The term genome, the basic gene complement of an individual, is almost synonymous with the chromosome complement of both nucleus and organelles. Refinements in cellular, genetic and molecular methods in recent years have opened up unexplored avenues in genome research. The modern tools of gene and genome analyses, coupled with analysis of finer segments of gene sequences in chromosomes utilizing molecular hybridization, are now applied on a wider scale in different groups of plants, ranging from algae to angiosperms. The present series on Plant Genomics: Biodiversity and Evolution aims to cover, in successive volumes, comprehensive reviews, concepts and discussions on the results of genome analysis and their impact on systematics, taxonomy, phylogeny and evolution of all plant groups. This volume touches upon the Lower Groups of plants.
Author(s): A K Sharma
Edition: 1
Publisher: Science Publishers
Year: 2006
Language: English
Pages: 542
PLANT GENOME: BIODIVERSITY AND EVOLUTION—Volume 2, Part B......Page 4
Copyright......Page 5
Preface to the Series "Plant Genome"......Page 6
Preface to this Edition......Page 8
Contents......Page 10
List of Contributors......Page 12
ABSTRACT......Page 16
INTRODUCTION......Page 17
The Small Nucleolar RNAs (snoRNAs)......Page 19
The Transfer Messenger RNAs (tmRNAs)......Page 20
The Small Interfering RNAs (siRNA)......Page 21
The Small Temporal RNAs (stRNA)......Page 22
The X Inactive-Specific Transcript RNAs (Xist RNA)......Page 23
The Class I Introns......Page 24
THE SMALL SELF-CLEAVING RNAs FAMILY......Page 26
Structure......Page 29
Catalytic mechanism......Page 31
Structure......Page 33
Catalytic Mechanism......Page 36
Structure......Page 37
Catalytic mechanism......Page 39
Structure......Page 41
Catalytic mechanism......Page 43
References......Page 45
ABSTRACT......Page 54
INTRODUCTION......Page 55
ASSESSING THE ALGAL AND PROTISTS EVOLUTION......Page 59
PRIMARY ENDOSYMBIOSIS: THE BIRTH OF PLASTIDS......Page 63
SECONDARY ENDOSYMBIOSIS: SPREADING THE PLASTIDS......Page 72
The Green Secondary Plastids......Page 74
The 'Red' Secondary Plastids......Page 77
The 'chromalveolate 'hypothesis'......Page 81
PLASTID REPLACEMENTS IN DINOFLAGELLATES......Page 84
ACKNOWLEDGMENTS......Page 88
References......Page 89
ABSTRACT......Page 104
EARLY EVOLUTION OF DINOFLAGELLATES......Page 105
THE DINOFLAGELLATE "MESOKARYOTIC" NATURE, HISTONE-LIKE PROTEINS AND EVOLUTION OF THE LIQUID CRYSTAL GENOME......Page 106
Overview......Page 108
Description of the Major Orders of Dinoflagellates......Page 111
MULTI-SPECIES COMPLEX......Page 114
INTRA-SPECIFIC VARIATION......Page 116
PLASTID GENOMES OF DINOFLAGELLATES......Page 120
ACKNOWLEDGMENTS......Page 124
References......Page 125
ABSTRACT......Page 132
INTRODUC TION......Page 133
MORPHOLOGY OF THE SILICA FRUSTULE......Page 134
TAXONOMY BASED ON CHARACTERISTICS OF THE SILICA FRUSTULE......Page 138
PHYLOGENIES BASED ON CHARACTERISTICS OF THE SILICA FRUSTULE......Page 148
A PHYLOGENY INFERRED FROM NUCLEAR SSU rDNA SEQUENCES......Page 149
The Radial Centrics (Fig. 36a)......Page 153
The Multipolar Centrics (Fig. 36a)......Page 154
The araphid pennates (Fig. 36b)......Page 159
The Raphid Pennates (Fig. 36c)......Page 163
PHYLOGENETIC SIGNAL IN THE LIFE CYCLE AND AUXOSPORE ONTOGENY......Page 166
Gamete Formation......Page 168
Auxospore development......Page 170
PHYLOGENETIC SIGNAL IN CYTOPLASMIC ULTRASTRUCTURAL FEATURES......Page 172
PALAEONTOLOGY AND PHYLOGENY......Page 176
NEW DIRECTIONS IN DIATOM PHYLOGENY......Page 180
References......Page 184
ABSTRACT......Page 194
INTRODUCTION......Page 195
Fungal Biodiversity......Page 197
Anamorph, Teleomorph, Holomorph......Page 198
Species Concepts Used in Fungal Taxonomy......Page 200
SYSTEMATICS BASED ON MORPHOLOGICAL CHARACTERS......Page 202
MOLECULAR APPROACHES TO FUNGAL PHYLOGENETICS......Page 203
Genome analysis of Saccharomyces cerevisiae......Page 207
Genome analysis of Ashbya gossypii......Page 208
Comparative genomics among Hemiascomycetes......Page 211
Organization of Introns of Hemiascomycetous Yeasts......Page 212
Genome analysis of Schizosaccharomyces pombe......Page 214
Genome analysis of Euascomycetes......Page 215
Ascomycete-specific Genes......Page 218
PHYLOGENETIC RELATIONSHIPS AMONG THE ASCOMYCOTA AND THEIR ANAMORPHS......Page 219
Hemiascomycetes......Page 222
Archiascomycetes......Page 225
Euascomycetes......Page 227
Plectomycetidae......Page 228
Pyrenomycetidae......Page 231
Loculoascomytidae......Page 237
Discomycetes......Page 239
References......Page 242
INTRODUCTION......Page 256
DEFINITION OF YEAST......Page 257
MORPHOLOGICAL DIVERSITY......Page 258
ULTRASTRUCTURE OF THE CELL WALL AND HYPHAL SEPTA......Page 262
Life Cycle of Ascomycetous Yeasts......Page 264
Life Cycle of Basidiomycetous Yeasts......Page 266
CELL WALL COMPOSITION......Page 269
G+C CONTENT......Page 271
CoQ TYPE......Page 272
5S rRNA......Page 274
18S rDNA......Page 275
26S rDNA......Page 277
Sequencing of the whole genome......Page 278
Genome sequencing and the theory of whole genome duplication......Page 280
Ascomycetous yeasts......Page 281
Basidiomycetous yeasts......Page 287
CONCLUSION......Page 291
References......Page 292
ABSTRACT......Page 300
Aspergillus Species as Pathogens of Plants and Animals......Page 301
Mycotoxins Produced by Aspergilli......Page 302
Aspergillus Species in the Food and Pharmaceutical Industries......Page 303
Aspergillus section Aspergillus......Page 304
Aspergillus section Nigri......Page 310
Aspergillus section Flavi......Page 313
Aspergillus section Circumdati......Page 321
Aspergillus section Terrei......Page 322
Aspergillus sections Cervini, Candidi and Cremi......Page 325
Aspergillus section Fumigati......Page 326
Aspergillus section Clavati......Page 334
CONCLUSION AND FUTURE PROSPECTS......Page 336
References......Page 337
ABSTRACT......Page 348
TAXONOMY......Page 349
PCR-BASED METHODS......Page 351
1. Random Amplified Polymorphic DNA (RAPD-PCR)......Page 352
2. Restriction Fragment Length Polymorphism (RFLP)......Page 356
3. Ribosomal RNA (rRNA) and Ribosomal DNA (rDNA) Sequence Comparisons......Page 358
ITS regions......Page 362
4. Micro- and Minisatellites......Page 365
5. DGGE......Page 366
6. Amplified Fragment Length Polymorphism (AFLP)......Page 367
References......Page 369
ABSTRACT......Page 380
INTRODUCTION......Page 381
THE BROWN STEM ROT PATHOSYSTEM......Page 382
Molecular Markers for Separating the Pathogen from other co-colonizing Fungi......Page 383
Molecular Markers for Separating Formae Speciales of P. gregata......Page 384
Nuclear rDNA marker......Page 385
Microsatellite markers......Page 388
Anomymous DNA markers......Page 389
Correspondence of molecular markers with pathotypes......Page 390
Correlation of molecular markers with host cultivar preference......Page 391
Association of Independent Genetic Traits and Clonal Reproduction......Page 393
References......Page 395
ABSTRACT......Page 400
INTRODUCTION......Page 401
LOCATION AND GENERAL FEATURES OF THE ITS......Page 403
Amplification and Sequencing......Page 407
Sequence Alignment......Page 408
Phylogenetkc Analysis......Page 409
PHYLOGENETIC UTILITY AND LIMITATIONS......Page 411
CONCLUSION......Page 413
References......Page 414
ABSTRACT......Page 424
INTRODUCTION......Page 425
Sampling of sequences......Page 426
Alignment, Secondary Structures and Statistics......Page 427
Phylogenetic analyses......Page 428
Sequences......Page 429
Length and GC-conetent......Page 430
Alignments, repeats, and sequence variation......Page 432
Promoter Elements......Page 434
Hairpin Secondary Structures......Page 436
Phylogenetic Inference......Page 438
CONCLUSION......Page 441
References......Page 442
ABSTRACT......Page 448
SPECIES RANGES: TRADITIONAL CONCEPTS......Page 449
SUPRASPECIFIC CLASSIFICATION OF PLAGIOCHILA BASED ON MORPHOLOGY......Page 450
Molecular Markers......Page 451
NATURAL SPECIES GROUPS SPAN SEVERAL FLORISTIC KINGDOMS......Page 452
MOLECULAR TOPOLOGIES AND MORPHOLOGY: THE CASE STUDY PLAGIOCHILA SECT. SUPERBAE......Page 458
MORPHOLOGICAL DATASETS OF PLAGIOCHILA HAVE A HIGH CONTENT OF HOMOPLASY......Page 462
TAXONOMIC DECISIONS BASED ON MOLECULAR TOPOLOGIES: PLAGIOCHILA DETECTA, PLAGIOCHILA MADERENSIS, PLAGIOCHILA RUTILANS AND RHODOPLAGIOCHILA......Page 464
PHYLOGEOGRAPHY......Page 465
References......Page 467
The Host Cacti......Page 474
Cactophilic Insects......Page 475
The Cactophilic Yeast......Page 477
Cactus-Yeast Interactions......Page 478
Drosophila-Yeast Interactions......Page 480
GENOME STUDIES OF CACTOPHILIC YEAST......Page 481
The Pichia cactophila Species Complex......Page 482
The Pichia Klyveri Complex......Page 483
The Sporopachydermia cereana Species Complex......Page 486
Clavispora opuntiae......Page 487
CONCLUSION......Page 488
Reference......Page 489
Author Index......Page 496
Detailed Contents of Volume 2, Part B......Page 534
