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Chapter 3 : Comparative Genomics of Species

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Abstract:

This chapter focuses on the species within the CTG clade. Several of the species (, , , , and ) 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 . The precise number of agglutinin-like sequence (ALS) genes in the other species is likely to be overestimated, caused by difficulties in assembling the repeated regions. Species-specific amplifications have also occurred in the other species. The large-scale analysis of genomes confirmed that many of the multigene families described for are also present in the genomes of other pathogenic species. and are the only two species that generate true filaments, although is much less efficient. The change in the genetic code may have helped protect species from infection by RNA-based viruses. Comparative genomic tools for 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 species.

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

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Candida albicans
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Candida tropicalis
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Figures

Image of FIGURE 1
FIGURE 1

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

Citation: Butler G. 2012. Comparative Genomics of Species, p 27-43. In Calderone R, Clancy C (ed), and Candidiasis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817176.ch3
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Image of FIGURE 2
FIGURE 2

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

Citation: Butler G. 2012. Comparative Genomics of Species, p 27-43. In Calderone R, Clancy C (ed), and Candidiasis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817176.ch3
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Image of FIGURE 3
FIGURE 3

Comparative analysis of sequences from species. (Top panel) Genomic distribution of genes in , , and . (Bottom panel) Maximum-likelihood phylogeny of 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. is present only in . Reproduced from ( ) with permission from the publisher. doi:10.1128/9781555817176.ch3.f3

Citation: Butler G. 2012. Comparative Genomics of Species, p 27-43. In Calderone R, Clancy C (ed), and Candidiasis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817176.ch3
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Image of FIGURE 4
FIGURE 4

(A) Organization of MTL in species. α-specific genes are shown in white and -specific genes in black. 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

Citation: Butler G. 2012. Comparative Genomics of Species, p 27-43. In Calderone R, Clancy C (ed), and Candidiasis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817176.ch3
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Image of FIGURE 5
FIGURE 5

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

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

Generic image for table
TABLE 1

Sequenced genomes in the CTG clade

Citation: Butler G. 2012. Comparative Genomics of Species, p 27-43. In Calderone R, Clancy C (ed), and Candidiasis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817176.ch3
Generic image for table
TABLE 2

Telomere sequences in species

Citation: Butler G. 2012. Comparative Genomics of Species, p 27-43. In Calderone R, Clancy C (ed), and Candidiasis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817176.ch3
Generic image for table
TABLE 3

Gene families enriched in pathogenic species

Citation: Butler G. 2012. Comparative Genomics of Species, p 27-43. In Calderone R, Clancy C (ed), and Candidiasis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817176.ch3
Generic image for table
TABLE 4

Loss of genes from mating signal transduction and meiotic pathways in species

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

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