Dot matrix comparison of the <i>C. parapsilosis</i> and <i>C. orthopsilosis</i> genomes.

<p>The horizontal axis represents a joining of the 8 largest <i>C. parapsilosis</i> superscaffolds, sorted by decreasing length. The vertical axis represents a joining of the 8 <i>C. orthopsilosis</i> superscaffolds, sorted and named by decreasing length. Sequence aligning between the two species is represented in black if in the same direction, and in red if in the opposite direction.</p

Horizontal Gene Transfer of a member of the MAT/GAT family in <i>C. orthopsilosis</i>.

<p>(<b>A</b>) Gene order surrounding the MAT/GAT gene in <i>C. orthopsilosis</i>, and the syntenic regions in <i>C. parapsilosis</i> and <i>L. elongisporus</i>. The grey, green and blue arrows represent conserved genes in all three species. The solid red arrow represents an intact ORF in <i>C. orthopsilosis</i>; the transparent red arrow represents a pseudogene in <i>C. parapsilosis</i>. (<b>B</b>) Multiple alignment of the predicted MAT/GAT proteins from <i>Sphingobacterium</i> (Sb1 = ZP_03969495.1, Sb2 = YP_004319944.1), <i>Pedobacter</i> (Pb, YP_003093425.1), <i>C. orthopsilosis</i> (Co) and <i>C. parapsilosis</i> (Cp). Yellow squares mark the presence of frameshifts (forward slash) and internal stop codons (x) that result in a pseudogene in <i>C. parapsilosis</i>.</p

Expansion of a Hyr/Iff gene cluster in <i>C. parapsilosis</i>.

<p>The diagram is redrawn from CGOB, and represents the gene order from 11 genomes of 10 species in the <i>Candida</i> clade. Horizontal blocks of color indicate chromosomes in individual species, and pillars contain orthologs. Adjacent genes are joined by gray lines. The arrows indicate the direction of transcription. Genes 301290–301330 represent a tandem amplification of 5 Hyr/Iff genes that is unique to <i>C. parapsilosis.</i></p

Sequence and Analysis of the Genome of the Pathogenic Yeast <em>Candida orthopsilosis</em>

<div><p><em>Candida orthopsilosis</em> is closely related to the fungal pathogen <em>Candida parapsilosis.</em> However, whereas <em>C. parapsilosis</em> is a major cause of disease in immunosuppressed individuals and in premature neonates, <em>C. orthopsilosis</em> is more rarely associated with infection. We sequenced the <em>C. orthopsilosis</em> genome to facilitate the identification of genes associated with virulence. Here, we report the <em>de novo</em> assembly and annotation of the genome of a Type 2 isolate of <em>C. orthopsilosis</em>. The sequence was obtained by combining data from next generation sequencing (454 Life Sciences and Illumina) with paired-end Sanger reads from a fosmid library. The final assembly contains 12.6 Mb on 8 chromosomes. The genome was annotated using an automated pipeline based on comparative analysis of genomes of <em>Candida</em> species, together with manual identification of introns. We identified 5700 protein-coding genes in <em>C. orthopsilosis</em>, of which 5570 have an ortholog in <em>C. parapsilosis.</em> The time of divergence between <em>C. orthopsilosis</em> and <em>C. parapsilosis</em> is estimated to be twice as great as that between <em>Candida albicans</em> and <em>Candida dubliniensis</em>. There has been an expansion of the Hyr/Iff family of cell wall genes and the JEN family of monocarboxylic transporters in <em>C. parapsilosis</em> relative to <em>C. orthopsilosis</em>. We identified one gene from a Maltose/Galactoside O-acetyltransferase family that originated by horizontal gene transfer from a bacterium to the common ancestor of <em>C. orthopsilosis</em> and <em>C. parapsilosis</em>. We report that <em>TFB3</em>, a component of the general transcription factor TFIIH, undergoes alternative splicing by intron retention in multiple <em>Candida</em> species. We also show that an intein in the vacuolar ATPase gene <em>VMA1</em> is present in <em>C. orthopsilosis</em> but not <em>C. parapsilosis</em>, and has a patchy distribution in <em>Candida</em> species. Our results suggest that the difference in virulence between <em>C. parapsilosis</em> and <em>C. orthopsilosis</em> may be associated with expansion of gene families.</p> </div

Potential in-frame translation of unspliced introns in <i>Candida TFB3</i> genes.

<p>The 5′ end of <i>TFB3</i> genes from 14 yeast species are shown, ending at a conserved region coding for the amino acid sequence DMCPICK. Exons and introns are written in upper and lower case, respectively. Gray backgrounds indicate potential in-frame translation of introns. Spliced and unspliced mRNAs have been identified in three species: <i>C. orthopsilosis</i>, <i>C. parapsilosis</i> and <i>C. albicans.</i> Probable intron branch sites are underlined. Upstream in-frame stop codons are boxed. Two possible alternative gene structures are shown for <i>D. hansenii</i>. Arrows mark two Cys residues that form part of the RING finger domain. The topology of the phylogenetic tree is from Fitzpatrick et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035750#pone.0035750-Fitzpatrick4" target="_blank">[126]</a>.</p

Phylogeny and sequence divergence in the <i>C. orthopsilosis</i> clade.

<p>(<b>A</b>) Phylogenetic relationship among 7 species, from maximum likelihood analysis of concatenated partial sequences of 1334 proteins. Numbers indicate branch lengths. Bootstrap values on all branches are 100%. (<b>B</b>) Histogram of distributions of nonsynonymous substitution levels (<i>dN</i>) in 5091 orthologous genes for two independent interspecies comparisons (<i>C. orthopsilosis</i> vs. <i>C. parapsilosis</i>, and <i>C. albicans</i> vs. <i>C. dubliniensis</i>). (<b>C</b>) Scatter plot showing the correlation of <i>dN</i> values for individual genes in the same two comparisons. The regression line has been forced through the origin.</p

Identification of intein sequences in the Vma1 proteins of Candida species.

<p>The figure shows the alignment of the intein (VDE) sequences only; the alignment of the entire Vma1 proteins is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035750#pone.0035750.s005" target="_blank">Figure S5</a>. The motifs are labeled according to the nomenclature of Perler et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035750#pone.0035750-Perler1" target="_blank">[102]</a>. Motifs A, B, F and G are important for self-splicing. Motifs C, D, E and H are associated with homing. Two aspartic acids within the LAGLIDADG motifs in C and E that are required for homing are indicated with asterisks. The protein sequences were aligned and visualized using SeaView <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035750#pone.0035750-Gouy1" target="_blank">[122]</a>.</p

Efg1 in Candida parapsilosis

Efg1 (a member of the APSES family) is an important regulator of hyphal growth and of the white-to-opaque transition in C. albicans and very closely related species. We show that in Candida parapsilosis Efg1 is a major regulator of a different morphological switch at the colony level, from a concentric to smooth morphology. The rate of switching is at least 20-fold increased in an efg1 knockout relative to wild type. Efg1 deletion strains also have reduced biofilm formation, attenuated virulence in an insect model, and increased sensitivity to SDS and caspofungin. Biofilm reduction is more dramatic in in vitro than in in vivo models. An Efg1 paralog (Efh1) is restricted to Candida species, and does not regulate concentric-smooth phenotype switching, biofilm formation or stress response. We used ChIP-seq to identify the Efg1 regulon. 931 promoter regions bound by Efg1 are highly enriched for transcription factors and regulatory proteins. Efg1 also binds to its own promoter, and negatively regulates its expression. Efg1 targets are enriched in binding sites for 93 additional transcription factors, including Ndt80. Our analysis suggests that Efg1 has an ancient role as regulator of development in fungi, and is central to several regulatory networks.Irish Research CouncilScience Foundation IrelandOTKAERA-Net PathoGenomics ProgramEMBO Installation GrantDM, 09/12/201

Role of Genomics and RNA-seq in Studies of Fungal Virulence

Since its introduction in the last decade, massive parallel sequencing, or "next-generation sequencing", has revolutionized our access to genomic information, providing accurate data with increasingly higher yields and lower costs with respect to first-generation technology. Massive parallel sequencing of cDNA, or RNA-seq, is progressively replacing array-based technology as the method of choice for transcriptomics. This review describes some of the most recent applications of next-generation sequencing technology to the study of pathogenic fungi, including Candida, Aspergillus and Cryptococcusspecies. Several integrated approaches illustrate the power and accuracy of RNA-seq for studying the biology of human fungal pathogens. In addition, the lack of consistency in data analysis is discussed.Copyright: "It is fully accessible to all users at libraries and institutions that have purchased a SpringerLink license. If your article is published under one of our Open Access programs, it will be freely accessible to any user." Also, the journal is "Current Fungal Infection Reports", not the "Current Rheumatology" I used. This new journal was not on the list. Please add it.Have asked Research for journal to be added ([email protected]) 2012-11-23 J