Review
The long hard road to a completed Candida albicans genome

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Abstract

After almost a decade of work, the sequencing, assembly, and annotation of the genome of the fungal pathogen Candida albicans is finally close at hand. This review covers the early history of the C. albicans genome project, from the release of early assemblies that provided the impetus for an explosion in functional genomics research, to a community-based annotation and a preview of the work that was necessary for the production of a final genome assembly.

Introduction

Candida albicans, a normal component of the micro-flora of mucosal surfaces and the digestive system, is the most common cause of opportunistic fungal infections in immuno-compromized patients. Most at risk for systemic candidiasis are premature infants, organ transplant recipients taking immunosuppressive drugs, HIV-positive patients and those with either chemotherapy-induced neutropenia or being treated with broad-spectrum antibiotics (Mathews and Witek-Janusek, 2002, Romani, 2002). The incidence of fungal sepsis had increased threefold between 1979 and 2000, with Candida accounting for 70–90% of all invasive mycoses (Bille et al., 2005). Immuno-compromised patients treated with fungistatic drugs are often unable to completely clear the pathogen which results in persistent cycles of fungal infections. Furthermore, the most effective antifungals have significant toxic side-effects. Thus, the mortality rate for systemic candidiasis can vary from 25 to 60 percent (Vincent et al., 1998).

It has long been argued that whole genome sequencing of this important fungal pathogen is necessary for the application of knowledge from the biology of other model organisms such as the budding yeast Saccharomyces cerevisiae, for the proper interpretation of functional genomic studies and, most importantly, for the identification of novel antifungal targets whose inhibition is less likely to have deleterious effects on the host. Following the 1996 release of the completed genome sequence for S. cerevisiae (Goffeau et al., 1996), work began on elucidating the slightly larger C. albicans genome. After eight years of efforts, the production of a complete C. albicans genome annotation and assembly is almost at hand, but has proven to be an especially arduous challenge. The reasons for these difficulties were numerous but, ultimately, not insurmountable. The first of these is that C. albicans is a diploid with homologous chromosomes that show substantial divergence so that many genes are present as two distinctive alleles. Most software packages that are used to assemble shotgun-sequencing data cannot effectively segregate reads between two alleles. To complicate matters, the genome is rich in long and short repeated sequences as well as recently diverged gene families that increase the chances for misassemblies and are easily confused with alleles. Sequence contigs that end in repeated sequences can usually be joined with the help of higher order information from the genome’s organization. Unfortunately, C. albicans’ lack of a complete sexual cycle has precluded the production of a high-density genetic map while a complete physical map of the C. albicans genome has only become available in recent years.

Section snippets

The early years

Our first look of the global organization of the C. albicans genome took place in 1997–1998 with a pilot sequencing project conducted at the Sanger Institute (Tait et al., 1997) and the publication of a physical map for chromosome 7 (Chibana et al., 1998).

Ted Jones, Stuart Scherer, and their colleagues at the Stanford Genome Technology Centre (SGTC) produced a much more extensive shotgun sequencing of the genome of C. albicans laboratory strain SC5314 (Jones et al., 2004). A preliminary

Sequence and annotation of the C. albicans genome

The diploid genome sequence of C. albicans was finally published in May 2004 (Jones et al., 2004). This report describes the whole-genome shotgun sequencing to 10.9X coverage and the construction of Assembly 6 with PHRAP (http://www.phrap.org). Since the sum of the Assembly 6 contigs significantly exceeded the haploid genome size, additional efforts were necessary. The diploid assembly began with an all-against-all pairwise BLASTN comparison of the Assembly 6 contigs followed by a manual

Other chromosomal landmarks

In addition to large-scale collaborative projects, others have used biological techniques, as well as the available genome sequences, to identify and map significant landmarks on the C. albicans chromosomes. For example, Goodwin and Poulter (2000) have demonstrated that the C. albicans genome contains 34 distinct families of long terminal repeat (LTR) retrotransposons, many of which are nonfunctional and of low copy number. In comparison, the S. cerevisiae genome contains only five families,

Finishing the genome assembly

As I write these lines, researchers from the NRC-BRI and the Magees’ laboratory at the University of Minnesota are applying the finishing touches to a final C. albicans genome assembly in which all of the sequence contigs have been ordered and fused to produce an almost contiguous sequence for each of the 8 chromosomes. Chibana et al. (2005) have already used data from Assembly 19, a physical map based on contiguous fosmids, as well as PCR-based validation, to assemble 16 of the contigs into an

Acknowledgment

My research of C. albicans is currently funded by CHIR Grant HOP 67260.

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