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Comparative genomics : using fungi as models / edited by Per Sunnerhagen, Jure Piskur. — New York : Springer, 2006.—(58.1481/C737c) |
Contents
Contents
Comparative genomics and gene finding in fungi 1
Marina Axelson-Fisk and Per Sunnerhagen 1
Abstract 1
1 Comparative genomics 1
2 Gene finding in fungal genomes 8
3 Extending the applications of fungal comparative genomics 17
Acknowledgements 20
References 21
Taxonomy and phylogenetic diversity among the yeasts 29
Cletus P. Kurtzman and Jure Piskur 29
Abstract 29
1 Introduction 29
2 Whole genome comparisons from measurements of DNA reassociation 30
3 Identification of species from analysis of gene sequence divergence 33
4 Relationships of fungi from phylogenetic analysis of gene sequence divergence 36
5 Evolution and timing of modern yeast traits 39
6 Future prospects 41
References 41
Structural features of fungal genomes 47
Phatthanaphong Wanchanthuek， Peter F. Hallin， Rodrigo Gouveia-Oliveira， and David Ussery 47
Abstract 47
1 Introduction 47
2 Overview of the fungal genomes 49
3 A global view of fungal genomes 55
4 Genome Atlases for visualization of DNA structural properties in chromosomes 57
5 Comparison of significance of DNA structure in fungal genomes 60
6 Analyses of promoter area and coding regions 64
7 Proteome comparisons 68
8 Conclusions 69
Acknowledgements 70
References 70
Duplication of genes and genomes in yeasts 79
Simon Wong and Kenneth H. Wolfe 79
Abstract 79
1 The ‘true’ yeasts 79
2 Taxonomy and phylogeny 81
3 Yeast genome sequencing projects 83
4 The origin of new genes 84
5 Whole genome duplication 86
6 Intraspecific detection of genome duplication 88
7 Interspecific detection of genome duplication 90
8 Genes lost， genes kept 92
References 94
Telomeres in fungi 101
Marita Cohn， Gianni Liti， David BH Barton 101
Abstract 101
1 Introduction 101
2 Telomeres in sequencing projects 103
3 The structure and maintenance of telomeric repeats 104
4 Telomerase structure 105
5 Other telosome proteins 108
6 Telomere length 111
7 Strand bias and telomeric DNA conformation 111
8 Telomere-associated elements 112
9 Subtelomeric homology regions， multiple gene families， and adaptation 116
10 Nuclear architecture: influence of spatial positioning on genomic dynamics 119
11 The future revealed by comparative genomics of telomeres 120
Acknowledgements 122
References 122
Employing protein size in the functional analysis of orthologous proteins， as illustrated with the yeast HOG pathway 131
Marcus Krantz and Stefan Hohmann 131
Abstract 131
1 Introduction 131
2 0rthologue identification 132
3 Functional analysis 134
4 Protein size 136
5 Conclusions 141
Acknowledgements 142
References 142
Lager brewing yeast 145
Yukiko Kodama， Morten C. Kielland-Brandt， Jorgen Hansen 145
Abstract 145
1 Introduction 145
2 The whole genome sequence of lager brewing yeast 151
3 Chromosomal structure 155
4 Diversity of chromosome structure of lager brewing yeasts and their relatives 158
5 Concluding remarks 158
Acknowledgements 160
References 160
Genome evolution: Lessons from Genolevures 165
Monique Bolotin-Fukuhara， Serge Casaregola， and Michel Aigle 165
Abstract 165
1 Introduction 165
2 Structural aspects 168
3 Functional aspects 176
4 Conclusions 191
Acknowledgements 192
References 192
The genome of the filamentous fungus Ashbya gossypii: annotation and evolutionary implications 197
Sophie Brachat， Fred Dietrich， Sylvia Voegeli， Tom Gaflhey， and Peter Philippsen 197
Abstract 197
1 Introduction 198
2 Sequence analysis and annotation of the A. gossypii genome 199
3 Evolutionary implications of the A. gossypii genome sequences 207
4 Gene pairs (twins) originating from the genome duplication 215
5 Evolution of chromosome number in A. gossypii 220
6 Material and methods 223
Acknowledgments 225
References 226
Schizosaccharomycespombe comparative genomics; from sequence to systems 233
Valerie Wood 233
Abstract 233
1 Introduction 233
2 Genome features 235
3 Genome and proteome sequence comparisons 248
4 Comparative and functional genomics 258
5 Curation 265
6 Future prospects 273
Acknowledgements 274
References 274
Index 287
