events that occurred in the original cross. This idea was tested by hybridizing DNA from the MATα parent NIH12 to the JEC21 array, and this analysis revealed a reciprocal pattern of similar and divergent regions as compared with the results with NIH433 (Figure 2). The averages and standard deviations (SDs) of Log2 ratios of the hybridization intensity of these regions along all chromosomes were consistent with the visual observations, in which regions of divergence generally have a higher SD than regions of similarity (Additional data file 1). This measure of divergence is illustrated quite clearly by signals from the MAT locus. That is, the SD of the MATa locus of NIH433 is 1.778 (average Log2 ratio of -1.632) upon comparison with the MATα locus of JEC21. In contrast, the SD for the homologous MATα locus of NIH12 is 0.229 (average Log2 ratio 0.090).

The putative recombination sites were observed in 10 of the 14 chromosomes and the number of these sites ranged from one on chromosome 7 to seven on chromosome 2 (Figure 2). Based on the current annotation, these sites occur in both intragenic and intergenic regions (Additional data file 2). Chromosomes 10, 11, 13, and 14 did not exhibit variability in Log2 ratios and different segments could not be distinguished. The SD of the hybridization ratios indicated that all of chromosome 10 may have originated from strain NIH12, with little or no contribution from NIH433. On the other hand, chromosomes 11, 13, and 14 are remarkably similar to NIH433 but divergent from NIH12, although one of the telomeres on chromosome 14 exhibited variability (Figure 2). Overall, these findings indicated that CGH with the JEC21 tiling array could detect sequence polymorphisms between strains of the same serotype and that these could be used to track recombination history. For C. neoformans and other fungal pathogens, the detection of recombination sites may have utility for mapping quantitative traits that contribute to virulence. Similar approaches have been used to examine breakpoints in the chromosomes of tumors and to characterize genetic diversity in Saccharomyces cerevisiae 4760.

The CGH analysis also allowed an examination of the MAT regions of the serotype D strains NIH12 and NIH433 in comparison with that of JEC21. Specifically, we observed that the flanking regions of the MAT locus on chromosome 4 contained putative sites of recombination presumably from the cross of NIH12 and NIH433 (Figure 3) 59. The observed sites are consistent with the previous identification of regions flanking the mating locus that are apparent hotspots of recombination 16. In agreement, CGH revealed two potential recombination sites in a region of about 6 kb (chromosome 4: 1,525,471 to 1,531,510 and 1,514,930 to 1,520,952), as well as a third more distant site on the left side, and one site in a region approximately 27 kb to the right of the MAT locus (chromosome 4: 1,639,910-1,667,015; Figure 3). Within the mating-type locus, two divergently transcribed genes, RPO41 and BSP2 (chromosome 4: 1,585,174 to 1,591,759), were presumed to be involved in gene conversion because they are 99% identical between the two mating-type alleles in phylogenetic analyses 1516. Consistent with this finding, CGH yielded a Log2 ratio near zero, indicating high sequence similarity (-0.089 and 0.069 for NIH433 and NIH12, respectively; Figure 3). Three neighboring genes, LPD1, CID1, and GEF1 (chromosome 4: 1,592,529 to 1,602,117), share similar properties with RPO41 and BSP2, and Fraser and coworkers 15 described this area as a species-specific, syntenic region in the MAT locus.

Examination of the CGH data outside the MAT locus identified several candidate regions of difference between JEC21 and the progenitor strains NIH12 and NIH433. For example, two regions appeared to be present in single copy in NIH433 but duplicated in NIH12. One of these regions of approximately 20 kb (chromosome coordinates 1,218,400 to 1,239,200; average Log2 ratio of -0.062 in NIH433 and 0.997 in NIH12) is present on chromosome 3 and contains genes encoding several putative functions (PM-scl autoantigen, nicotinate-nucleotide diphosphorylase [carboxylating], phosphate transporter, and kynureninase). The other region of approximately 13 kb on chromosome 13 (chromosome coordinates 508,400-521,200) encodes putative functions including a metal transporter, a carboxylesterase, a (R, R)-butanediol dehydrogenase, and a formaldehyde dehydrogenase (glutathione; average Log2 ratio of 0.016 in NIH433 and 01.284 in NIH12). Additionally, an approximately 29 kb segment near the right telomere of chromosome 5 (encoding mostly hypothetical proteins) was highly divergent in NIH433 (average Log2 ratio of -3.232, SD of 1.496) and had an average Log2 ratio of 0.829 (SD of 0.382) in NIH12 (Figure 2). This region is part of an approximately 40 kb so-called 'identity island' in the genomes of the serotype A and D strains H99 and JEC21 61. The sequences of the region share 98.5% identity between the two genomes - a level that is approximately 10% higher than the average identity across the entire genomes. Kavanaugh and coworkers 61 found that the approximately 40 kb identity island was the apparent result of a nonreciprocal transfer event from a serotype A genome to a serotype D genome about 2 million years ago. They also surveyed 12 serotype D strains and found that ten (including NIH12) had the identity island that originated from the serotype A sequence and that two strains, NIH430 and NIH433, retained the original serotype D version of the sequence. Therefore, the analysis reported here for NIH12 and NIH433 matches the findings of Kavanaugh and coworkers 61, and thus demonstrates the utility of the CGH approach for detecting these types of sequence anomalies in C. neoformans genomes.

NIH433 and NIH12 are both virulent, but NIH433 requires more time than NIH12 to cause equal mortality when injected intravenously into mice 59. In addition to the MAT locus, differences in genetic background were proposed to be important contributors to the virulence of these strains 59. In this context, the differences observed for chromosomes 3, 5, and 13 or undetected polymorphisms (single nucleotide changes) could potentially influence virulence. For example, one region on chromosome 3 (2,022,000 to 2,024,000; Log2 ratio -3.161) contains a gene for a predicted O-acetyltransferase (CNC06920) that is deleted in NIH433, as confirmed by PCR (data not shown). O-acetyl substituents are found on the polysaccharide capsule that is the major virulence determinant of C. neoformans, and a mutant defective in O-acetylation was found to be hypervirulent 6263.

Serotype A strains of C. neoformans are responsible for the majority of clinical cases of cryptococcosis, particularly in AIDS patients, and three molecular subtypes (VNI, VNII, and VNB) have been identified by MLST and AFLP analyses 2293839. Given that CGH detected variation within the serotype D strains, we next considered whether the same approach would detect genomic differences in serotype A strains of opposite mating type and different molecular subtypes. The majority of serotype A isolates have the VNI molecular subtype and the MATα mating type. MATa strains are rare among clinical and environmental isolates compared with the prevalence of the MATα mating type. In fact, MATa strains of serotype A were thought to be extinct or to exist as a vestigial, nonfunctional form until two clinical strains were identified: 125.91 from Tanzania 64 and IUM 96-2828 from Italy 65. Strain 125.91 (VNI) was found to mate with a subset of MATα serotype A strains, but was unable to mate with the reference strain H99 1264. Recently, detailed MLST and AFLP analyses of a large population of serotype A strains from a global collection identified MATa isolates among the VNB molecular subtype that is uniquely present in Botswana; these isolates included strain Bt63, which can mate with H99 3839. With the emerging view of the serotype A population in mind, we examined the genomes of two MATa strains (125.91 and Bt63), a VNII strain (WM626 [MATα]), and a VNI strain (CNB7779 [MATα]) reported to have a small genome 32. For this analysis, we employed the tiling array based on the sequence of the VNI strain H99 and the corresponding chromosome numbers from the genome sequence assembly 61.

Our analysis of strains 125.91 and Bt63 revealed that, as expected, the Log2 ratios of hybridization signals in the MAT locus region were highly variable and ranged from -4.345 to 0.445, and from -4.24 to 0.488, respectively. This indicates extensive sequence divergence between these MATa regions and the MATα locus of H99 (Figures 1 and 4, and Additional data file 3). Note that the MAT locus is on chromosome 5 in the serotype A strain H99 used for the analysis of the MAT regions of the serotype A strains 125.91 and Bt63; MAT is on chromosome 4 in strain JEC21 (serotype D). The average Log2 ratios were -2.200 (SD 1.319) and -2.204 (SD 1.401) for 125.91 and Bt63, respectively. These results mirror the comparisons of the MATa and MATα alleles for the serotype D strains presented above (Figures 1 to 3). Outside the MAT locus, the relative extent of divergence in hybridization signals between Bt63 and H99 (molecular subtypes VNB and VNI, respectively) versus 125.91 and H99 (both VNI) suggested that a higher level of genome variability exists between, versus within, molecular subtypes (Table 1). A large number of regions of difference were detected for both 125.91 and Bt63 relative to H99 (Additional data files 3 and 4). Several regions were also different between the two MATa strains. These include the region from 339,600 to 350,000 on chromosome 1 that appears to be absent from or highly divergent in 125.91 but potentially amplified in Bt63 (Additional data file 4) and an approximately 1.2 kb deletion (1,443,600 to 1,445,200) on chromosome 3 in Bt63 that was confirmed by PCR (Log2 ratio of -2.868 in the deleted region; data not shown). In addition, Bt63 appears to have a duplication of a region (1,776,000 to 1,786,400) on chromosome 5 that contains genes encoding putative myoinositol transporters. This observation is interesting because Xue and coworkers 66 recently showed that inositol stimulates mating in C. neoformans, and it is known that Bt63 mates more robustly with H99 than does 125.91 64.

The genome variability between VNI and VNB strains revealed by CGH prompted us to compare the genome of the VNII strain WM626 with the H99 genome. VNII strains may represent up to 20% of the serotype A population worldwide, and WM626 is a clinical isolate from Sydney, Australia 29. The results indicated that the WM626 genome is quite divergent from the H99 genome (Figure 4, Table 1, and Additional data file 3), suggesting considerable variation between the VNI and VNII subtypes (although a larger survey is needed). Compared with the results for 125.91 and Bt63, the CGH data for WM626 revealed a large number of highly divergent or deleted regions on 12 of the 14 chromosomes relative to the corresponding locations in Bt63 (Additional data file 4).

We also used CGH to examine the genome content of the clinical strain CBS7779 (VNI) from Argentina that was reported to have a small genome size as estimated by electrophoretic karyotype analysis 32. Specifically, the genome size for CBS7779 was estimated to be 15 Mb, which is considerably smaller than the approximately 19 Mb genomes of the sequenced strains. We initially confirmed the published karyotype of CBS7779 (data not shown), and subsequent CGH analysis of the genome of this strain with H99 revealed Log2 ratios near zero for all of the chromosomes, suggesting a close relationship between the two strains (Figure 4 and Table 1). The similarities in the genomes were particularly evident in contrast to the results for the hybridizations with Bt63 and WM626 (Figure 4). These results suggested that CBS7779 shared most, if not all, of its genome with H99, and missing sequences that would account for the smaller estimated genome size were not found. This outcome may reflect the challenge in using electrophoretic karyotyping to measure genome size, particularly for strains that exhibit chromosome length polymorphisms that may result in co-migrating chromosomes. It is also possible that the genomes of these strains may contain different amounts of repetitive DNA. The comparison of the CBS7779 and H99 genomes did reveal a relatively small number of short regions of divergence. Two larger differences for CBS7779 relative to H99 included an apparent deleted or divergent region of 17 kb on chromosome 10 and an amplified region of 20 kb on chromosome 5 (Additional data file 4).

The evaluation of the serotype A strains also allowed a more detailed look at the 'identity island' discussed above. This region is on the left end of chromosome 5, based the assembled H99 genome sequence, and Kavanaugh and coworkers 61 found that several genes (The Institute for Genomic Research [TIGR] IDs: CNE05310, CNE05340, and CNE05350) in this region were present in H99 and 125.91, but not Bt63. CGH confirmed these findings and further revealed that other genes within the region (CNE05250, CNE05290, CNE05320, CNE05330, CNE05300, and CNE00020) were present in 125.91 (VNI) but absent in Bt63 (VNB; Additional data file 4). Interestingly, several genes within the region (CNE05310, CNE05340, CNE05350, CNE05320, and CNE05330) appeared to be duplicated in CBS7779 (VNI; Additional data file 4). These genes were also present in the VNII strain WM626, although a region of about 6 kb on the telomere proximal side appeared to be lost. For another region of high sequence identity between H99 (chromosome 10) and JEC21 (chromosome 13) 61, CGH revealed that three consecutive genes, namely CNM02580, CNM02590 and CNM02600, were conserved in all of the strains (H99, Bt63, 125.91, and CBS7779). However, CNM02570, which encodes a putative receptor protein near to the telomere, was present in H99, Bt63, CBS7779, and WM626, but not in 125.91. Kavanaugh and coworkers 61 found that repetitive elements were associated with the identity island on chromosome 5 and suggested that one of these (Cnl1) may have participated in translocation of the island in the serotype D strain. It is possible that these elements also contribute to the variability in these and other regions observed by CGH.

The CGH analysis also revealed an anomaly in the hybridization signals for chromosome 13 in strains CBS7779 and WM626, such that the Log2 ratio was above zero (0.562 and 0.721, respectively) across the entire chromosome (Table 1, Figure 4, and Additional data file 3). The simplest explanation for this is that chromosome 13 in these strains is present in more than one copy in some or all of the cells. Alternatively, duplicated chromosome 13 segments could reside elsewhere in the genome, but this is less likely, given that the entire chromosome exhibited an elevated Log2 ratio. Quantitative real-time PCR with three loci on chromosome 13 in strains H99, WM626, and CBS7779 supported the conclusion of an increased copy number in the latter two strains (Additional data files 5 and 6). Furthermore, replacement of the APT1 gene on chromosome 13 with a neomycin marker confirmed the presence of two copies of the gene in WM626, compared with the single copy found upon transformation of strain H99 (Additional data file 7). However, integration at the APT1 gene in strain CBS7779 yielded transformants with only the neomycin marker replacement of the gene. We hypothesize that instability at chromosome 13 in this strain may have resulted in the loss of one copy during the transformation process (see Additional data file 8). This idea is supported by quantitative real-time PCR data that confirmed a difference in copy number for chromosome 13 before and after transformation of the strain (Additional data files 5 and 6). Strains H99, WM626, and CBS7779 also exhibit phenotypic differences (for instance, in melanin formation) that could potentially result from the difference in chromosome content or the regions of divergence detected by CGH (Additional data file 9).

Other studies have documented genome anomalies for C. neoformans, including segmental duplications for serotype D strains 67 and chromosome length polymorphisms 3268. The possibility of elevated copy number for specific chromosomes in C. neoformans suggests that there is potentially greater genome variability among isolates than was previously appreciated. Chromosome copy number variation may have implications for differences in phenotypic properties between isolates. For example, variability in virulence has been observed for clinical isolates of serotype A and among A, D, and AD strains 6970. Additionally, C. neoformans exhibits phenotypic switching that influences the expression of virulence traits, interactions with the host immune system, the outcome of chronic infection and symptom development (specifically, intracranial pressure) 71. It is possible that switching could result from changes in chromosome copy number, perhaps through a positive or negative influence on gene expression. In this regard, Torres and coworkers 72 recently showed that the gain of extra chromosomes in S. cerevisiae had a major influence on cellular processes, including gene expression, proliferation, metabolism, and protein turnover.

Taken together, the CGH data with selected serotype A strains revealed extensive variability, in agreement with the classification of the strains into different molecular subtypes. Specifically, variation in the Log2 ratios and SDs for each chromosome supports the grouping of H99 with the other VNI strains 125.91 and CBS7779 (lower SDs) and indicates divergence from the VNII strain WM626 and the VNB strain Bt63 (higher SDs; Table 1). Although we examined a small number of strains that may not be completely representative, the variable regions may define signature differences that could facilitate further characterization of molecular subtypes and epidemiologic studies. A wide variety of hypothetical genes and genes with predicted functions were present in the regions of difference, but no clear pattern of variation was observed, with the exception that variability was often associated with repetitive elements and/or present at subtelomeric regions (Additional data file 4). As described above, repeated sequences such as those associated with mobile genetic elements may contribute to genome instability and examples have been noted for C. neoformans 61. For the telomeric and subtelomeric regions, the observed variability probably reflects rapid structural evolution of these regions in C. neoformans, similar to that observed at telomeric or subtelomeric regions of S. cerevisiae, A. fumigatus, Magnaporthe grisea, and many other organisms 477374757677. For example, CGH experiments with the genome of Aspergillus fumigatus strain Af293 as a reference revealed 2,557 genes that are absent or diverged in two additional strains of A. fumigatus and three closely related species, namely A. clavatus, Neosartorya fischeri, and N. fennelliae 75. These absent or divergent genes exhibited a bias toward subtelomeric locations 74. The identification of similar variable segments in C. neoformans may guide future analyses to assess whether genome variation contributes to the differences in virulence between serotype A strains 70. Of course, the approach reported here would not detect regions that are present in the test genomes but not in H99.

Clinical and environmental isolates of C. neoformans are normally haploid, and the diploid phase is a transient part of the sexual phase of the life cycle. Some clinical and environmental isolates possess a hybrid AD serotype and are presumed to result from natural fusions between A and D parental strains 78. Fluorescence-activated cell sorting and PCR analyses also revealed that AD strains are diploid or aneuploid (>1n but <2n) 926. We used the tiling arrays for the reference genomes of H99 (serotype A) and JEC21 (serotype D) to determine the utility of the CGH approach for characterizing hybrid strains. Three hybrid strains (KW5, CDC228, and CDC304) were chosen because they had previously been characterized with respect to virulence and they exhibited serotype-specific differences at some loci, including genes at the MAT locus 9.

Hybridization of DNA from the AD strains to the JEC21 and H99 arrays suggested that most chromosomes (chromosomes 2 to 4 and 9 to 14 [numbers based on the JEC21 genome]) were represented by copies from both the A and D genomes because the average Log2 ratios were close to zero (Figure 5; Additional data file 10). This observation was supported by the finding that other chromosomes of the A and D genomes were not equally represented in the three AD hybrid strains (Figure 5 and Additional data file 10). Specifically, Log2 ratios for chromosome 1 in the AD strains ranged from -1 to -4 upon hybridization to the JEC21 array, suggesting the absence of sequences of chromosome 1 originating from a D genome, whereas the ratios for hybridization to the H99 array were 0.5 to 1, suggesting the presence of one or two copies of chromosome 1 from the parental A genome. Note that the VN molecular subtype of the parental strains for the hybrids is not known, and the variation in the Log2 ratios may reflect sequence divergence between H99 and the serotype A parent. The average Log2 ratios for each chromosome of the three strains are listed in Additional data file 10. Overall, the results indicated that chromosome 1 of KW5, CDC208, and CDC304 originated from an A genome, suggesting that the D genome version of chromosome 1 may have been lost. Similarly, based on the Log2 ratios, chromosomes 6 and 7 of KW5 may have only a serotype A version, chromosome 8 of KW5 appears to be from a D genome, and chromosome 5 of CDC304 may have only a serotype D version.

The predictions about the presence of specific chromosomes were tested by PCR-RFLP analysis of selected regions. Specifically, tests were performed with chromosome 5 as a representative chromosome only from serotype D in CDC304 and with chromosome 1 as representative of a chromosome only from serotype A in all three strains. For comparison, chromosomes 2 and 3 were included as examples of chromosomes that were present from both serotype A and D parents (Figure 5). Initially, PCR-RFLP analysis of a region in the JEC21 gene CNE04380 on chromosome 5 that was conserved between the A and D genomes confirmed that KW5 and CDC228 have both a serotype A and serotype D copy of chromosome 5, whereas CD304 only has the serotype D sequence of this region (Figure 6). Digestion with a different enzyme confirmed these results and revealed that the serotype A copy in KW5 has a different RFLP pattern from that in CDC228, most likely due to restriction site polymorphisms. Parallel PCR-RFLP analyses for chromosomes 2 and 3 confirmed the CGH prediction that the AD hybrids contained these chromosomes from both the A and D genomes.

Chromosome 1 in the AD hybrids was also examined by PCR-RFLP analysis of a segment of the conserved JEC21 gene CNA01230 (Figure 6). This analysis initially indicated that all three strains had only a serotype A version of chromosome 1, although closer examination revealed faint additional bands from strain CDC304 that could result from incomplete digestion, sequence polymorphisms at the site, or the presence of the serotype D version of chromosome 1. Restriction digests with additional enzymes suggested that CDC304 might have a serotype D version of chromosome 1 present at a low level (Figure 6). One possibility was that strain CDC304 contained a mixed population of cells in which the majority had a serotype A copy of chromosome 1 and a minority also contained a copy from serotype D. To test this hypothesis, we isolated and analyzed four different colonies of CDC304 and found that the cells in three colonies had only a serotype A version of chromosome 1. The other colony contained cells in which the serotype A and D versions of chromosome 1 were present in approximately equal abundance (data not shown). We therefore hypothesize that most cells in strain CDC304 have lost the serotype D copy of chromosome 1, but that a minor population retains this chromosome. Thus, CDC304 may still be in the process of losing chromosomes from the original A and D parents, and this observation is consistent with the genome instability observed for AD hybrid strains 9.

The AD hybrid strains of Cryptococcus examined in this study showed that chromosomes of both A and D serotypes are not equally represented in each AD hybrid strain. That is, specific chromosomes were represented by sequences from only one serotype. Although, we have not determined the copy number for chromosomes that are represented by a single serotype sequence, the possibility exists that these chromosomes are present in two copies because the average Log2 ratios were about 0.4. It is notable that all three AD strains preferentially contained chromosome 1 sequences from the serotype A parental strain but not from the D strain. To strengthen the conclusion that chromosome 1 from serotype A is preferentially retained in hybrids, we obtained 16 additional AD hybrid strains and examined the origin of chromosome 1 using the RFLP-PCR method (Additional data file 11). We found that 11 possessed chromosome 1 sequences only from serotype A and the other five had copies of chromosome 1 from both A and D parents. These results agree with those of Nakamura and coworkers 79 and Okabayashi and colleagues 80, who used CAP59 gene sequences from chromosome 1 to examine phylogenetic relationships between serotypes. They found that the three AD hybrid strains that they tested grouped with serotype A strains, suggesting that these strains also had only the serotype A allele of CAP59. Similarly, Xu and coworkers 24 found evidence for loss of heterozygosity in AD hybrid strains using MSLT analysis with four genes and identified strains that cluster with serotype A strains as well as others that lacked consistent grouping with one serotype.

The emerging picture of frequent loss of heterozygosity in hybrid strains and the retention of specific chromosomes raises questions about the mechanisms of loss and retention. It is possible that chromosome 1 of serotype A carries a gene or genes that confer a selective advantage relative to the serotype D version of the chromosome, and/or that the latter chromosome has a disadvantageous combination of genes. In this case, hybrids that spontaneously lose chromosome 1 from serotype A might be at a selective disadvantage. It is also possible that chromosome 1 from the serotype D parent has an inherent defect in replication or transmission, such that it is preferentially lost or that incompatibility exists for some chromosomes. The mechanisms underlying these patterns of chromosome content, and possible relevance for virulence, remain to be investigated. It is interesting, however, that the AD strains are clinical isolates, which raises the possibility that retention of chromosome 1 from the serotype A genome (serotype A strains are known to be more virulent) contributes a selective advantage in the mammalian host environment.

A set of genes or regions in the AD hybrids have been amplified and compared previously 9. We examined the CGH data for these sequences, and the Log2 ratios are consistent with the interpretations of chromosome content (data not shown). The three AD strains have also been tested previously for virulence in comparison with strain H99 9. These assays indicated that the AD hybrids are less virulent than H99 and differ from each other. Specifically, infected mice succumbed to H99 by day 25, to KW5 by day 100, and to CDC228 or CDC304 by day 150. It is known that serotype A strains are generally more virulent that serotype D strains, although strain variation exists in both groups 6970. Differences in chromosomal content could potentially influence virulence through the contributions of specific alleles, such that a greater content of the A genome (as found in KW5) may result in enhanced virulence. Of course, other explanations are possible, including the accumulation of mutations in key virulence traits in the less virulent AD strains and epigenetic phenomena. Barchiesi and coworkers 69 suggested that the presence of the serotype A, MATα mating type allele in either haploid or diploid (aneuploid) strains is correlated with virulence, whereas the MATa in serotype A or MATα allele in serotype D is associated with moderate or no virulence. In this regard, Lengeler and colleagues 9 showed that KW5 is heterozygous for the mating-type locus with the serotype D MATa and the serotype A MATα loci present. In contrast, the CDC228 and CDC304 strains have the MATα locus from a serotype D parent and appear to have the MATa locus from a serotype A parent. Therefore, the contributions of mating type to virulence are unclear, with contributions likely both from specific alleles and variable chromosome complements in the AD hybrids.

Additional data file 12 lists the strains used in this study. The strains were maintained on yeast extract, peptone, dextrose medium (YPD; Difco, Sparks, MD, USA) and the genomic DNA for hybridization experiments was isolated as previously described 85. The genome sequences of strain JEC21 46 and strain H99 were obtained from public databases 8687. The assembled sequences were used by NimbleGen Systems, Inc. (Madison, WI, USA) 88 to design and manufacture high-density oligonucleotide genomic arrays. The design for the arrays was the same for each genome, with oligonucleotide probes that cover all 14 chromosomes for each genome tiled at an average interval spacing of 44 bp on one strand. The average length of the probes was 50 bp (range 45 to 85 bp) and the average melting temperature (Tm) of the probes on each array was 76°C. The number of oligonucleotide probes for each genome were as follows: 386,279 for H99 and 380,236 for JEC21. The probes for each array were designed to uniquely match a single sequence in the genome, and highly repetitive centromeric regions and the rDNA repeat cluster were not included. In H99, a region of the mating locus (chromosome 5: 203,813 to 220,976) was considered repetitive and not included on the array. The comparative standard operation procedures of NimbleGen Systems, Inc. were followed for hybridization (42°C), array scanning, and data acquisition, as described previously 60. Genomic DNA from the test strains was labelled with Cy3 and that of reference strains with Cy5. The data were expressed as Log2 ratios of Cy3/Cy5 fluorescence intensity. The arrays are available from NimbleGen Systems, Inc.

The data were extracted from scanned array images using NimbleScan 2.0 software (NimbleGen Systems, Inc.) and were provided to us as an initial DNA segmentation analysis of the normalized data. This analysis included a window averaging step, in which the probes that fell into a defined base pair window size were averaged using the Tukey biweight mean. The adjacent windows were averaged to reduce the size of the dataset and the noise in the data. In the present study, the data were analyzed using 400, 800, and 2,000 bp windows for averaging; these sizes represent 10, 20, and 50 times the length of an average probe. In most cases, a 400 bp window was used for the analysis. The segmentation of the averaged log2 ratio data was determined based on a circular binary segmentation algorithm 89. We also examined the data for each individual probe in the analyses shown in Figure 1 and Additional data file 4. The sample key for the raw hybridization data is provided in Additional data file 13 and the actual data files are available on our website 90.

The CGH results were viewed and analyzed as GFF files with SignalMap (NimbleGen Systems, Inc.) using 400, 800, and 2,000 bp windows for averaging. The data for the MAT loci (Figure 1) were analyzed using Log2 ratios from segmentations based on a 400 bp window and the nucleotide sequence identity for the corresponding region of available homologous sequences from 20 genes in the loci. The sequences of the MAT loci were obtained from GenBank, and sequence identity was determined from alignments with the BioEdit Sequence Alignment Editor 91. The accession numbers for the sequences are as follows: serotype A strains H99 (MATα, AF542529) and 125.91 (MATa, AF542528), and serotype D strains JEC21 (MATα, AF542531) and JEC20 (MATa, AF542530). The relationship between Log2 ratio values and sequence identity was examined by linear regression analysis in Excel.

Selected regions identified by CGH as candidates for deleted, duplicated, or divergent sequences were examined by PCR amplification and sequence analysis. PCR amplification from genomic DNA was performed as described by Hu and Kronstad 85, with primers designed from the sequences flanking each predicted region of difference, so that the amplified fragment spanned the region. The primers were obtained from Invitrogen (Burlington, Ontario, Canada) and their sequences are listed in Additional data file 14. PCR-amplified DNA fragments were either sequenced using the dideoxy chain-termination method or digested with selected restriction enzymes in the case of AD hybrids. Primers for the analysis of AD hybrid strains were designed to target highly conserved regions in the genome to ensure that the primers would bind to both the serotype A and D alleles in these strains. These conserved regions were identified by aligning the sequences from H99 (representing serotype A) and JEC21 (representing serotype D) with BioEdit 91.