Descriptions

Outline

Click the species name for a description of the organism

C. albicans WO-1

Status

The Candida albicans sequencing project is part of the Broad Institute Fungal Genome Initiative. Its goal is to release an annotated assembly with 8X genome sequence coverage for Candida albicans strain WO-1.

The specific aims for this organism are:

  1. Generate and assemble sequence reads yielding 8X coverage of the C. albicans genome through whole genome shotgun sequencing.
  2. Perform automated annotation of the sequence assembly.
  3. Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server at the Broad and by deposition of the sequence assembly in GenBank.

We produced whole genome shotgun sequence from two plasmid libraries (4kb and 10kb inserts) and a Fosmid library. The resulting 10X assembly was made public in March, 2006, and the results of automated genome annotation will be made public in future releases.

Organism Information

Candida species are the most common human fungal pathogens. The high prevalence of Candida compared with other fungi is likely because it is generally a benign commensal that resides on mucosal surfaces. Candida cause severe systemic disease in individuals who are immunocompromised, post-surgery, or taking broad-spectrum antibiotics. The diploid yeast C. albicans is the most frequent cause of candidemia, accounting for roughly half of Candida infections.

The estimated diploid genome size of C. albicans WO-1 is ~30 Mb contained in 8 pairs of homologous chromosomes.

Dr. Thyagarajan Srikantha in the laboratory of Dr. David Soll at the University of Iowa provided the genomic DNA for the sequencing project.

Questions about the project should be directed to annotation-webmaster@broad.mit.edu.

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C. tropicalis

Status

The Candida tropicalis sequencing project is part of the Broad Institute Fungal Genome Initiative. Its goal is to release an annotated assembly with 8X genome sequence coverage for Candida tropicalis strain MYA-3404.

Our specific aims are as follows:

  1. Generate and assemble sequence reads yielding 8X coverage of the C. tropicalis genome through whole genome shotgun sequencing.
  2. Perform automated annotation of the sequence assembly.
  3. Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server at the Broad and by deposition of the sequence assembly in GenBank.

We produced whole genome shotgun sequence from two plasmid libraries (4kb and 10kb inserts) and a Fosmid library. The resulting 10X assembly was made public in January of 2005, and the results of automated genome annotation will be made public in future 2005 releases.

Organism Information

The diploid yeast C. tropicalis is one of the most frequent non-albicans causes of candidemia. Unlike C. albicans, which is a normal commensal on human mucous membranes, the detection of C. tropicalis is more often associated with the development of deep fungal infections. However, many other virulence properties are shared between these two species. In a study of eight medically important Candida species, C. tropicalis appeared to be the second most virulent species in animal models; only C. albicans was more virulent. This may be explained in part by the high observed adherence property of C. tropicalis and C. albicans relative to other infectious Candidas. Like many other Candidas, C. tropicalis is capable of forming pseudohyphae. In rare cases C. tropicalis can also form true hyphae, a property uniquely shared with C. albicans. C. tropicalis also undergoes colony morphology switching, like C. albicans. These similarities mirror the phylogenetic relationship of these species. C. tropicalis forms a closely related taxon with C. albicans, C. dubliniensis, and C. parapsilosis. Like C. albicans, the CTG codon encodes serine rather than leucine in C. tropicalis as a consequence of the CTG capture event which occurred 100-200 million years ago in this clade of pathogenic yeasts.

The estimated diploid genome size of C. tropicalis is ~30 Mb contained in 5-6 pairs of homologous chromosomes.

Dr. Srikantha Thyagarajan in the laboratory of Dr. David Soll at the University of Iowa provided the genomic DNA for the sequencing project.

Questions about the project should be directed to annotation-webmaster@broad.mit.edu.

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L. elongisporus

Status

The Lodderomyces elongisporus sequencing project is part of the Broad Institute Fungal Genome Initiative. Its goal is to release an annotated assembly from 12X genome sequence coverage for Lodderomyces elongisporus diploid strain NRLL YB-4239, which was provided by Dr. Cletus Kurtzman at the National Center for Agricultural Utilization Research, ARS/USDA.

Our specific aims are as follows:

  1. Generate 12X coverage of the L. elongisporus genome through whole genome shotgun sequencing and generate a high quality genome assembly.
  2. Perform automated annotation of the sequence assembly.
  3. Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server at the Broad and by deposition of the sequence assembly in GenBank.

We produced whole genome shotgun sequence from two plasmid libraries (4kb and 10kb inserts) and a Fosmid library. The resulting 8.7X assembly was made public in June of 2006, and the results of automated genome annotation will be made public in future 2006 releases.

Organism Information

Lodderomyces elongisporus is the only known ascosporogenous species in the C. albicans clade, usually producing a single ascospore. While L. elongisporus does not appear pathogenic, many members of the C. albicans clade are important human pathogens. L. elongisporus is closely related to C. parapsilosis, C. albicans, and C. tropicalis (1).

1 Kurtzman, C. P. and C. J. Robnett. 1998. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek 73:331-371.

Genomic DNA from this strain was prepared by Jennifer Reedy in the laboratory of Dr. Joseph Heitman, Duke University Medical Center.

Questions about the project should be directed to annotation-webmaster@broad.mit.edu.

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C. guilliermondii

Status

The Candida guilliermondii sequencing project is part of the Broad Institute Fungal Genome Initiative. Its goal is to release an annotated assembly with 7X genome sequence coverage for Candida guilliermondii strain ATCC6260.

Our specific aims are as follows:

  1. Generate and assemble sequence reads yielding 7X coverage of the C. guilliermondii genome through whole genome shotgun sequencing.
  2. Perform automated annotation of the sequence assembly.
  3. Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server at the Broad and by deposition of the sequence assembly in GenBank.

We produced whole genome shotgun sequence from two plasmid libraries (4kb and 10kb inserts) and a Fosmid library. The resulting 12X assembly was made public in January of 2005, and the results of automated genome annotation will be made public in future 2005 releases.

January 2005 - Release 1 consists of a 12X whole-genome shotgun assembly generated at the Broad.

Release 2 will provide the results of automated genome annotation and analysis.

Organism Information

Candida guilliermondii (teleomorph Pichia guilliermondii) is a rarely observed pathogen, accounting for a few percent of all Candidemias. However, for cancer patients, C. guilliermondii is the primary cause of fungemia. C. guilliermondii is more distantly related to C. albicans than C. tropicalis, but is more closely related than C. lusitaniae. Like C. lusitaniae, C. guillermondii is haploid and has retained a complete sexual cycle including meiosis and sporulation. C. guillermondii shares in common with C. albicans, C. tropicalis, and C. lusitaniae the fact that CTG encodes serine rather than leucine, which is a marked distinction from other more distantly related hemiascomycetes including Ashbya gossypii, Saccharomyces cerevisiae, and Candida glabrata.

Jennifer Reedy in the laboratory of Dr. Joseph Heitman at Duke University provided the genomic DNA for the sequencing project.

Questions about the project should be directed to annotation-webmaster@broad.mit.edu.

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C. lusitaniae

Status

The Candida lusitaniae sequencing project is part of the Broad Institute Fungal Genome Initiative. Its goal is to release an annotated assembly with 7X genome sequence coverage for Candida lusitaniae strain ATCC 42720.

Our specific aims are as follows:

  1. Generate and assemble sequence reads yielding 7X coverage of the C. lusitaniae genome through whole genome shotgun sequencing.
  2. Perform automated annotation of the sequence assembly.
  3. Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server at the Broad and by deposition of the sequence assembly in GenBank.

We produced whole genome shotgun sequence from two plasmid libraries (4kb and 10kb inserts) and a Fosmid library. The resulting 9X assembly was made public in January of 2005, and the results of automated genome annotation will be made public in future 2005 releases.

Organism Information

Candida lusitaniae (teleomorph Clavispora lusitaniae) is an infrequently observed pathogen. Despite its low prevalence, C. lusitaniae poses unique therapeutic challenges as strains resistant to amphotericin B are frequently isolated from patients. Resistance of strains to azole drugs has also been reported. As a laboratory model, C. lusitaniae is experimentally tractable haploid organism offering transformation, gene disruption by homologous recombination, and congenic a and alpha strains constructed for genetic studies. C. lusitaniae is more distantly related to C. albicans than C. guilliermondii. The comparison of the genome sequence of C. lusitaniae to those of C. albicans, C. tropicalis, and C. guilliermondii will allow comprehensive analysis of protein conservation across very distantly related but infectious Candida species, including those that are haploid and have maintained a complete sexual cycle (including meiosis and sporulation) such as C. lusitaniae and C. guillermondii compared to those that are diploid and only rarely mate and complete only a parasexual cycle (C. albicans).

Jennifer Reedy in the laboratory of Dr. Joseph Heitman at Duke University provided the genomic DNA for the sequencing project.

Questions about the project should be directed to annotation-webmaster@broad.mit.edu.

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C. parapsilosis

Status and Organism Information

Details can be found at Wellcome Trust Sanger Institute

 

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Debaryomyces hansenii

Status and Organism Information

Details can be found at Genolevures

 

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