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Small chromosomes among Danish Candida glabrata isolates originated through different mechanisms.

Ahmad KM, Ishchuk OP, Hellborg L, Jørgensen G, Skvarc M, Stenderup J, Jørck-Ramberg D, Polakova S, Piškur J - Antonie Van Leeuwenhoek (2013)

Bottom Line: Regarding the year, patient and hospital, these C. glabrata strains had independent origin and the analyzed small chromosomes were structurally not related to each other (i.e. they contained different sets of genes).The first type of small chromosomes carrying duplicated genes exhibited mitotic instability, while the second type, which contained the corresponding genes in only one copy in the genome, was mitotically stable.Apparently, in patients C. glabrata chromosomes are frequently reshuffled resulting in new genetic configurations, including appearance of small chromosomes, and some of these resulting "mutant" strains can have increased fitness in a certain patient "environment".

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden. khadija_mohamed.ahmad@biol.lu.se

ABSTRACT
We analyzed 192 strains of the pathogenic yeast Candida glabrata from patients, mainly suffering from systemic infection, at Danish hospitals during 1985-1999. Our analysis showed that these strains were closely related but exhibited large karyotype polymorphism. Nine strains contained small chromosomes, which were smaller than 0.5 Mb. Regarding the year, patient and hospital, these C. glabrata strains had independent origin and the analyzed small chromosomes were structurally not related to each other (i.e. they contained different sets of genes). We suggest that at least two mechanisms could participate in their origin: (i) through a segmental duplication which covered the centromeric region, or (ii) by a translocation event moving a larger chromosome arm to another chromosome that leaves the centromere part with the shorter arm. The first type of small chromosomes carrying duplicated genes exhibited mitotic instability, while the second type, which contained the corresponding genes in only one copy in the genome, was mitotically stable. Apparently, in patients C. glabrata chromosomes are frequently reshuffled resulting in new genetic configurations, including appearance of small chromosomes, and some of these resulting "mutant" strains can have increased fitness in a certain patient "environment".

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Phylogenetic relationship, as deduced by Neighbor-joining method, based on the IGS region located between the CDH1 and EPR6 genes. 35 (plus CBS 138) different haplotypes (representing isolate sequences which had the available 474 positions) were deduced. The strain numbers correspond to the museum numbers of the initial collection and can be found in Supplementary materials Table 1. The names of the strains with small chromosomes are followed by a capital letter pointing out which CBS 138 chromosome is related to the small chromosome. Among the analyzed strains several sequences belonged to the same haplotype. The appearance of each haplotype, in addition to the shown strain (and if different from 1), is written in the brackets following the strain/sequence designation. The strains belonging to each of these haplotypes can be found in Supplementary methods Table S1. The group 002574 (analyzed for their karyotypes in Fig. 3) is arrowed. The bootstrap values are shown on some branches and the tree is not rooted
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Fig2: Phylogenetic relationship, as deduced by Neighbor-joining method, based on the IGS region located between the CDH1 and EPR6 genes. 35 (plus CBS 138) different haplotypes (representing isolate sequences which had the available 474 positions) were deduced. The strain numbers correspond to the museum numbers of the initial collection and can be found in Supplementary materials Table 1. The names of the strains with small chromosomes are followed by a capital letter pointing out which CBS 138 chromosome is related to the small chromosome. Among the analyzed strains several sequences belonged to the same haplotype. The appearance of each haplotype, in addition to the shown strain (and if different from 1), is written in the brackets following the strain/sequence designation. The strains belonging to each of these haplotypes can be found in Supplementary methods Table S1. The group 002574 (analyzed for their karyotypes in Fig. 3) is arrowed. The bootstrap values are shown on some branches and the tree is not rooted

Mentions: In this study we analysed the identity and phylogenetic relationship of our clinical isolates through the sequencing of two genetic loci. Initially, we could see that ten strains from the original collection had quite a distinct D1/D2 domain (belonging to the nuclear 26S rDNA locus) polymorphism and apparently did not belong to C. glabrata based on the yeast species definition (Kurtzman 2006). Also the karyotypes of these strains were different from the C. glabrata ones (data not shown). Likely, these strains were misclassified during the initial determination and deposition and we later excluded them from further experiments and from the analysis shown in Fig. 1 and they are not shown in Supplementary materials Table S1. We obtained in total (including 40 previously determined ones, see Poláková et al. 2009) 192 sequences of the D1/D2 domain, and 192 sequences of IGS, mapping between the nuclear CDH1 and ERP6 genes, and these can be found in Supplementary materials Table S1. Seven different haplotypes of the D1/D2 locus, based on the analyzed 489 positions were obtained (Fig. 1). The difference between the CBS 138 sequence and the least related strain 003338 was observed at five positions (see also Fig. 1). According to the yeast species definition (Kurtzman 2006) this means that all strains belong to C. glabrata. When the fast evolving IGS locus was analyzed, a more pronounced polymorphism was detected (Fig. 2). Therefore, in Fig. 2 more distinctive sub-groupings than in Fig. 1 could be observed. Neighbor-joining and Maximum Parsimony methods defined the same small chromosome containing sub-groups (data not shown). In short, these experiments confirmed which of the strains in the collection were indeed C. glabrata and provided a basis to explain the origin of different molecular events (see later sections).Fig. 1


Small chromosomes among Danish Candida glabrata isolates originated through different mechanisms.

Ahmad KM, Ishchuk OP, Hellborg L, Jørgensen G, Skvarc M, Stenderup J, Jørck-Ramberg D, Polakova S, Piškur J - Antonie Van Leeuwenhoek (2013)

Phylogenetic relationship, as deduced by Neighbor-joining method, based on the IGS region located between the CDH1 and EPR6 genes. 35 (plus CBS 138) different haplotypes (representing isolate sequences which had the available 474 positions) were deduced. The strain numbers correspond to the museum numbers of the initial collection and can be found in Supplementary materials Table 1. The names of the strains with small chromosomes are followed by a capital letter pointing out which CBS 138 chromosome is related to the small chromosome. Among the analyzed strains several sequences belonged to the same haplotype. The appearance of each haplotype, in addition to the shown strain (and if different from 1), is written in the brackets following the strain/sequence designation. The strains belonging to each of these haplotypes can be found in Supplementary methods Table S1. The group 002574 (analyzed for their karyotypes in Fig. 3) is arrowed. The bootstrap values are shown on some branches and the tree is not rooted
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3672514&req=5

Fig2: Phylogenetic relationship, as deduced by Neighbor-joining method, based on the IGS region located between the CDH1 and EPR6 genes. 35 (plus CBS 138) different haplotypes (representing isolate sequences which had the available 474 positions) were deduced. The strain numbers correspond to the museum numbers of the initial collection and can be found in Supplementary materials Table 1. The names of the strains with small chromosomes are followed by a capital letter pointing out which CBS 138 chromosome is related to the small chromosome. Among the analyzed strains several sequences belonged to the same haplotype. The appearance of each haplotype, in addition to the shown strain (and if different from 1), is written in the brackets following the strain/sequence designation. The strains belonging to each of these haplotypes can be found in Supplementary methods Table S1. The group 002574 (analyzed for their karyotypes in Fig. 3) is arrowed. The bootstrap values are shown on some branches and the tree is not rooted
Mentions: In this study we analysed the identity and phylogenetic relationship of our clinical isolates through the sequencing of two genetic loci. Initially, we could see that ten strains from the original collection had quite a distinct D1/D2 domain (belonging to the nuclear 26S rDNA locus) polymorphism and apparently did not belong to C. glabrata based on the yeast species definition (Kurtzman 2006). Also the karyotypes of these strains were different from the C. glabrata ones (data not shown). Likely, these strains were misclassified during the initial determination and deposition and we later excluded them from further experiments and from the analysis shown in Fig. 1 and they are not shown in Supplementary materials Table S1. We obtained in total (including 40 previously determined ones, see Poláková et al. 2009) 192 sequences of the D1/D2 domain, and 192 sequences of IGS, mapping between the nuclear CDH1 and ERP6 genes, and these can be found in Supplementary materials Table S1. Seven different haplotypes of the D1/D2 locus, based on the analyzed 489 positions were obtained (Fig. 1). The difference between the CBS 138 sequence and the least related strain 003338 was observed at five positions (see also Fig. 1). According to the yeast species definition (Kurtzman 2006) this means that all strains belong to C. glabrata. When the fast evolving IGS locus was analyzed, a more pronounced polymorphism was detected (Fig. 2). Therefore, in Fig. 2 more distinctive sub-groupings than in Fig. 1 could be observed. Neighbor-joining and Maximum Parsimony methods defined the same small chromosome containing sub-groups (data not shown). In short, these experiments confirmed which of the strains in the collection were indeed C. glabrata and provided a basis to explain the origin of different molecular events (see later sections).Fig. 1

Bottom Line: Regarding the year, patient and hospital, these C. glabrata strains had independent origin and the analyzed small chromosomes were structurally not related to each other (i.e. they contained different sets of genes).The first type of small chromosomes carrying duplicated genes exhibited mitotic instability, while the second type, which contained the corresponding genes in only one copy in the genome, was mitotically stable.Apparently, in patients C. glabrata chromosomes are frequently reshuffled resulting in new genetic configurations, including appearance of small chromosomes, and some of these resulting "mutant" strains can have increased fitness in a certain patient "environment".

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden. khadija_mohamed.ahmad@biol.lu.se

ABSTRACT
We analyzed 192 strains of the pathogenic yeast Candida glabrata from patients, mainly suffering from systemic infection, at Danish hospitals during 1985-1999. Our analysis showed that these strains were closely related but exhibited large karyotype polymorphism. Nine strains contained small chromosomes, which were smaller than 0.5 Mb. Regarding the year, patient and hospital, these C. glabrata strains had independent origin and the analyzed small chromosomes were structurally not related to each other (i.e. they contained different sets of genes). We suggest that at least two mechanisms could participate in their origin: (i) through a segmental duplication which covered the centromeric region, or (ii) by a translocation event moving a larger chromosome arm to another chromosome that leaves the centromere part with the shorter arm. The first type of small chromosomes carrying duplicated genes exhibited mitotic instability, while the second type, which contained the corresponding genes in only one copy in the genome, was mitotically stable. Apparently, in patients C. glabrata chromosomes are frequently reshuffled resulting in new genetic configurations, including appearance of small chromosomes, and some of these resulting "mutant" strains can have increased fitness in a certain patient "environment".

Show MeSH
Related in: MedlinePlus