Comparative Genomics of Candida Species

Geraldine Butler

doi:10.1128/9781555817176.ch3

Chapter 3 : Comparative Genomics of Candida Species

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Affiliations: 1: School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland

Content Type: Monograph

Publication Year: 2012

Category: Fungi and Fungal Pathogenesis; Clinical Microbiology

Book DOI: 10.1128/9781555817176

Chapter DOI: 10.1128/9781555817176.ch3

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Abstract:

This chapter focuses on the Candida species within the CTG clade. Several of the species (Candida albicans, Candida dubliniensis, Candida tropicalis, Candida parapsilosis, and Lodderomyces elongisporus) have diploid genomes, so it is possible to compare the single nucleotide polymorphisms (SNPs) between the homologous chromosomes. Families of long terminal repeat (LTR) and non-LTR retrotransposons have been well characterized in C. albicans. The precise number of agglutinin-like sequence (ALS) genes in the other Candida species is likely to be overestimated, caused by difficulties in assembling the repeated regions. Species-specific amplifications have also occurred in the other Candida species. The large-scale analysis of Candida genomes confirmed that many of the multigene families described for C. albicans are also present in the genomes of other pathogenic Candida species. C. albicans and C. dubliniensis are the only two Candida species that generate true filaments, although C. dubliniensis is much less efficient. The change in the genetic code may have helped protect Candida species from infection by RNA-based viruses. Comparative genomic tools for Candida species are available from the Broad Institute, the Pasteur Institute, and University College Dublin. In conclusion, analysis of the vast array of genomic data available has already made, and is likely to continue to make, major contributions to our understanding of the biology of Candida species.

Citation: Butler G. 2012. Comparative Genomics of Candida Species, p 27-43. In Calderone R, Clancy C (ed), Candida and Candidiasis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817176.ch3

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Comparative Genomics of Candida Species

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FIGURE 1

Phylogenetic relationship of the sequenced Candida species. The tree was constructed using a supertree approach, including all 10 genomes from the CTG clade and C. glabrata and S. cerevisiae. Methods are described in the work of Fitzpatrick et al. ( 41 ). The subclades that contain haploid and diploid genomes are indicated. doi:10.1128/9781555817176.ch3.f1

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FIGURE 1

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FIGURE 2

Distribution of SNPs in L. elongisporus. SNP frequency (SNPs per kilobase, normalized by the fraction of high-quality aligned positions) for 10-kb windows is plotted along L. elongisporus scaffolds. sc, supercontig, approximately corresponding to chromosomes. Reproduced from reference 12 with permission. doi:10.1128/9781555817176.ch3.f2

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FIGURE 2

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FIGURE 3

Comparative analysis of ALS sequences from Candida species. (Top panel) Genomic distribution of ALS genes in C. albicans, C. dubliniensis, and C. tropicalis. (Bottom panel) Maximum-likelihood phylogeny of ALS genes from the three species shown in the top panel. Terminal nodes are labeled with the same symbols and gene names as shown in the top panel. A conserved 14-amino-acid sequence at the C terminus is shown. ALS3 is present only in C. albicans. Reproduced from Genome Research ( 73 ) with permission from the publisher. doi:10.1128/9781555817176.ch3.f3

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FIGURE 3

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FIGURE 4

(A) Organization of MTL in Candida species. MTLα-specific genes are shown in white and MTL a-specific genes in black. C. albicans names are used for adjacent genes. Gene losses are indicated with crosses. Idiomorphs from heterothallic isolates are linked with braces. Genomic regions are not drawn to scale, and not all ORFs are shown. (B) Placement of gene losses on the phylogenetic tree. doi:10.1128/9781555817176.ch3.f4

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FIGURE 4

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FIGURE 5

HGT of a proline racemase gene into C. parapsilosis. The species and gene names are shown in the individual boxes. Clavispora lusitaniae is equivalent to C. lusitaniae, and P. guilliermondii is equivalent to C. guilliermondii. Orthologous genes are stacked in columns, or pillars. Gene order is conserved on the left-hand side; on the right-hand side synteny between C. parapsilosis and L. elongisporus is conserved, except for an insertion of a PR and a neutral amino acid transporter (AA) in C. parapsilosis. There is no conservation in synteny in this region between C. parapsilosis/L. elongisporus and the other Candida species. Reproduced from reference 40 with permission. doi:10.1128/9781555817176.ch3.f5

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Tables

Comparative Genomics of Candida Species

/content/10.1128/9781555817176.ch03.ch03tab01

TABLE 1

Sequenced genomes in the CTG clade

TABLE 1

Sequenced genomes in the CTG clade

/content/10.1128/9781555817176.ch03.ch03tab02

TABLE 2

Telomere sequences in Candida species

TABLE 2

Telomere sequences in Candida species

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TABLE 3

Gene families enriched in pathogenic Candida speciesa

TABLE 3

Gene families enriched in pathogenic Candida speciesa

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TABLE 4

Loss of genes from mating signal transduction and meiotic pathways in Candida speciesa

TABLE 4

Loss of genes from mating signal transduction and meiotic pathways in Candida speciesa