Marsupial Genetics and Genomics (eBook)

Marsupial Genetics and Genomics 2
Preface 5
Contents 8
Contributors 11
Abbreviations 15
Part I Marsupial Breeding 18
Chapter 1 Breeding and Genetic Management of Captive Marsupial Populations 21
1.1 Introduction 21
1.2 Aspects of Species Biology Influencing Captive Breeding 25
1.2.1 Reproductive Strategies 26
1.2.2 Embryonic Diapause 29
1.2.3 Monitoring Reproductive Status 29
1.2.4 Reproductive Behaviour and Mating Systems 30
1.3 Captive Breeding Strategies to Maintain Genetic Diversity 34
1.4 Case Study: Management of a Research Colony of a Model Marsupial ( Macropus eugenii ) 41
1.5 Future Research and Conclusions 42
References 43
References 20
Part II Marsupial Chromosomes and Gene Maps 49
Chapter 2 The Conserved Marsupial Karyotype: Chromosome Painting and Evolution 52
2.1 Marsupial Karyotype Comparison by G-Banding 52
2.2 Marsupial Karyotype Comparison by Cross-Species Chromosome Painting 56
2.2.1 History 56
2.2.2 Marsupial Chromosome Painting 57
2.3 Marsupial Karyotype Phylogeny and Chromosome Evolution 59
2.4 Centromere Dynamics in Chromosome Evolution 64
2.5 Marsupial Whole Genome Sequencing 64
2.6 Conclusion 65
References 66
Chapter 3 Marsupial Centomeres and Telomeres: Dynamic Chromosome Domains 69
3.1 Centromere Evolution in Marsupials 19
3.1.1 Satellite Sequence Convergence in Macropus 69
3.1.2 KERV, Centromeres and Evolutionary Breakpoints 75
3.2 Centromere Function 76
3.2.1 KERV and Small RNAs 76
3.3 Hybrid Dysgenesis and Karyotypic Change 78
3.4 Telomeres 80
3.5 Looking Forward: Centromere and Chromosome Biology in the Age of Genomics 82
References 83
Chapter 4 Marsupial Linkage Maps 88
4.1 Introduction 88
4.2 Why Construct Linkage Maps? 90
4.3 Pioneering Linkage Studies in Marsupials 91
4.4 Linkage Maps of Marsupials 94
4.4.1 The Tammar Wallaby Linkage Map 95
4.4.2 Gray, Short-Tailed Opossum Linkage Maps 97
4.5 Implications of Low Recombination Rates 102
4.6 Sex-Role Reversal in Recombination Rates 103
4.7 Applications of the Linkage Maps 105
4.7.1 Map Integration 105
4.7.2 QTL Mapping 106
4.7.3 Determinants of Sex-Specific Recombination Rates 108
References 109
Chapter 5 Physical and Comparative Gene Maps in Marsupials 113
5.1 Introduction 113
5.2 Species Used for Physical Mapping 114
5.3 Physical Mapping in the Pre-genomics Era 114
5.4 Physical Mapping in the Genomics Era 116
5.4.1 The Important Role of Gene Mapping in the Opossum Genome Project 117
5.4.2 The Wallaby Genome and a New Strategy for Physical Map Construction 119
5.4.3 Genes that Break the Rules 122
5.4.4 Integrating the Linkage and Physical Maps 122
5.5 Mapping in Other Marsupials 124
5.6 Conclusion 125
References 125
References 51
Part III Marsupial Genome Sequencing 128
Chapter 6 Marsupial Sequencing Projects and Bioinformatics Challenges 131
6.1 Marsupial Sequencing Projects The State of Play 131
6.2 Bioinformatics Tools 134
6.2.1 Sequence Alignment 134
6.2.2 Gene Prediction 135
6.2.3 Sequence Assembly 136
6.3 Bioinformatics Challenges 136
6.3.1 Dealing with Next Generation Data 136
6.3.2 Next Generation Transcriptome Assembly 137
6.3.3 Finding Divergent Gene Sequences in Marsupial Genomes 138
6.4 Conclusion 140
References 141
Chapter 7 Insight into Evolution of Gene Regulation Networks from the Opossum Genome 143
7.1 Introduction 143
7.2 Opossum Genome Features 144
7.3 Protein Coding Genes 146
7.4 Evolution of Non Protein Coding Regulatory Sequences 148
7.5 Exaptation of Line Elements in XCI 151
7.6 Conclusion 153
References 154
References 130
Part IV Marsupial Sex Chromosomes 157
Chapter 8 Organization and Evolution of the Marsupial X Chromosome 160
8.1 Introduction 161
8.2 Marsupial Karyotypes and Sex Chromosomes 162
8.3 Marsupial X Chromosome Structure and Organization 163
8.3.1 X Chromosome Size and Gene Content 163
8.3.2 The Marsupial X Chromosome Centromere 164
8.3.3 Absence of Pseudoautosomal Region 164
8.3.4 Nucleolus Organizer Region (NOR) 165
8.3.5 Repeated Sequences and Isochore Structure of the Marsupial X Chromosome 166
8.3.6 Non-coding Transcripts from the Marsupial X Chromosome 167
8.3.7 Gene Maps and Evolution of Marsupial Sex Chromosomes 168
8.3.7.1 Identification of Evolutionary Layers on the Eutherian X Chromosome 168
8.3.7.2 Gene Arrangement on the Marsupial X Chromosome 170
8.3.8 Mutation Rates on the Marsupial X Chromosome 172
8.3.9 Marsupial X Chromosome Sequence and X Inactivation 173
8.3.10 Somatic X Inactivation in Marsupials 173
8.3.11 Meiotic Sex Chromosome Inactivation 175
8.4 Conclusion 175
References 176
Chapter 9 Gene Content of the Mammalian X Chromosome 181
9.1 Introduction 181
9.2 Y Chromosome Gene Content 183
9.3 X Chromosome Gene Content 183
9.4 Sex and Reproduction-Related Genes Within Large Inverted Repeats 184
9.5 Meiotic Sex Chromosome Inactivation 184
9.6 Postmeiotic Expression of Testis-Specific X Chromosome genes 185
9.7 Retrotransposition of Genes On and Off the X Chromosome 188
9.8 X-Linked Genes with a Function in the Brain 189
9.9 Conclusion 191
References 191
Chapter 10 Marsupial Sex Chromosome Behaviour During Male Meiosis 194
10.1 Marsupial Sex Chromosomes 194
10.2 Sex Chromosome Behaviour During Meiosis in Mammals 197
10.3 Sex Chromosome Pairing in Marsupials 198
10.4 Sex Chromosome Segregation in Marsupials 202
10.5 Sex Chromosome Inactivation 204
10.6 Future Prospects 206
References 208
Chapter 11 Compact but Complex The Marsupial Y Chromosome 214
11.1 Introduction 214
11.2 Heterogametic Sex Chromosomes 215
11.2.1 Sex Chromosomes of Birds and Mammals 217
11.2.2 General Properties of Y Chromosomes 218
11.3 Sex Chromosomes of Therian Mammals 219
11.3.1 Sex Chromosomes of Eutherian Mammals 219
11.3.1.1 Human Sex Chromosomes 220
11.4 Marsupial Y Chromosomes 221
11.4.1 Marsupial Sex Determination 221
11.4.2 Genes on the Marsupial Y 222
11.4.2.1 SRY 223
11.4.2.2 RBMY 225
11.4.2.3 KDM5D 225
11.4.2.4 UBE1Y 226
11.4.2.5 RPS4Y 227
11.4.2.6 ATRY 227
11.4.2.7 PHF6Y and HUWE1Y 228
11.4.3 Summary of Genes on the Marsupial Y 229
11.5 Conclusion 229
References 230
References 158
Part V Marsupial Epigenetics 236
Chapter 12 The Evolution of Genomic Imprinting A Marsupial Perspective 239
12.1 Introduction 239
12.1.1 Genomic Imprinting: Definition and Relevance 240
12.1.2 Evolution of Genomic Imprinting in Mammals: Why Marsupials Are Important 241
12.2 Imprinted Clusters in Marsupials 241
12.2.1 IGF2/H19 and CDKN1C Locus 243
12.2.2 INS 244
12.2.3 IGF2R 245
12.2.4 PEG10Locus 246
12.3 Clusters Not Imprinted in Marsupials 247
12.3.1 Prader-Willi and Angelman's Syndrome Locus 247
12.3.2 Callipyge Locus 248
12.4 Distribution of Repeats in Mammalian Genomes and the Host Defence Hypothesis 249
12.5 The X-Chromosome 249
12.6 Regulators of Imprinting in Marsupials 250
12.6.1 Evolution of the DNA Methyltransferase 3 Family 250
12.6.2 Evolution of CTCF and BORIS 251
12.7 Why Did Genomic Imprinting Evolve? 252
12.7.1 Genomic Imprinting and the Evolution of the Placenta 253
12.7.2 The Kinship Hypothesis of Genomic Imprinting 254
12.7.3 Alternative Theories: Ovarian Time-Bomb and Co-adaptation 255
12.8 Conclusions/Future Research 256
References 257
Chapter 13 Marsupial Genetics Reveals Insights into Evolution of Mammalian X Chromosome Inactivation 264
13.1 Introduction 264
13.2 Evolution of Mammalians Sex Chromosomes 265
13.3 Evolution of Dosage Compensation 266
13.4 X Chromosome Inactivation 267
13.4.1 Eutherian X-Inactivation 267
13.4.1.1 X-Inactivation in Eutherian Development 268
13.4.1.2 Imprinted X-Inactivation 268
13.4.1.3 Random X-Inactivation 269
13.4.1.4 Transcriptional Silencing of the Inactive X Chromosome 269
13.4.1.5 Escape from Inactivation 270
13.4.2 Marsupial X-Inactivation 271
13.4.2.1 X-Inactivation in Marsupial Development 271
13.4.2.2 Molecular Mechanism of Marsupial X-Inactivation 272
13.5 Evolution of Dosage Compensation and X-Inactivation 275
13.5.1 Evolution of Dosage Compensation in Monotremes 275
13.5.2 Evolution of X-Inactivation in Therian Mammals 276
13.6 Conclusion 279
References 280
References 237
Part VI Marsupial Reproductive and Developmental Genetics 286
Chapter 14 Molecular Regulation of Marsupial Reproduction and Development 289
14.1 Introduction 289
14.2 Early Embryonic Development 291
14.3 Embryonic Diapause 293
14.4 Fetal and Placental Development 295
14.5 Post Natal Growth 296
14.6 Gonadotrophic Control of Reproduction and the Developing Pituitary 297
14.7 Gametes and Germ Cells 298
14.7.1 The Ooctye and the Adult Ovary 300
14.7.2 Spermatozoa and the Adult Testis 301
14.8 Sex Determination and Sexual Differentiation 303
14.8.1 Localisation and Characterisation of the Testis Determining Factor SRY 304
14.8.2 Pouch and Scrotum 304
14.8.3 X-Linked Genes Involved in Sexual Differentiation 305
14.8.4 Autosomal Genes Involved in Sexual Differentiation 307
14.8.5 The Effect of Oestrogen on Sex Determination 310
14.8.6 Androgens and Virilization 311
14.9 Conclusions 312
References 312
Chapter 15 Marsupial Milk Identifying Signals for Regulating Mammary Function and Development of the Young 321
15.1 Introduction 321
15.2 The Lactation Cycle in the Tammar Wallaby ( Macropus eugenii ) 322
15.3 Regulation of the Lactation Cycle 325
15.4 Identification of Milk Bioactives in Tammar Milk Using a Functional Genomics Platform 326
15.5 Changes in Milk Composition Regulates Growth of the Tammar Pouch Young 326
15.6 A Role for Milk in Regulation of Stomach Maturation 327
15.7 The Role of Gastric Microflora in Regulating Stomach Development 330
15.8 A Role for Milk in the Control of Mammary Function in the Tammar 331
15.9 Conclusion 335
References 335
References 288
Part VII Marsupial Immune Genes 339
Chapter 16 The Marsupial Major Histocompatibility Complex 342
16.1 Introduction 342
16.2 Marsupial MHC Class I Genes 343
16.3 Marsupial MHC Class II Genes 346
16.4 Marsupial Class III Genes 348
16.5 Genetic Organization of Marsupial MHC 350
16.6 The Level of MHC Diversity in Marsupials 352
16.6.1 MHC Diversity and Wildlife Health 354
16.6.2 MHC Diversity and Immunocontraception 355
16.7 Future Perspectives 355
References 356
Chapter 17 Marsupial Immunoglobulin and T Cell Receptor Genomics 360
17.1 Introduction 360
17.2 Marsupial B Cell Development, Antibody Responses, and Ig Genetics 363
17.2.1 The Immunoglobulin Heavy Chain Locus 363
17.2.2 The Ig Light Chain Loci 369
17.2.3 Marsupial B Cell Ontogeny and Immuno-Competence 369
17.3 T Cell Receptor Genomics 370
17.3.1 TCR /Locus 372
17.3.2 TCR Locus 375
17.3.3 TCR Locus 375
17.3.4 Genomic Organization Influences Early Diversity of T Cells 375
17.3.5 A Novel TCR in Marsupials 376
17.4 Conclusion 378
References 379
Chapter 18 Use of Genomic Information to Gain Insights into Immune Function in Marsupials: A Review of Divergent Immune Genes 384
18.1 Introduction 384
18.2 Cytokines 385
18.2.1 Marsupial Tumour Necrosis Factors 388
18.2.2 Marsupial Interleukins 389
18.2.3 Interferons 390
18.2.4 Identifying Marsupial Cytokines In Silico 390
18.2.5 Uses for Marsupial Cytokine Sequence Data 393
18.3 Natural Killer Cell Receptors 394
18.4 Antimicrobial Peptides 395
18.4.1 Defensins 396
18.4.2 Cathelicidins 397
18.4.3 Potential Uses for Marsupial Antimicrobial Peptides 398
18.5 Conclusion 399
References 400
References 340
Part VIII Marsupial Genes and Gene Evolution 404
Chapter 19 Visual Pigments and Colour Vision in Marsupials and Monotremes 406
19.1 Introduction 406
19.2 Marsupial Cone Visual Pigments and Colour Vision 409
19.2.1 Australian Marsupials 409
19.2.2 South American Marsupials 412
19.2.3 Topography of Retinal Photoreceptors in Marsupials and Colour Vision 413
19.3 Cone Visual Pigments and Genes of Monotremes 414
19.4 Future Experiments 415
References 416
Chapter 20 The Evolutionary History of Globin Genes: Insights from Marsupials and Monotremes 418
20.1 Introduction 418
20.2 Unique Globin Properties in Marsupial Newborns 419
20.3 How Did-and-Globin Clusters Evolve in Jawed Vertebrates? 420
20.3.1 History of Globin Gene Evolution 420
20.3.2 The Discovery of a Novel Marsupial Globin Gene: Implications for Globin Gene Evolution 423
20.3.3 A New Model for Globin Gene Evolution: Insights from Monotremes 424
20.3.4 What Was the Mechanism Behind Transposition? 429
20.4 Regulation of - and-Globin Genes 429
20.4.1 How Did Transposition Affect the Regulation of the Globin Clusters? 430
20.5 Unsolved Questions and Future Work 431
References 433
Chapter 21 The Olfactory Receptor Gene Family of Marsupials 437
21.1 Introduction 437
21.1.1 The Importance of Olfaction 438
21.1.2 Structure of the Olfactory Epithelium 438
21.1.3 The Organization of the Olfactory System 438
21.2 Olfactory Receptor Genes 440
21.2.1 Regulation of OR Gene Expression 441
21.2.2 Vertebrate Olfactory Receptor Gene Families 443
21.2.3 Ectopic Expression of OR Genes 445
21.2.4 Evolution of OR Genes 446
21.3 The Olfactory System in Marsupials 448
21.4 Olfactory Apparatus of Marsupials 449
21.5 Marsupial OR Repertoire 449
21.6 Conclusion 454
References 455
References 405
Part IX Marsupial Conservation Genetics 459
Chapter 22 Marsupial Population and Conservation Genetics 462
22.1 Introduction 462
22.2 Microsatellites 463
22.2.1 Genetic Diversity at Microsatellite Loci 464
22.3 Mitochondrial DNA 479
22.3.1 Genetic Diversity at the mtDNA Control Region 482
22.4 Managing Genetic Diversity 482
22.5 Genetics Informing Management 485
22.6 Future Directions 486
References 489
Chapter 23 Devil Facial Tumour Disease (DFTD): Using Genetics and Genomics to Investigate Infectious Disease in an Endangered Marsupial 499
23.1 The Tasmanian Devil and the Emergence of DFTD 499
23.2 DFTD Pathogenesis 500
23.3 DFTD Cytogenetics: Evidence for Cellular Transmission 501
23.4 Immunogenetics of Transmissible Tumours 504
23.5 DFTD Epidemiology and Impact 505
23.6 Disease Management 508
23.7 A Role for Genomics in Tasmanian Devil Conservation 509
23.8 Implications of DFTD for Conservation Biology and Future Directions 511
References 512
References 460
Index 516