Marsupial Genetics and Genomics

✍ Scribed by Paul D. Waters (editor), Janine E. Deakin (editor), Jennifer A. Marshall Graves (editor)

• Publisher: Springer
• Year: 2010
• Tongue: English
• Leaves: 518
• Category: Library

✦ Synopsis

Marsupials belong to the Class Mammalia, sharing some features with other mammals, yet they also possess many unique features. It is their differences from the more traditionally studied mammals, such as mice and humans, that is of greatest value to comparative studies. Sequencing of genomes from two distantly related marsupials, the short grey-tailed opossum from South America and the Australian tammar wallaby, has launched marsupials into the genomics era and accelerated the rate of progress in marsupial research. With the current worldwide concern for the plight of the endangered Tasmanian devil, marsupial genetics and genomics research is even more important than ever if this species is to be saved from extinction. This volume recounts some of the history of research in this field and highlights the most recent advances in the many different areas of marsupial genetics and genomics research.

✦ Table of Contents

Marsupial Genetics and Genomics
Preface
Contents
Contributors
Abbreviations
Part I Marsupial Breeding
References
Chapter 1 Breeding and Genetic Management of Captive Marsupial Populations
1.1 Introduction
1.2 Aspects of Species Biology Influencing Captive Breeding
1.2.1 Reproductive Strategies
1.2.2 Embryonic Diapause
1.2.3 Monitoring Reproductive Status
1.2.4 Reproductive Behaviour and Mating Systems
1.3 Captive Breeding Strategies to Maintain Genetic Diversity
1.4 Case Study: Management of a Research Colony of a Model Marsupial ( Macropus eugenii )
1.5 Future Research and Conclusions
References
Part II Marsupial Chromosomes and Gene Maps
References
Chapter 2 The Conserved Marsupial Karyotype: Chromosome Painting and Evolution
2.1 Marsupial Karyotype Comparison by G-Banding
2.2 Marsupial Karyotype Comparison by Cross-Species Chromosome Painting
2.2.1 History
2.2.2 Marsupial Chromosome Painting
2.3 Marsupial Karyotype Phylogeny and Chromosome Evolution
2.4 Centromere Dynamics in Chromosome Evolution
2.5 Marsupial Whole Genome Sequencing
2.6 Conclusion
References
Chapter 3 Marsupial Centomeres and Telomeres: Dynamic Chromosome Domains
3.1 Centromere Evolution in Marsupials
3.1.1 Satellite Sequence Convergence in Macropus
3.1.2 KERV, Centromeres and Evolutionary Breakpoints
3.2 Centromere Function
3.2.1 KERV and Small RNAs
3.3 Hybrid Dysgenesis and Karyotypic Change
3.4 Telomeres
3.5 Looking Forward: Centromere and Chromosome Biology in the Age of Genomics
References
Chapter 4 Marsupial Linkage Maps
4.1 Introduction
4.2 Why Construct Linkage Maps?
4.3 Pioneering Linkage Studies in Marsupials
4.4 Linkage Maps of Marsupials
4.4.1 The Tammar Wallaby Linkage Map
4.4.2 Gray, Short-Tailed Opossum Linkage Maps
4.5 Implications of Low Recombination Rates
4.6 Sex-Role Reversal in Recombination Rates
4.7 Applications of the Linkage Maps
4.7.1 Map Integration
4.7.2 QTL Mapping
4.7.3 Determinants of Sex-Specific Recombination Rates
References
Chapter 5 Physical and Comparative Gene Maps in Marsupials
5.1 Introduction
5.2 Species Used for Physical Mapping
5.3 Physical Mapping in the Pre-genomics Era
5.4 Physical Mapping in the Genomics Era
5.4.1 The Important Role of Gene Mapping in the Opossum Genome Project
5.4.2 The Wallaby Genome and a New Strategy for Physical Map Construction
5.4.3 Genes that Break the Rules
5.4.4 Integrating the Linkage and Physical Maps
5.5 Mapping in Other Marsupials
5.6 Conclusion
References
Part III Marsupial Genome Sequencing
References
Chapter 6 Marsupial Sequencing Projects and Bioinformatics Challenges
6.1 Marsupial Sequencing Projects The State of Play
6.2 Bioinformatics Tools
6.2.1 Sequence Alignment
6.2.2 Gene Prediction
6.2.3 Sequence Assembly
6.3 Bioinformatics Challenges
6.3.1 Dealing with Next Generation Data
6.3.2 Next Generation Transcriptome Assembly
6.3.3 Finding Divergent Gene Sequences in Marsupial Genomes
6.4 Conclusion
References
Chapter 7 Insight into Evolution of Gene Regulation Networks from the Opossum Genome
7.1 Introduction
7.2 Opossum Genome Features
7.3 Protein Coding Genes
7.4 Evolution of Non Protein Coding Regulatory Sequences
7.5 Exaptation of Line Elements in XCI
7.6 Conclusion
References
Part IV Marsupial Sex Chromosomes
References
Chapter 8 Organization and Evolution of the Marsupial X Chromosome
8.1 Introduction
8.2 Marsupial Karyotypes and Sex Chromosomes
8.3 Marsupial X Chromosome Structure and Organization
8.3.1 X Chromosome Size and Gene Content
8.3.2 The Marsupial X Chromosome Centromere
8.3.3 Absence of Pseudoautosomal Region
8.3.4 Nucleolus Organizer Region (NOR)
8.3.5 Repeated Sequences and Isochore Structure of the Marsupial X Chromosome
8.3.6 Non-coding Transcripts from the Marsupial X Chromosome
8.3.7 Gene Maps and Evolution of Marsupial Sex Chromosomes
8.3.7.1 Identification of Evolutionary Layers on the Eutherian X Chromosome
8.3.7.2 Gene Arrangement on the Marsupial X Chromosome
8.3.8 Mutation Rates on the Marsupial X Chromosome
8.3.9 Marsupial X Chromosome Sequence and X Inactivation
8.3.10 Somatic X Inactivation in Marsupials
8.3.11 Meiotic Sex Chromosome Inactivation
8.4 Conclusion
References
Chapter 9 Gene Content of the Mammalian X Chromosome
9.1 Introduction
9.2 Y Chromosome Gene Content
9.3 X Chromosome Gene Content
9.4 Sex and Reproduction-Related Genes Within Large Inverted Repeats
9.5 Meiotic Sex Chromosome Inactivation
9.6 Postmeiotic Expression of Testis-Specific X Chromosome genes
9.7 Retrotransposition of Genes On and Off the X Chromosome
9.8 X-Linked Genes with a Function in the Brain
9.9 Conclusion
References
Chapter 10 Marsupial Sex Chromosome Behaviour During Male Meiosis
10.1 Marsupial Sex Chromosomes
10.2 Sex Chromosome Behaviour During Meiosis in Mammals
10.3 Sex Chromosome Pairing in Marsupials
10.4 Sex Chromosome Segregation in Marsupials
10.5 Sex Chromosome Inactivation
10.6 Future Prospects
References
Chapter 11 Compact but Complex The Marsupial Y Chromosome
11.1 Introduction
11.2 Heterogametic Sex Chromosomes
11.2.1 Sex Chromosomes of Birds and Mammals
11.2.2 General Properties of Y Chromosomes
11.3 Sex Chromosomes of Therian Mammals
11.3.1 Sex Chromosomes of Eutherian Mammals
11.3.1.1 Human Sex Chromosomes
11.4 Marsupial Y Chromosomes
11.4.1 Marsupial Sex Determination
11.4.2 Genes on the Marsupial Y
11.4.2.1 SRY
11.4.2.2 RBMY
11.4.2.3 KDM5D
11.4.2.4 UBE1Y
11.4.2.5 RPS4Y
11.4.2.6 ATRY
11.4.2.7 PHF6Y and HUWE1Y
11.4.3 Summary of Genes on the Marsupial Y
11.5 Conclusion
References
Part V Marsupial Epigenetics
References
Chapter 12 The Evolution of Genomic Imprinting A Marsupial Perspective
12.1 Introduction
12.1.1 Genomic Imprinting: Definition and Relevance
12.1.2 Evolution of Genomic Imprinting in Mammals: Why Marsupials Are Important
12.2 Imprinted Clusters in Marsupials
12.2.1 IGF2/H19 and CDKN1C Locus
12.2.2 INS
12.2.3 IGF2R
12.2.4 PEG10Locus
12.3 Clusters Not Imprinted in Marsupials
12.3.1 Prader-Willi and Angelman's Syndrome Locus
12.3.2 Callipyge Locus
12.4 Distribution of Repeats in Mammalian Genomes and the Host Defence Hypothesis
12.5 The X-Chromosome
12.6 Regulators of Imprinting in Marsupials
12.6.1 Evolution of the DNA Methyltransferase 3 Family
12.6.2 Evolution of CTCF and BORIS
12.7 Why Did Genomic Imprinting Evolve?
12.7.1 Genomic Imprinting and the Evolution of the Placenta
12.7.2 The Kinship Hypothesis of Genomic Imprinting
12.7.3 Alternative Theories: Ovarian Time-Bomb and Co-adaptation
12.8 Conclusions/Future Research
References
Chapter 13 Marsupial Genetics Reveals Insights into Evolution of Mammalian X Chromosome Inactivation
13.1 Introduction
13.2 Evolution of Mammalians Sex Chromosomes
13.3 Evolution of Dosage Compensation
13.4 X Chromosome Inactivation
13.4.1 Eutherian X-Inactivation
13.4.1.1 X-Inactivation in Eutherian Development
13.4.1.2 Imprinted X-Inactivation
13.4.1.3 Random X-Inactivation
13.4.1.4 Transcriptional Silencing of the Inactive X Chromosome
13.4.1.5 Escape from Inactivation
13.4.2 Marsupial X-Inactivation
13.4.2.1 X-Inactivation in Marsupial Development
13.4.2.2 Molecular Mechanism of Marsupial X-Inactivation
13.5 Evolution of Dosage Compensation and X-Inactivation
13.5.1 Evolution of Dosage Compensation in Monotremes
13.5.2 Evolution of X-Inactivation in Therian Mammals
13.6 Conclusion
References
Part VI Marsupial Reproductive and Developmental Genetics
References
Chapter 14 Molecular Regulation of Marsupial Reproduction and Development
14.1 Introduction
14.2 Early Embryonic Development
14.3 Embryonic Diapause
14.4 Fetal and Placental Development
14.5 Post Natal Growth
14.6 Gonadotrophic Control of Reproduction and the Developing Pituitary
14.7 Gametes and Germ Cells
14.7.1 The Ooctye and the Adult Ovary
14.7.2 Spermatozoa and the Adult Testis
14.8 Sex Determination and Sexual Differentiation
14.8.1 Localisation and Characterisation of the Testis Determining Factor SRY
14.8.2 Pouch and Scrotum
14.8.3 X-Linked Genes Involved in Sexual Differentiation
14.8.4 Autosomal Genes Involved in Sexual Differentiation
14.8.5 The Effect of Oestrogen on Sex Determination
14.8.6 Androgens and Virilization
14.9 Conclusions
References
Chapter 15 Marsupial Milk Identifying Signals for Regulating Mammary Function and Development of the Young
15.1 Introduction
15.2 The Lactation Cycle in the Tammar Wallaby ( Macropus eugenii )
15.3 Regulation of the Lactation Cycle
15.4 Identification of Milk Bioactives in Tammar Milk Using a Functional Genomics Platform
15.5 Changes in Milk Composition Regulates Growth of the Tammar Pouch Young
15.6 A Role for Milk in Regulation of Stomach Maturation
15.7 The Role of Gastric Microflora in Regulating Stomach Development
15.8 A Role for Milk in the Control of Mammary Function in the Tammar
15.9 Conclusion
References
Part VII Marsupial Immune Genes
References
Chapter 16 The Marsupial Major Histocompatibility Complex
16.1 Introduction
16.2 Marsupial MHC Class I Genes
16.3 Marsupial MHC Class II Genes
16.4 Marsupial Class III Genes
16.5 Genetic Organization of Marsupial MHC
16.6 The Level of MHC Diversity in Marsupials
16.6.1 MHC Diversity and Wildlife Health
16.6.2 MHC Diversity and Immunocontraception
16.7 Future Perspectives
References
Chapter 17 Marsupial Immunoglobulin and T Cell Receptor Genomics
17.1 Introduction
17.2 Marsupial B Cell Development, Antibody Responses, and Ig Genetics
17.2.1 The Immunoglobulin Heavy Chain Locus
17.2.2 The Ig Light Chain Loci
17.2.3 Marsupial B Cell Ontogeny and Immuno-Competence
17.3 T Cell Receptor Genomics
17.3.1 TCR /Locus
17.3.2 TCR Locus
17.3.3 TCR Locus
17.3.4 Genomic Organization Influences Early Diversity of T Cells
17.3.5 A Novel TCR in Marsupials
17.4 Conclusion
References
Chapter 18 Use of Genomic Information to Gain Insights into Immune Function in Marsupials: A Review of Divergent Immune Genes
18.1 Introduction
18.2 Cytokines
18.2.1 Marsupial Tumour Necrosis Factors
18.2.2 Marsupial Interleukins
18.2.3 Interferons
18.2.4 Identifying Marsupial Cytokines In Silico
18.2.5 Uses for Marsupial Cytokine Sequence Data
18.3 Natural Killer Cell Receptors
18.4 Antimicrobial Peptides
18.4.1 Defensins
18.4.2 Cathelicidins
18.4.3 Potential Uses for Marsupial Antimicrobial Peptides
18.5 Conclusion
References
Part VIII Marsupial Genes and Gene Evolution
References
Chapter 19 Visual Pigments and Colour Vision in Marsupials and Monotremes
19.1 Introduction
19.2 Marsupial Cone Visual Pigments and Colour Vision
19.2.1 Australian Marsupials
19.2.2 South American Marsupials
19.2.3 Topography of Retinal Photoreceptors in Marsupials and Colour Vision
19.3 Cone Visual Pigments and Genes of Monotremes
19.4 Future Experiments
References
Chapter 20 The Evolutionary History of Globin Genes: Insights from Marsupials and Monotremes
20.1 Introduction
20.2 Unique Globin Properties in Marsupial Newborns
20.3 How Did-and-Globin Clusters Evolve in Jawed Vertebrates?
20.3.1 History of Globin Gene Evolution
20.3.2 The Discovery of a Novel Marsupial Globin Gene: Implications for Globin Gene Evolution
20.3.3 A New Model for Globin Gene Evolution: Insights from Monotremes
20.3.4 What Was the Mechanism Behind Transposition?
20.4 Regulation of - and-Globin Genes
20.4.1 How Did Transposition Affect the Regulation of the Globin Clusters?
20.5 Unsolved Questions and Future Work
References
Chapter 21 The Olfactory Receptor Gene Family of Marsupials
21.1 Introduction
21.1.1 The Importance of Olfaction
21.1.2 Structure of the Olfactory Epithelium
21.1.3 The Organization of the Olfactory System
21.2 Olfactory Receptor Genes
21.2.1 Regulation of OR Gene Expression
21.2.2 Vertebrate Olfactory Receptor Gene Families
21.2.3 Ectopic Expression of OR Genes
21.2.4 Evolution of OR Genes
21.3 The Olfactory System in Marsupials
21.4 Olfactory Apparatus of Marsupials
21.5 Marsupial OR Repertoire
21.6 Conclusion
References
Part IX Marsupial Conservation Genetics
References
Chapter 22 Marsupial Population and Conservation Genetics
22.1 Introduction
22.2 Microsatellites
22.2.1 Genetic Diversity at Microsatellite Loci
22.3 Mitochondrial DNA
22.3.1 Genetic Diversity at the mtDNA Control Region
22.4 Managing Genetic Diversity
22.5 Genetics Informing Management
22.6 Future Directions
References
Chapter 23 Devil Facial Tumour Disease (DFTD): Using Genetics and Genomics to Investigate Infectious Disease in an Endangered Marsupial
23.1 The Tasmanian Devil and the Emergence of DFTD
23.2 DFTD Pathogenesis
23.3 DFTD Cytogenetics: Evidence for Cellular Transmission
23.4 Immunogenetics of Transmissible Tumours
23.5 DFTD Epidemiology and Impact
23.6 Disease Management
23.7 A Role for Genomics in Tasmanian Devil Conservation
23.8 Implications of DFTD for Conservation Biology and Future Directions
References
Index