Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes
Background: The 10.9× genomic sequence of Candida albicans, the most important human fungal pathogen, was published in 2004. Assembly 19 consisted of 412 supercontigs, of which 266 were a haploid set, since this fungus is diploid and contains an extensive degree of heterozygosity but lacks a complet...
| Main Authors: | , , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
BioMed Central Ltd
2010
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| Online Access: | http://hdl.handle.net/1721.1/58917 |
| _version_ | 1826193070337556480 |
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| author | van het Hoog, Marco Rast, Timothy J Martchenko, Mikhail Grindle, Suzanne Dignard, Daniel Hogues, Herve Cuomo, Christina Berriman, Matthew Scherer, Stewart Whiteway, Malcolm Chibana, Hiroji Nantel, Andre Magee, P. T. Magee, B. B. |
| author2 | Broad Institute of MIT and Harvard |
| author_facet | Broad Institute of MIT and Harvard van het Hoog, Marco Rast, Timothy J Martchenko, Mikhail Grindle, Suzanne Dignard, Daniel Hogues, Herve Cuomo, Christina Berriman, Matthew Scherer, Stewart Whiteway, Malcolm Chibana, Hiroji Nantel, Andre Magee, P. T. Magee, B. B. |
| author_sort | van het Hoog, Marco |
| collection | MIT |
| description | Background: The 10.9× genomic sequence of Candida albicans, the most important human fungal pathogen, was published in 2004. Assembly 19 consisted of 412 supercontigs, of which 266 were a haploid set, since this fungus is diploid and contains an extensive degree of heterozygosity but lacks a complete sexual cycle. However, sequences of specific chromosomes were not determined. Results: Supercontigs from Assembly 19 (183, representing 98.4% of the sequence) were assigned to individual chromosomes purified by pulse-field gel electrophoresis and hybridized to DNA microarrays. Nine Assembly 19 supercontigs were found to contain markers from two different chromosomes. Assembly 21 contains the sequence of each of the eight chromosomes and was determined using a synteny analysis with preliminary versions of the Candida dubliniensis genome assembly, bioinformatics, a sequence tagged site (STS) map of overlapping fosmid clones, and an optical map. The orientation and order of the contigs on each chromosome, repeat regions too large to be covered by a sequence run, such as the ribosomal DNA cluster and the major repeat sequence, and telomere placement were determined using the STS map. Sequence gaps were closed by PCR and sequencing of the products. The overall assembly was compared to an optical map; this identified some misassembled contigs and gave a size estimate for each chromosome. Conclusion: Assembly 21 reveals an ancient chromosome fusion, a number of small internal duplications followed by inversions, and a subtelomeric arrangement, including a new gene family, the TLO genes. Correlations of position with relatedness of gene families imply a novel method of dispersion. The sequence of the individual chromosomes of C. albicans raises interesting biological questions about gene family creation and dispersion, subtelomere organization, and chromosome evolution. |
| first_indexed | 2024-09-23T09:33:18Z |
| format | Article |
| id | mit-1721.1/58917 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T09:33:18Z |
| publishDate | 2010 |
| publisher | BioMed Central Ltd |
| record_format | dspace |
| spelling | mit-1721.1/589172022-09-30T15:15:18Z Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes van het Hoog, Marco Rast, Timothy J Martchenko, Mikhail Grindle, Suzanne Dignard, Daniel Hogues, Herve Cuomo, Christina Berriman, Matthew Scherer, Stewart Whiteway, Malcolm Chibana, Hiroji Nantel, Andre Magee, P. T. Magee, B. B. Broad Institute of MIT and Harvard Cuomo, Christina Background: The 10.9× genomic sequence of Candida albicans, the most important human fungal pathogen, was published in 2004. Assembly 19 consisted of 412 supercontigs, of which 266 were a haploid set, since this fungus is diploid and contains an extensive degree of heterozygosity but lacks a complete sexual cycle. However, sequences of specific chromosomes were not determined. Results: Supercontigs from Assembly 19 (183, representing 98.4% of the sequence) were assigned to individual chromosomes purified by pulse-field gel electrophoresis and hybridized to DNA microarrays. Nine Assembly 19 supercontigs were found to contain markers from two different chromosomes. Assembly 21 contains the sequence of each of the eight chromosomes and was determined using a synteny analysis with preliminary versions of the Candida dubliniensis genome assembly, bioinformatics, a sequence tagged site (STS) map of overlapping fosmid clones, and an optical map. The orientation and order of the contigs on each chromosome, repeat regions too large to be covered by a sequence run, such as the ribosomal DNA cluster and the major repeat sequence, and telomere placement were determined using the STS map. Sequence gaps were closed by PCR and sequencing of the products. The overall assembly was compared to an optical map; this identified some misassembled contigs and gave a size estimate for each chromosome. Conclusion: Assembly 21 reveals an ancient chromosome fusion, a number of small internal duplications followed by inversions, and a subtelomeric arrangement, including a new gene family, the TLO genes. Correlations of position with relatedness of gene families imply a novel method of dispersion. The sequence of the individual chromosomes of C. albicans raises interesting biological questions about gene family creation and dispersion, subtelomere organization, and chromosome evolution. National Institute of Allergy and Infectious Diseases (U.S.) (contract N01 AI05406) National Institute of Allergy and Infectious Diseases (U.S.) (grant R01 AI 16567) National Research Council (U.S.). Genome Health Initiative Canadian Institutes for Health Research (grant HOP 67260) Canadian Institutes for Health Research (grant MOP 42516) Ministry of Education, Culture, Sports, Science and Technology of Japan (Grant-in-Aid for Scientific Research) 2010-10-06T19:35:30Z 2010-10-06T19:35:30Z 2007-04 2006-10 2010-09-03T16:14:06Z Article http://purl.org/eprint/type/JournalArticle 1474-760X 1465-6914 http://hdl.handle.net/1721.1/58917 Genome Biology. 2007 Apr 09;8(4):R52 en http://dx.doi.org/10.1186/gb-2007-8-4-r52 Genome Biology Creative Commons Attribution http://creativecommons.org/licenses/by/2.0 van het Hoog et al.; licensee BioMed Central Ltd. application/pdf BioMed Central Ltd BioMed Central Ltd |
| spellingShingle | van het Hoog, Marco Rast, Timothy J Martchenko, Mikhail Grindle, Suzanne Dignard, Daniel Hogues, Herve Cuomo, Christina Berriman, Matthew Scherer, Stewart Whiteway, Malcolm Chibana, Hiroji Nantel, Andre Magee, P. T. Magee, B. B. Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes |
| title | Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes |
| title_full | Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes |
| title_fullStr | Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes |
| title_full_unstemmed | Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes |
| title_short | Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes |
| title_sort | assembly of the candida albicans genome into sixteen supercontigs aligned on the eight chromosomes |
| url | http://hdl.handle.net/1721.1/58917 |
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