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In the spring of 2005, we had access to 18 fully sequenced fungal genomes, and more are coming rapidly. New approaches and methods are being developed to harvest this information source to derive functional predictions and understanding of genome anatomy. Comparative genomics also tells us stories about the evolution of yeasts and filamentous fungi, and the genome rearrangements that marked their history. For example, several genes encoding proteins required for heterochromatin formation and RNA interference have been lost uniformly throughout the Hemiascomycetes , although some genes remain in a few species in a scattered pattern. Being the first eukaryote to have its genome fully sequenced, Saccharomyces cerevisiae was the forerunner for in silico methods of genome annotation in general, and gene finding in particular. Lessons learned from the comparatively simple genome of this budding yeast have paved the way for efficient genome analysis in other fungi as well as eukaryotes in general. Several fungal species are of important applied interest for mankind, and so it is essential to utilise comparative genomics to derive functional information about them. The set of fungal genomes: simple, related in evolution, and with a high density of functional information, can serve as a highly efficient test bed for the further development of comparative genomics.

Yeasts are among the economically and scientifically most important eukaryotic microorganisms known. At present, there are 1,500 recognized species, which are distributed between the ascomycetes and the basidiomycetes, but only a small fraction of these species have undergone extensive genetic analyses. In this chapter, we discuss application of molecular methods for identification of species and for their classification from phylogenetic analysis of gene sequences. The resulting phylogeny is considered in the context of comparative genomics and evolution, and provides a useful background for selection of additional species for whole genome sequencing as well as for new biotechnological applications.

Eighteen fungal genomes have been sequenced to date from a variety of taxonomic groups, with fifteen Ascomycota , two Basidomycota and one Microsporidia species represented. The genomes vary in size more than tenfold, from approximately 2.5 Mbp to 38.8 Mbp. We have performed a computational analysis of DNA structural features of all 18 fungal genomes. The sequenced genomes can be visualised with Genome Atlases, which are graphical representations of the chromosomes, showing DNA structural properties (including the location of potentially highly expressed genes), DNA repeats, and DNA base-composition properties, such as AT-content and GC-skew. A comparison of DNA structural features in the various fungal genomes shows an over-representation of purine stretches of >10 bp in length; that is, there is a tendency for stretches containing only A’s or G’s on the same strand of the DNA helix. This strand bias is pronounced in all of the fungal chromosomes examined. The purine and pyrimidine/purine stretches are localized mainly within non-coding regions of the chromosomes. Another common structural feature for all of the fungal genomes is that the upstream promoter regions of genes are more AT rich than downstream coding regions. Codon usage patterns are different in the three phyla of fungi examined, as well as amino acid usage. Finally, a protein comparison of the predicted gene products gives an overview of the similarity based on protein homology and localization.

The molecular evolution of the group of yeasts closely related to Saccharomyces cerevisiae has been profoundly affected by an ancient polyploidy event that resulted in duplication of the whole genome. This event occurred in the common ancestor of the Saccharomyces sensu stricto and sensu lato species, including Candida glabrata . Recent progress in genome sequencing has allowed the molecular sorting-out process after genome duplication to be investigated in detail. The loci where both copies of the gene were retained, as opposed to deletion of one copy, appear to be those that have either been subject to selection for high dosage of the gene product, or where functional divergence between the two copies was achieved rapidly.

Telomeres are the functional elements concluding and defining each linear chromosome in eukaryotes. They play an essential role in protecting genetic material and preventing genome loss during cell division. At the same time, and in stark contrast, they are remarkably dynamic regions: initial analyses of yeast genomes have shown, through comparative genomics, that regions close to telomeres are prone to rearrangements and duplication and thus are particularly variable between strains and species. This propensity for variation leads to the birth of new and alternative gene functions and helps to accelerate genome evolution and divergence. However, this special property, while making telomeric regions of even greater scientific interest, complicates investigation. Firstly, repetitive DNA is problematic to clone and sequence properly. Secondly, the reoccurring rearrangements and associated lack of synteny between the telomeric regions of even very closely related species creates daunting challenges for the comparative approach. This drives the development of special cloning and bioinformatic strategies. Such efforts should be fruitful, since a comparative approach of telomeres and subtelomeres promises many insights of significance to the research of ageing and cancer, chromosome dynamics in cell division, and the processes of evolution and speciation.

Comparative genomics has provided us with a new handle on the interpretation of protein sequences. The sequencing of numerous fungal genomes has offered the possibility to compare genomes over a degree of evolutionary divergence. More importantly, the large number of sequenced genomes provides for a statistical analysis of orthologues, which allows analysis of protein size in addition to primary sequence. Like protein structure, size is expected to be conserved between orthologues. As significant deviations in size are indicative of altered protein domain structure, we propose size analysis as a supplementary tool for interspecies sequence comparison. Herein, we summarize a comparative analysis of the yeast HOG pathway and highlight the use of protein size analysis in identification and comparison of orthologues, and for evaluation of sequencing and annotation. Such comparisons were used to define differences in the signalling pathway architecture between species, such as absent components or components with altered domain structure. Furthermore, they provide a powerful complement to functional protein analysis, such as discovery of novel, and evaluation of characterised, functional domains, as well as evaluation of potential sites for posttranslational modification. The fungal genome sequences provide a unique resource that should facilitate the functional analysis of any fungal proteins.

Lager brewing yeast is a group of closely related strains of Saccharomyces pastorianus/S. carlsbergensis used for lager beer production all over the world, making it one of the most important industrial yeasts. The pure cultivation of yeast was established in the early 1880’s with immediate practical success for lager brewing yeast. However, almost a century would elapse before its genetics could be approached in detail, despite the development of the genetics of Saccharomyces cerevisiae , starting in the 1930’s. During the last few decades, the complex nature of the genome of lager brewing yeast was elucidated, showing that it is a hybrid between Saccharomyces cerevisiae and another Saccharomyces species. Here we review current knowledge on genetics and genomics of lager brewing yeast and introduce the most updated information about its whole genome sequence. These studies throw further light on the complex chromosomal structure of this yeast. They may also open the door for the elucidation of how inter-species hybrids maintain their chromosomes.

In the past years, yeast genome-sequencing programs have been widely developed. Two of them, namely Genolevures I and II, were devoted to the exploration of hemiascomycetous yeasts. The first one covered 13 species with partial random sequencing (0.2-0.4X coverage). The second one led to the complete genome sequence (8-11X coverage) of four species. The overall evolution of genome structures and the phylogeny could already be deduced from the partial sequencing data, while their mechanisms needed the analysis of complete genome. The main results that came out of these projects are that evolution superimposes stochastic discrete events to the continuous mutation flow. Concerning functional aspects, examination of partial sequences revealed only general trends. Here, we performed a detailed analysis of the genes involved in central metabolism and in the anaerobiosis/aerobiosis pathways on the complete genome of three representative yeasts, Saccharomyces cerevisiae , Kluyveromyces lactis , and Yarrowia lipolytica . This comparison revealed subtle and relevant differences in gene content, which explain in a satisfactory way the known physiological specificities of these three species. This analysis outlines the need for high quality and complete genome sequence when comparing biological processes and functions.

The 9.2 Mb genome of the filamentous fungus Ashbya gossypii consists of seven chromosomes carrying 4718 protein coding genes, 194 tRNA genes, at least 60 small RNA genes, and 40-50 copies of rRNA genes. With respect to both, the size and the number of genes, this presently represents the smallest known genome of a free-living eukaryote. Over 95% of the A. gossypii open reading frames encode proteins with homology to Saccharomyces cerevisiae proteins. In addition, 90% of A. gossypii genes show both, homology and a particular pattern of synteny (conservation of gene order), with the genome of budding yeast. Gene orders in the two species are not strictly co-linear because individual clusters of A. gossypii genes are always syntenic to two distinct S. cerevisiae chromosomal regions but frequently homologous genes are missing in either of the two regions. These gene clusters of ancient synteny (CLAS) were found to cover over 90% of both genomes. Specifically, 95% of the S. cerevisiae genes can be paired in duplicate blocks that match the gene order of single A. gossypii gene groups. The almost complete coverage of both genomes by clusters of ancient synteny provides compelling evidence that both species originate from a common ancestor and that the evolution of S. cerevisiae included a whole genome duplication subsequently followed by random deletions of one gene copy in 90% of the duplicated genes. The alignment of both genomes revealed a complete list of the 10% still remaining duplicated genes (twin genes) in today’s genome of S. cerevisiae . The analysis of this comprehensive set of ancient twin genes in S. cerevisiae suggests that their evolution is asynchronous. Finally, interpretation of the synteny pattern between the sixteen S. cerevisiae centromere regions and the homologous gene regions in A. gossypii suggests that the common ancestor of the two species most likely carried eight chromosomes. The postulated reduction to seven chromosomes in the A. gossypii lineage very likely marked a key event in the development of this filamentous yeast as a novel species.

The fission yeast Schizosaccharomyces pombe is becoming increasingly important as a model for the characterization and study of many globally conserved genes, second only in importance to the budding yeast Saccharomyces cerevisiae . This chapter provides an updated inventory of gene number and genome contents for fission yeast compared to budding yeast. Functional and comparative genomics studies, and the insights these have provided into how the different genome contents of these two yeasts are manifested in their individual biologies are reviewed. Phylogenetic analysis, comparative genomics and experimental research support the choice of S. pombe as a model for the dissection of many biological processes, which are often more similar to the analogous processes in higher eukaryotes than those of the Saccharomytina . The review underlines the advantages of exploiting this organism through the integration of bench science, functional genomics, phylogenomics and systems biology in order to identify and interpret the minimal requirements for a eukaryotic cell.