A human-curated annotation of the Candida albicans genome

Burkhard R. Braun; Marco van het Hoog; Christophe d'Enfert; Mikhail Martchenko; Jan Dungan; Alan Kuo; Diane O. Inglis; M. Andrew Uhl; Hervé Hogues; Matthew Berriman; Michael Lorenz; Anastasia Levitin; Ursula Oberholzer; Catherine Bachewich; Doreen Harcus; Anne Marcil; Daniel Dignard; Tatiana Iouk; Rosa Zito; Lionel Frangeul; Fredj Tekaia; Kim Rutherford; Edwin Wang; Carol A. Munro; Steve Bates; Neil A. Gow; Lois L. Hoyer; Gerwald Köhler; Joachim Morschhäuser; George Newport; Sadri Znaidi; Martine Raymond; Bernard Turcotte; Gavin Sherlock; Maria Costanzo; Jan Ihmels; Judith Berman; Dominique Sanglard; Nina Agabian; Aaron P. Mitchell; Alexander D. Johnson; Malcolm Whiteway; André Nantel

doi:10.1371/journal.pgen.0010001

A human-curated annotation of the Candida albicans genome

Burkhard R. Braun, Marco van het Hoog, Christophe d'Enfert, Mikhail Martchenko, Jan Dungan, Alan Kuo, Diane O. Inglis, M. Andrew Uhl, Hervé Hogues, Matthew Berriman, Michael Lorenz, Anastasia Levitin, Ursula Oberholzer, Catherine Bachewich, Doreen Harcus, Anne Marcil, Daniel Dignard, Tatiana Iouk, Rosa Zito, Lionel FrangeulFredj Tekaia, Kim Rutherford, Edwin Wang, Carol A. Munro, Steve Bates, Neil A. Gow, Lois L. Hoyer, Gerwald Köhler, Joachim Morschhäuser, George Newport, Sadri Znaidi, Martine Raymond, Bernard Turcotte, Gavin Sherlock, Maria Costanzo, Jan Ihmels, Judith Berman, Dominique Sanglard, Nina Agabian, Aaron P. Mitchell, Alexander D. Johnson, Malcolm Whiteway, André Nantel

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Abstract

Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.

Original language	English
Pages (from-to)	36-57
Number of pages	22
Journal	PLoS Genetics
Volume	1
Issue number	1
DOIs	https://doi.org/10.1371/journal.pgen.0010001
State	Published - Jul 2005

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Braun, B. R., van het Hoog, M., d'Enfert, C., Martchenko, M., Dungan, J., Kuo, A., Inglis, D. O., Uhl, M. A., Hogues, H., Berriman, M., Lorenz, M., Levitin, A., Oberholzer, U., Bachewich, C., Harcus, D., Marcil, A., Dignard, D., Iouk, T., Zito, R., ... Nantel, A. (2005). A human-curated annotation of the Candida albicans genome. PLoS Genetics, 1(1), 36-57. https://doi.org/10.1371/journal.pgen.0010001

@article{05d910925008406698431bc5cd6f19ed,

title = "A human-curated annotation of the Candida albicans genome",

abstract = "Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.",

author = "Braun, {Burkhard R.} and {van het Hoog}, Marco and Christophe d'Enfert and Mikhail Martchenko and Jan Dungan and Alan Kuo and Inglis, {Diane O.} and Uhl, {M. Andrew} and Herv{\'e} Hogues and Matthew Berriman and Michael Lorenz and Anastasia Levitin and Ursula Oberholzer and Catherine Bachewich and Doreen Harcus and Anne Marcil and Daniel Dignard and Tatiana Iouk and Rosa Zito and Lionel Frangeul and Fredj Tekaia and Kim Rutherford and Edwin Wang and Munro, {Carol A.} and Steve Bates and Gow, {Neil A.} and Hoyer, {Lois L.} and Gerwald K{\"o}hler and Joachim Morschh{\"a}user and George Newport and Sadri Znaidi and Martine Raymond and Bernard Turcotte and Gavin Sherlock and Maria Costanzo and Jan Ihmels and Judith Berman and Dominique Sanglard and Nina Agabian and Mitchell, {Aaron P.} and Johnson, {Alexander D.} and Malcolm Whiteway and Andr{\'e} Nantel",

year = "2005",

month = jul,

doi = "10.1371/journal.pgen.0010001",

language = "English",

volume = "1",

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Braun, BR, van het Hoog, M, d'Enfert, C, Martchenko, M, Dungan, J, Kuo, A, Inglis, DO, Uhl, MA, Hogues, H, Berriman, M, Lorenz, M, Levitin, A, Oberholzer, U, Bachewich, C, Harcus, D, Marcil, A, Dignard, D, Iouk, T, Zito, R, Frangeul, L, Tekaia, F, Rutherford, K, Wang, E, Munro, CA, Bates, S, Gow, NA, Hoyer, LL, Köhler, G, Morschhäuser, J, Newport, G, Znaidi, S, Raymond, M, Turcotte, B, Sherlock, G, Costanzo, M, Ihmels, J, Berman, J, Sanglard, D, Agabian, N, Mitchell, AP, Johnson, AD, Whiteway, M & Nantel, A 2005, 'A human-curated annotation of the Candida albicans genome', PLoS Genetics, vol. 1, no. 1, pp. 36-57. https://doi.org/10.1371/journal.pgen.0010001

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T1 - A human-curated annotation of the Candida albicans genome

AU - Braun, Burkhard R.

AU - van het Hoog, Marco

AU - d'Enfert, Christophe

AU - Martchenko, Mikhail

AU - Dungan, Jan

AU - Kuo, Alan

AU - Inglis, Diane O.

AU - Uhl, M. Andrew

AU - Hogues, Hervé

AU - Berriman, Matthew

AU - Lorenz, Michael

AU - Levitin, Anastasia

AU - Oberholzer, Ursula

AU - Bachewich, Catherine

AU - Harcus, Doreen

AU - Marcil, Anne

AU - Dignard, Daniel

AU - Iouk, Tatiana

AU - Zito, Rosa

AU - Frangeul, Lionel

AU - Tekaia, Fredj

AU - Rutherford, Kim

AU - Wang, Edwin

AU - Munro, Carol A.

AU - Bates, Steve

AU - Gow, Neil A.

AU - Hoyer, Lois L.

AU - Köhler, Gerwald

AU - Morschhäuser, Joachim

AU - Newport, George

AU - Znaidi, Sadri

AU - Raymond, Martine

AU - Turcotte, Bernard

AU - Sherlock, Gavin

AU - Costanzo, Maria

AU - Ihmels, Jan

AU - Berman, Judith

AU - Sanglard, Dominique

AU - Agabian, Nina

AU - Mitchell, Aaron P.

AU - Johnson, Alexander D.

AU - Whiteway, Malcolm

AU - Nantel, André

PY - 2005/7

Y1 - 2005/7

N2 - Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.

AB - Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.

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U2 - 10.1371/journal.pgen.0010001

DO - 10.1371/journal.pgen.0010001

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VL - 1

SP - 36

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JO - PLoS Genetics

JF - PLoS Genetics

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A human-curated annotation of the Candida albicans genome

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