Sequence finishing and gene mapping for Candida albicans chromosome 7 and syntenic analysis against the Saccharomyces cerevisiae genome

Abstract

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.

Figure 1.—

Overview of gap closing. A physical map, previously published by Chibana et al. (1998), is presented with the shaded bar. Probes assigned to chromosome 7 are located on the map. Open boxes on the shaded bar describe sites for the probes that are mapped with random breakage mapping. SfiI sites are described with vertical open bars on the shaded bar. The location for ODP2 was corrected by the authors after publication. Two arrows on the shaded bar describe MRS. Although the MRSs are represented with a single repetitive sequence (RPS) (Iwaguchi et al. 1992) in this map, RPS is a tandem repeated sequence in some other MRS. The total length of chromosome 7 is 995 kbp in this map. Supercontigs assigned on chromosome 7 are described with a closed arrow headed by a solid bar. Probes with a known DNA sequence and mapped on the supercontigs are described with an open box. R2B9, SfiI, RBP1, ARS3, ARG4, and G2E10 were used as landmarks to assign the supercontigs on the physical map. To adjust the position of the landmarks, supercontig 19-10262 was cleaved with a spacer. A sequence deletion was identified on supercontig 19-20248 and indicated with a spacer. Gaps between the supercontigs and region including ambiguous sequences were amplified with PCR and are indicated by numbers 1–16 in parentheses. Ca35A5 represents a whole sequence of cosmid inserted DNA no. AL033396. The inserted DNA of the cosmid was isolated from strain 1161 and the sequence was determined using the methods described by Tait et al. (1997).

Figure 2.—

Gene maps for C. albicans chromosome 7. Class 1 and class 2 ORFs are shown as rectangles with thick and thin outlines, respectively. Class 3 ORFs are shown as rectangles with no outline. Each ORF was colored the same color as the best-hit species: red, blue, green, and yellow for S. cerevisiae, S. pombe, N. crassa, and Homo sapiens, respectively. Solid arrowheads pointing toward the coding sequence indicate the position of the intron. CDSs, which are reorganized in this work, are represented by asterisks. ORF number of assembly 19 is assigned in the column of C. albicans. Results of BlastX, Pfam, and more information are available as supplementary data at http://www.genetics.org/supplemental/

Figure 2.—

Gene maps for C. albicans chromosome 7. Class 1 and class 2 ORFs are shown as rectangles with thick and thin outlines, respectively. Class 3 ORFs are shown as rectangles with no outline. Each ORF was colored the same color as the best-hit species: red, blue, green, and yellow for S. cerevisiae, S. pombe, N. crassa, and Homo sapiens, respectively. Solid arrowheads pointing toward the coding sequence indicate the position of the intron. CDSs, which are reorganized in this work, are represented by asterisks. ORF number of assembly 19 is assigned in the column of C. albicans. Results of BlastX, Pfam, and more information are available as supplementary data at http://www.genetics.org/supplemental/

Figure 2.—

Gene maps for C. albicans chromosome 7. Class 1 and class 2 ORFs are shown as rectangles with thick and thin outlines, respectively. Class 3 ORFs are shown as rectangles with no outline. Each ORF was colored the same color as the best-hit species: red, blue, green, and yellow for S. cerevisiae, S. pombe, N. crassa, and Homo sapiens, respectively. Solid arrowheads pointing toward the coding sequence indicate the position of the intron. CDSs, which are reorganized in this work, are represented by asterisks. ORF number of assembly 19 is assigned in the column of C. albicans. Results of BlastX, Pfam, and more information are available as supplementary data at http://www.genetics.org/supplemental/

Figure 2.—

Gene maps for C. albicans chromosome 7. Class 1 and class 2 ORFs are shown as rectangles with thick and thin outlines, respectively. Class 3 ORFs are shown as rectangles with no outline. Each ORF was colored the same color as the best-hit species: red, blue, green, and yellow for S. cerevisiae, S. pombe, N. crassa, and Homo sapiens, respectively. Solid arrowheads pointing toward the coding sequence indicate the position of the intron. CDSs, which are reorganized in this work, are represented by asterisks. ORF number of assembly 19 is assigned in the column of C. albicans. Results of BlastX, Pfam, and more information are available as supplementary data at http://www.genetics.org/supplemental/

Figure 2.—

Gene maps for C. albicans chromosome 7. Class 1 and class 2 ORFs are shown as rectangles with thick and thin outlines, respectively. Class 3 ORFs are shown as rectangles with no outline. Each ORF was colored the same color as the best-hit species: red, blue, green, and yellow for S. cerevisiae, S. pombe, N. crassa, and Homo sapiens, respectively. Solid arrowheads pointing toward the coding sequence indicate the position of the intron. CDSs, which are reorganized in this work, are represented by asterisks. ORF number of assembly 19 is assigned in the column of C. albicans. Results of BlastX, Pfam, and more information are available as supplementary data at http://www.genetics.org/supplemental/

Figure 2.—

Gene maps for C. albicans chromosome 7. Class 1 and class 2 ORFs are shown as rectangles with thick and thin outlines, respectively. Class 3 ORFs are shown as rectangles with no outline. Each ORF was colored the same color as the best-hit species: red, blue, green, and yellow for S. cerevisiae, S. pombe, N. crassa, and Homo sapiens, respectively. Solid arrowheads pointing toward the coding sequence indicate the position of the intron. CDSs, which are reorganized in this work, are represented by asterisks. ORF number of assembly 19 is assigned in the column of C. albicans. Results of BlastX, Pfam, and more information are available as supplementary data at http://www.genetics.org/supplemental/

Figure 3.—

The longest syntenic region between the genome in S. cerevisiae and chromosome 7 in C. albicans. The region between DCC1 and PGS1 includes 11 ORFs encoding polypeptides with >100 aa. Of these, 8 ORFs were identified as sharing similarity in amino acid sequence with genes in S. cerevisiae with a score >50 in BLASTX results. Although linkage of these genes is conserved in C. albicans and S. cerevisiae, at least four inversions and three indels were identified.

Figure 4.—

Sequence indel between 19-10248 and 19-20248. The length of this indel is 7249 bp. LTR η (Goodwin and Poulter 2000) flanks this region. The best hits of three ORFs are YLT1, hypothetical protein YLT1 (TrEMBL no. Q9COUO) suggested to encode a fungal retroelement pol polyprotein in Yarrowia lypolytica (1e-44); YIL8, putative protein (TrEMBL no. Q94LP8) suggested to encode Gag or capsid-like proteins from LTR retrotransposons Oryza sativa (1e-25); and STA1, putative protein (TrEMBL no. PO8640) suggested to encode glucoamylase S1/S2 precursor (EC 3.2.1.3) (glucan 1,4-α-glucosidase) (1,4-α-d-glucan) in S. cerevisiae (9e-06).