Originally published as Genetics Published Articles Ahead of Print on June 3, 2005.

Genetics, Vol. 170, 1525-1537, August 2005, Copyright © 2005
doi:10.1534/genetics.104.034652

Sequence Finishing and Gene Mapping for Candida albicans Chromosome 7 and Syntenic Analysis Against the Saccharomyces cerevisiae Genome

Hiroji Chibana^*,1, Nao Oka^*, Hironobu Nakayama, Toshihiro Aoyama, B. B. Magee, P. T. Magee and Yuzuru Mikami^*,1

^* Research Center for Pathogenic Fungi and Microbial Toxicoses, Chiba University, Chiba 260-8673, Japan
Suzuka National College of Technology, Suzuka 510-0294, Japan
Department of Genetics, Cell Biology, and Development, University of Minnesota, Saint Paul, Minnesota 55108

¹ Corresponding author: Research Center for Pathogenic Fungi and Microbial Toxicoses, Chiba University, 1-8-1 Inohana Chuo-ku, Chiba 260-8673, Japan.
E-mail: chibana{at}faculty.chiba-u.jp

The size of the genome in the opportunistic fungus Candida albicans is 15.6 Mb. Whole-genome shotgun sequencing was carried out at Stanford University where the sequences were assembled into 412 contigs. C. albicans is a diploid basically, and analysis of the sequence is complicated due to repeated sequences and to sequence polymorphism between homologous chromosomes. Chromosome 7 is 1 Mb in size and the best characterized of the 8 chromosomes in C. albicans. We assigned 16 of the contigs, ranging in length from 7309 to 267,590 bp, to chromosome 7 and determined sequences of 16 regions. These regions included four gaps, a misassembled sequence, and two major repeat sequences (MRS) of >16 kb. The length of the continuous sequence attained was 949,626 bp and provided complete coverage of chromosome 7 except for telomeric regions. Sequence analysis was carried out and predicted 404 genes, 11 of which included at least one intron. A 7-kb indel, which might be caused by a retrotransposon, was identified as the largest difference between the homologous chromosomes. Synteny analysis revealed that the degree of synteny between C. albicans and Saccharomyces cerevisiae is too weak to use for completion of the genomic sequence in C. albicans.

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