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

Research output: Contribution to journalArticle

217 Citations (Scopus)

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 languageEnglish
Pages (from-to)36-57
Number of pages22
JournalPLoS Genetics
Volume1
Issue number1
DOIs
StatePublished - Jul 2005

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Candida albicans
Fungal Genome
genome
Genome
gene
Genes
genomics
malonyl coenzyme A
Fungi
genes
fungus
enzyme
Malonyl Coenzyme A
genome assembly
ketone bodies
Ketone Bodies
Reading Frames
therapeutics
fungi
bioinformatics

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Braun, B. R., van het Hoog, M., d'Enfert, C., Martchenko, M., Dungan, J., Kuo, A., ... 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
Braun, Burkhard R. ; van het Hoog, Marco ; d'Enfert, Christophe ; Martchenko, Mikhail ; Dungan, Jan ; Kuo, Alan ; Inglis, Diane O. ; Uhl, M. Andrew ; Hogues, Hervé ; Berriman, Matthew ; Lorenz, Michael ; Levitin, Anastasia ; Oberholzer, Ursula ; Bachewich, Catherine ; Harcus, Doreen ; Marcil, Anne ; Dignard, Daniel ; Iouk, Tatiana ; Zito, Rosa ; Frangeul, Lionel ; Tekaia, Fredj ; Rutherford, Kim ; Wang, Edwin ; Munro, Carol A. ; Bates, Steve ; Gow, Neil A. ; Hoyer, Lois L. ; Köhler, Gerwald ; Morschhäuser, Joachim ; Newport, George ; Znaidi, Sadri ; Raymond, Martine ; Turcotte, Bernard ; Sherlock, Gavin ; Costanzo, Maria ; Ihmels, Jan ; Berman, Judith ; Sanglard, Dominique ; Agabian, Nina ; Mitchell, Aaron P. ; Johnson, Alexander D. ; Whiteway, Malcolm ; Nantel, André. / A human-curated annotation of the Candida albicans genome. In: PLoS Genetics. 2005 ; Vol. 1, No. 1. pp. 36-57.
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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

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

In: PLoS Genetics, Vol. 1, No. 1, 07.2005, p. 36-57.

Research output: Contribution to journalArticle

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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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Braun BR, van het Hoog M, d'Enfert C, Martchenko M, Dungan J, Kuo A et al. A human-curated annotation of the Candida albicans genome. PLoS Genetics. 2005 Jul;1(1):36-57. https://doi.org/10.1371/journal.pgen.0010001