Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes

Genome Biology

Volumn 8, Issue 4, 2007, Pages

  Van het Hoog, Marco ^a   Rast, Timothy J ^b   Martchenko, Mikhail ^a   Grindle, Suzanne ^b   Dignard, Daniel ^a   Hogues, Hervé ^a   Cuomo, Christine ^c   Berriman, Matthew ^d   Scherer, Stewart ^e   Magee, B B ^b   Whiteway, Malcolm ^a   Chibana, Hiroji ^f   Nantel, André ^a   Magee, P T ^b  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^b UNIVERSITY OF MINNESOTA   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^e Paseo Grande ^*  (United States)

^f CHIBA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; TELOMERE BINDING PROTEIN;

ARTICLE; CANDIDA ALBICANS; CANDIDA DUBLINIENSIS; CHROMOSOME ANALYSIS; CHROMOSOME DUPLICATION; CHROMOSOME INVERSION; CHROMOSOME SIZE; CONTIG MAPPING; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA MICROARRAY; GENE ASSIGNMENT; GENE CLUSTER; GENE ORDER; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CONSERVATION; GENOMICS; MARKER GENE; MOLECULAR CLONING; NONHUMAN; POLYMERASE CHAIN REACTION; POSITION EFFECT; PULSED FIELD GEL ELECTROPHORESIS; SEQUENCE ALIGNMENT; SEQUENCE TAGGED SITE; STRUCTURAL BIOINFORMATICS; SYNTENY; TELOMERE; AMINO ACID SEQUENCE; CENTROMERE; CHEMISTRY; CHROMOSOME; GENETICS; GENOME; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; OPEN READING FRAME;

CANDIDA ALBICANS; CANDIDA DUBLINIENSIS; FUNGI;

AMINO ACID SEQUENCE; CANDIDA ALBICANS; CENTROMERE; CHROMOSOMES, FUNGAL; CONTIG MAPPING; GENOME, FUNGAL; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT; SYNTENY; TELOMERE-BINDING PROTEINS;

EID: 34250186544     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-4-r52     Document Type: Article

References (48)

1. Kullberg BJ Filler SG Candidemia. Candida and Candidiasis Washington, DC: ASM Press Calderone R 2002:327-340.
2. Chen X Magee BB Dawson D Magee PT Kumamoto CA Chromosome 1 trisomy compromises the virulence of Candida albicans. Mol Microbiol 2004, 51:551-65. 10.1046/j.1365-2958.2003.03852.x 14756793
3. Selmecki A Bergmann S Berman J Comparative genome hybridization reveals widespread aneuploidy in Candida albicans laboratory strains. Mol Microbiol 2005, 55:1553-1565. 10.1111/j.1365-2958.2005.04492.x 15720560
4. Lephart PR Chibana H Magee PT Effect of the major repeat sequence on chromosome loss in Candida albicans. Eukaryot Cell 2005, 4:733-741. 1087809 15821133 10.1128/EC.4.4.733-741.2005
5. Selmecki A Forche A Berman J Aneuploidy and isochromosome formation in drug-resistant Candida albicans. Science 2006, 313:367-370. 1717021 16857942 10.1126/science.1128242
6. Jones T Federspiel NA Chibana H Dungan J Kalman S Magee BB Newport G Thorstenson YR Agabian N Magee PT The diploid genome sequence of Candida albicans. Proc Natl Acad Sci USA 2004, 101:7329-7334. 409918 15123810 10.1073/pnas.0401648101
7. Nantel A The long hard road to a completed Candida albicans genome. Fungal Genet Biol 2006, 43:311-315. 10.1016/j.fgb.2006.01.002 16517185
8. Chibana H Magee BB Grindle S Ran Y Scherer S Magee PT A physical map of Chromosome 7 of Candida albicans. Genetics 1998, 149:1739-1752. 1460290 9691033
9. Lane S Birse C Zhou S Matson R Liu H DNA array studies demonstrate convergent regulation of virulence factors by Cph1, Cph2, and Efg1 in Candida albicans. J Biol Chem 2001, 276:48988-48996. 10.1074/ jbc.M104484200 11595734
10. Nantel A Dignard D Bachewich C Harcus D Marcil A Bouin AP Sensen CW Hogues H van het Hoog M Gordon P Transcription profiling of Candida albicans cells undergoing the yeast-to-hyphal transition. Mol Biol Cell 2002, 13:3452-3465. 129958 12388749 10.1091/mbc.E02-05-0272
11. Uhl MA Biery M Craig N Johnson AD Haploinsufficiency-based large-scale forward genetic analysis of filamentous growth in the diploid human fungal pathogen C. albicans. EMBO J 2003, 22:2668-2678. 156753 12773383 10.1093/emboj/cdg256
12. Hube B Naglik J Candida albicans proteinases: Resolving the mystery of a gene family. Microbiology 2001, 147:1997-2005. 11495978
13. Hoyer LL Hecht JE The ALS5 gene of Candida albicans and analysis of the Als5p N-terminal domain. Yeast 2001, 18:49-60. 10.1002/ 1097-0061(200101)18:1<49::AID-YEA646>3.0.CO;2-M 11124701
14. Kunze D Melzer I Bennett D Sanglard D MacCallum D Norskau J Coleman DC Odds FC Schafer W Hube B Functional analysis of the phospholipase C gene CaPLC1 and two unusual phospholipase C genes, CaPLC2 and CaPLC3, of Candida albicans. Microbiology 2005, 151:3381-3394. 10.1099/ mic.0.28353-0 16207920
15. Samaranayake YH Dassanayake RS Jayatilake JA Cheung BP Yau JY Yeung KW Samaranayake LP Phospholipase B enzyme expression is not associated with other virulence attributes in Candida albicans isolates from patients with human immunodeficiency virus infection. J Med Microbiol 2005, 54:583-593. 10.1099/jmm.0.45762-0 15888468
16. Roemer T Jiang B Davison J Ketela T Veillette K Breton A Tandia F Linteau A Sillaots S Marta C Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery. Mol Microbiol 2003, 50:167-181. 10.1046/j.1365-2958.2003.03697.x 14507372
17. Bruno VM Mitchell AP Large-scale gene function analysis in Candida albicans. Trends Microbiol 2004, 12:157-161. 10.1016/j.tim.2004.02.002 15051065
18. Chindamporn A Nakagawa Y Mizuguchi I Chibana H Doi M Tanaka K Repetitive sequences (RPSs) in the chromosomes of Candida albicans are sandwiched between two novel stretches, HOK and RB2, common to each chromosome. Microbiology 1998, 144:849-857. 9579060
19. Lasker BA Page LS Lot TJ Kobayashi GS Isolation, characterization, and sequencing of Candida albicans repetitive sequence element 2. Gene 1992, 116:51-57. 10.1016/0378-1119(92)90628-3 1628844
20. Thrash-Bingham C Gorman JA Identification, characterization and sequence of Candida albicans repetitive DNAs Rel-1 and Rel-2. Curr Genet 1993, 23:455-462. 10.1007/BF00312634 8319302
21. Chibana H Oka N Nakayama H Aoyama T Magee BB Magee PT Mikami Y Sequence finishing and gene mapping for Candida albicans chromosome 7, and syntenic analysis against Saccharomyces cerevisiae genome. Genetics 2005, 170:1525-1537. 1449773 15937140 10.1534/genetics.104.034652
22. Sanyal K Baum M Carbon J Centromeric DNA sequences in the pathogenic yeast Candida albicans are all different and unique. Proc Natl Acad Sci USA 2004, 101:11374-11379. 509209 15272074 10.1073/pnas.0404318101
23. Iwaguchi S Homma M Chibana H Tanaka K Isolation and characterization of a repeated sequence (RPS1) of Candida albicans. J Gen Microbiol 1992, 138:1893-1900. 1402790
24. Chibana H Iwaguchi S Homma M Chindamporn A Nakagawa Y Tanaka K Diversity of tandemly repetitive sequences due to short periodic repetitions in the chromosomes of Candida albicans. J Bacteriol 1994, 176:3851-3858. 205581 8021166
25. Chindamporn A Nakagawa Y Homma M Chibana H Doi M Tanaka K Analysis of the chromosomal localization of the repetitive sequences (RPSs) in Candida albicans. Microbiology 1995, 141:469-476. 7704277
26. Goodwin TJ Poulter RT Multiple LTR-retrotransposon families in the asexual yeast Candida albicans. Genome Res 2000, 10:174-191. 10.1101/ gr.10.2.174 10673276
27. Kaiser B Munder T Saluz HP Kunkel W Eck R Identification of a gene encoding the pyruvate decarboxylase gene regulator CaPdc2p from Candida albicans. Yeast 1999, 15:585-591. 10.1002/ (SICI)1097-0061(199905)15:7<585::AID-YEA401>3.0.CO;2-9 10341421
28. 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 A human-curated annotation of the Candida albicans genome. PLOS Genet 2005, 1:36-57. 1183520 16103911 10.1371/journal.pgen.0010001
29. Gaur M Choudhury D Prasad R Complete inventory of ABC proteins in human pathogenic yeast, Candida albicans. J Mol Microbiol Biotechnol 2005, 9:3-15. 10.1159/000088141 16254441
30. Pujol C Daniels KJ Lockhart SR Srikantha T Radke JB Geiger J Soll DR The closely related species Candida albicans and Candida dubliniensis can mate. Eukaryot Cell 2004, 3:1015-10127. 500882 15302834 10.1128/ EC.3.4.1015-1027.2004
31. Moran G Stokes C Thewes S Hube B Coleman DC Sullivan D Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis. Microbiology 2004, 150:3363-3382. 10.1099/mic.0.27221-0 15470115
32. Goodwin TJ Poulter RT The CARE-2 and rel-2 repetitive elements of Candida albicans contain LTR fragments of a new retrotransposon. Gene 1998, 218:85-93. 10.1016/S0378-1119(98)00362-X 9751806
33. Hube B Stehr F Bossenz M Mazur A Kretschmar M Schafer W Secreted lipases of Candida albicans: Cloning, characterisation and expression analysis of a new gene family with at least ten members. Arch Microbiol 2000, 174:362-374. 10.1007/s002030000218 11131027
34. Teng SC Zakian VA Telomere-telomere recombination is an efficient bypass pathway for telomere maintenance in Saccharomyces cerevisiae. Mol Cell Biol 1999, 19:8083-8093. 84893 10567534
35. Ciudad T Andaluz E Steinberg-Neifach O Lue NF Gow NA Calderone RA Larriba G Homologous recombination in Candida albicans: Role of CaRad52p in DNA repair, integration of linear DNA fragments and telomere length. Mol Microbiol 2004, 53:1177-1194. 10.1111/j.1365-2958.2004.04197.x 15306020
36. De Las Penas A Pan SJ Castano I Alder J Cregg R Cormack BP Virulence-related surface glycoproteins in the yeast pathogen Candida glabrata are encoded in subtelomeric clusters and subject to RAP1- and SIR-dependent transcriptional silencing. Genes Dev 2003, 17:2245-2258. 196462 12952896 10.1101/gad.1121003
37. Chu WS Magee BB Magee PT Construction of an SfiI macrorestriction map of the Candida albicans genome. J Bacteriol 1993, 175:6637-6651. 206775 8407841
38. Suzuki T Kanbe T Kuroiwa T Tanaka K Occurrence of ploidy shift in a strain of the imperfect yeast Candida albicans. J Gen Microbiol 1986, 132:443-453. 3519859
39. Ca-19 Chromosome Assignment http://candida.bri.nrc.ca/index.cfm?page= CaChrom
40. Broad Institute C. albicans Sequencing Project http://www.broad.mit.edu/ annotation/genome/candida_albicans/Info.html
41. Sequencher 4.7 http://www.sequencher.com
42. Goshorn AK Grindle SM Scherer S Gene isolation by complementation in Candida albicans and applications to physical and genetic mapping. Infect Immun 1992, 60:876-884. 257568 1541560
43. Kim UJ Shizuya H de Jong PJ Birren B Simon MI Stable propagation of cosmid sized human DNA inserts in an F factor based vector. Nucleic Acids Res 1992, 20:1083-1085. 312094 1549470 10.1093/nar/20.5.1083
44. Chibana H Heinecke EL Beckerman JL Magee PT A system of rapid isolation of end-DNA from a small amount of fosmid DNA, with vector-based PCR for chromosome walking. Genome 2001, 44:305-308. 10.1139/gen-44-2-305 11341742
45. C. albicans Physical Map http://albicansmap.ahc.umn.edu/
46. OpGen Technologies http://www.opgen.com/
47. CG Database http://www.candidagenome.org
48. Green Group http://www.phrap.org