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Dobry J, Zhu Z, Zhou Q, Wapstra E, Deakin JE, Ezaz T. Fixed allele differences associated with the centromere reveal chromosome morphology and rearrangements in a reptile (Varanus acanthurus BOULENGER). Mol Biol Evol 2023:7179469. [PMID: 37279881 DOI: 10.1093/molbev/msad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/03/2023] [Accepted: 05/23/2023] [Indexed: 06/08/2023] Open
Abstract
Chromosome rearrangements are often implicated with genomic divergence and are proposed to be associated with species evolution. Rearrangements alter the genomic structure and interfere with homologous recombination by isolating a portion of the genome. Integration of multi-platform next generation DNA sequencing technologies has enabled putative identification of chromosome rearrangements in many taxa, however, integrating these data sets with cytogenetics is still uncommon beyond model genetic organisms. Therefore, to achieve the ultimate goal for the genomic classification of eukaryotic organisms, physical chromosome mapping remains critical. The ridge-tailed goannas (Varanus acanthurus BOULENGER) are a group of dwarf monitor lizards comprised of several species found throughout Northern Australia. These lizards exhibit extreme divergence at both the genic and chromosomal levels. The chromosome polymorphisms are widespread extending across much of their distribution, raising the question if these polymorphisms are homologous within the V. acanthurus complex. We used a combined genomic and cytogenetic approach to test for homology across divergent populations with morphologically similar chromosome rearrangements. We showed that more than one chromosome pair was involved with the widespread rearrangements. This finding provides evidence to support de novo chromosome rearrangements have occurred within populations. These chromosome rearrangements are characterised by fixed allele differences originating in the vicinity of the centromeric region. We then compared this region with several other assembled genomes of reptiles, chicken and the platypus. We demonstrated that the synteny of genes in Reptilia remains conserved despite centromere repositioning across these taxa.
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Affiliation(s)
- Jason Dobry
- Institute for Applied Ecology, University of Canberra, Canberra, 2601, Australian Capital Territory, Australia
| | - Zexian Zhu
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Evolutionary & Organismal Biology Research Center, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Erik Wapstra
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, 2601, Australian Capital Territory, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, 2601, Australian Capital Territory, Australia
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2
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Zhang X, Wagner S, Holleley CE, Deakin JE, Matsubara K, Deveson IW, O'Meally D, Patel HR, Ezaz T, Li Z, Wang C, Edwards M, Graves JAM, Georges A. Sex-specific splicing of Z- and W-borne nr5a1 alleles suggests sex determination is controlled by chromosome conformation. Proc Natl Acad Sci U S A 2022; 119:e2116475119. [PMID: 35074916 PMCID: PMC8795496 DOI: 10.1073/pnas.2116475119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/03/2021] [Indexed: 11/18/2022] Open
Abstract
Pogona vitticeps has female heterogamety (ZZ/ZW), but the master sex-determining gene is unknown, as it is for all reptiles. We show that nr5a1 (Nuclear Receptor Subfamily 5 Group A Member 1), a gene that is essential in mammalian sex determination, has alleles on the Z and W chromosomes (Z-nr5a1 and W-nr5a1), which are both expressed and can recombine. Three transcript isoforms of Z-nr5a1 were detected in gonads of adult ZZ males, two of which encode a functional protein. However, ZW females produced 16 isoforms, most of which contained premature stop codons. The array of transcripts produced by the W-borne allele (W-nr5a1) is likely to produce truncated polypeptides that contain a structurally normal DNA-binding domain and could act as a competitive inhibitor to the full-length intact protein. We hypothesize that an altered configuration of the W chromosome affects the conformation of the primary transcript generating inhibitory W-borne isoforms that suppress testis determination. Under this hypothesis, the genetic sex determination (GSD) system of P. vitticeps is a W-borne dominant female-determining gene that may be controlled epigenetically.
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Affiliation(s)
- Xiuwen Zhang
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Susan Wagner
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Clare E Holleley
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
- Australian National Wildlife Collection, Commonwealth Scientific and Industrial Research Organisation, Crace, ACT 2911, Australia
| | - Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Kazumi Matsubara
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Hardip R Patel
- Genome Sciences Department, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Zhao Li
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Chexu Wang
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Melanie Edwards
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Jennifer A Marshall Graves
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia;
- School of Life Sciences, La Trobe University, Bundoora, VIC 3186, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia;
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Ingles ED, Deakin JE. Telomeres, species differences, and unusual telomeres in vertebrates: presenting challenges and opportunities to understanding telomere dynamics. AIMS Genetics 2021. [DOI: 10.3934/genet.2016.1.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
AbstractThere has been increasing interest in the use of telomeres as biomarkers of stress, cellular ageing and life-histories. However, the telomere landscape is a diverse feature, with noticeable differences between species, a fact which is highlighted by the unusual telomeres of various vertebrate organisms. We broadly review differences in telomere dynamics among vertebrates, and emphasize the need to understand more about telomere processes and trends across species. As part of these species differences, we review unusual telomeres in vertebrates. This includes mega-telomeres, which are present across a diverse set of organisms, but also focusing on the unusual telomeres traits of marsupials and monotremes, which have seen little to no prior discussion, yet uniquely stand out from other unusual telomere features discovered thus far. Due to the presence of at least two unique telomere features in the marsupial family Dasyuridae, as well as to the presence of physiological strategies semelparity and torpor, which have implications for telomere life-histories in these species, we suggest that this family has a very large potential to uncover novel information on telomere evolution and dynamics.
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Affiliation(s)
- Emory D. Ingles
- Institute of Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Janine E. Deakin
- Institute of Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
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Deakin JE, Potter S. Marsupial chromosomics: bridging the gap between genomes and chromosomes. Reprod Fertil Dev 2020; 31:1189-1202. [PMID: 30630589 DOI: 10.1071/rd18201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 12/05/2018] [Indexed: 12/12/2022] Open
Abstract
Marsupials have unique features that make them particularly interesting to study, and sequencing of marsupial genomes is helping to understand their evolution. A decade ago, it was a huge feat to sequence the first marsupial genome. Now, the advances in sequencing technology have made the sequencing of many more marsupial genomes possible. However, the DNA sequence is only one component of the structures it is packaged into: chromosomes. Knowing the arrangement of the DNA sequence on each chromosome is essential for a genome assembly to be used to its full potential. The importance of combining sequence information with cytogenetics has previously been demonstrated for rapidly evolving regions of the genome, such as the sex chromosomes, as well as for reconstructing the ancestral marsupial karyotype and understanding the chromosome rearrangements involved in the Tasmanian devil facial tumour disease. Despite the recent advances in sequencing technology assisting in genome assembly, physical anchoring of the sequence to chromosomes is required to achieve a chromosome-level assembly. Once chromosome-level assemblies are achieved for more marsupials, we will be able to investigate changes in the packaging and interactions between chromosomes to gain an understanding of the role genome architecture has played during marsupial evolution.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Sally Potter
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
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Abstract
Marsupial genomes, which are packaged into large chromosomes, provide a powerful resource for studying the mechanisms of genome evolution. The extensive and valuable body of work on marsupial cytogenetics, combined more recently with genome sequence data, has enabled prediction of the 2n = 14 karyotype ancestral to all marsupial families. The application of both chromosome biology and genome sequencing, or chromosomics, has been a necessary approach for various aspects of mammalian genome evolution, such as understanding sex chromosome evolution and the origin and evolution of transmissible tumors in Tasmanian devils. The next phase of marsupial genome evolution research will employ chromosomics approaches to begin addressing fundamental questions in marsupial genome evolution and chromosome evolution more generally. The answers to these complex questions will impact our understanding across a broad range of fields, including the genetics of speciation, genome adaptation to environmental stressors, and species management.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2617, Australia;
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA;
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Deakin JE, Potter S, O'Neill R, Ruiz-Herrera A, Cioffi MB, Eldridge MDB, Fukui K, Marshall Graves JA, Griffin D, Grutzner F, Kratochvíl L, Miura I, Rovatsos M, Srikulnath K, Wapstra E, Ezaz T. Chromosomics: Bridging the Gap between Genomes and Chromosomes. Genes (Basel) 2019; 10:genes10080627. [PMID: 31434289 PMCID: PMC6723020 DOI: 10.3390/genes10080627] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/10/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023] Open
Abstract
The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term 'chromosomics' as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia.
| | - Sally Potter
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
- Australian Museum Research Institute, Australian Museum, 1 William St Sydney, NSW 2010, Australia
| | - Rachel O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Marcelo B Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP 13565-905, Brazil
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, 1 William St Sydney, NSW 2010, Australia
| | - Kichi Fukui
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871, Osaka, Japan
| | - Jennifer A Marshall Graves
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia
- School of Life Sciences, LaTrobe University, Melbourne, VIC 3168, Australia
| | - Darren Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Frank Grutzner
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Ikuo Miura
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Michail Rovatsos
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics & Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Erik Wapstra
- School of Natural Sciences, University of Tasmania, Hobart 7000, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia.
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7
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Edwards AM, Cameron EZ, Deakin JE, Ezaz T, Pereira JC, Ferguson‐Smith MA, Robert KA. Sexual conflict in action: An antagonistic relationship between maternal and paternal sex allocation in the tammar wallaby, Notamacropus eugenii. Ecol Evol 2019; 9:4340-4348. [PMID: 31031909 PMCID: PMC6476839 DOI: 10.1002/ece3.4813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 11/22/2018] [Indexed: 01/29/2023] Open
Abstract
Sex ratio biases are often inconsistent, both among and within species and populations. While some of these inconsistencies may be due to experimental design, much of the variation remains inexplicable. Recent research suggests that an exclusive focus on mothers may account for some of the inconsistency, with an increasing number of studies showing variation in sperm sex ratios and seminal fluids. Using fluorescent in-situ hybridization, we show a significant population-level Y-chromosome bias in the spermatozoa of wild tammar wallabies, but with significant intraindividual variation between males. We also show a population-level birth sex ratio trend in the same direction toward male offspring, but a weaning sex ratio that is significantly female-biased, indicating that males are disproportionately lost during lactation. We hypothesize that sexual conflict between parents may cause mothers to adjust offspring sex ratios after birth, through abandonment of male pouch young and reactivation of diapaused embryos. Further research is required in a captive, controlled setting to understand what is driving and mechanistically controlling sperm sex ratio and offspring sex ratio biases and to understand the sexually antagonistic relationship between mothers and fathers over offspring sex. These results extend beyond sex allocation, as they question studies of population processes that assume equal input of sex chromosomes from fathers, and will also assist with future reproduction studies for management and conservation of marsupials.
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Affiliation(s)
- Amy M. Edwards
- Department of Ecology, Environment and Evolution, School of Life SciencesLa Trobe UniversityMelbourneVictoriaAustralia
| | - Elissa Z. Cameron
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Janine E. Deakin
- Institute for Applied EcologyUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Tariq Ezaz
- Institute for Applied EcologyUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Jorge C. Pereira
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
- Cytocell Ltd.CambridgeUK
| | | | - Kylie A. Robert
- Department of Ecology, Environment and Evolution, School of Life SciencesLa Trobe UniversityMelbourneVictoriaAustralia
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8
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Deakin JE, Ezaz T. Understanding the Evolution of Reptile Chromosomes through Applications of Combined Cytogenetics and Genomics Approaches. Cytogenet Genome Res 2019; 157:7-20. [DOI: 10.1159/000495974] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Studies of reptile (nonavian reptiles) chromosomes began well over a century ago (1897) with the initial report on the description of sand lizard (Lacerta agilis) chromosomes. Since then, chromosome analysis in reptiles has contributed significantly to understanding chromosome evolution in vertebrates. Reptile karyotypes are also unique, as being the only vertebrate group where the majority of the species possess variable numbers of macro- and microchromosomes, which was first reported for iguanids and teiids in 1921. In addition, many reptiles have microchromosomes as sex chromosomes, highlighting their evolutionary significance, yet very little is known about their evolutionary origin and significance in shaping amniote genomes. Advances in genomic technologies in recent years have accelerated our capacity to understand how sequences are arranged within a genome. However, genomic and cytogenetic analyses have been combined for only 3 species to provide a deeper understanding of reptile chromosome evolution and sequence organization. In this review, we highlight how a combined approach of cytogenetic analysis and sequence analysis in reptiles can help us answer fundamental questions of chromosome evolution in reptiles, including evolution of microchromosomes and sex chromosomes.
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Johnson RN, O'Meally D, Chen Z, Etherington GJ, Ho SYW, Nash WJ, Grueber CE, Cheng Y, Whittington CM, Dennison S, Peel E, Haerty W, O'Neill RJ, Colgan D, Russell TL, Alquezar-Planas DE, Attenbrow V, Bragg JG, Brandies PA, Chong AYY, Deakin JE, Di Palma F, Duda Z, Eldridge MDB, Ewart KM, Hogg CJ, Frankham GJ, Georges A, Gillett AK, Govendir M, Greenwood AD, Hayakawa T, Helgen KM, Hobbs M, Holleley CE, Heider TN, Jones EA, King A, Madden D, Graves JAM, Morris KM, Neaves LE, Patel HR, Polkinghorne A, Renfree MB, Robin C, Salinas R, Tsangaras K, Waters PD, Waters SA, Wright B, Wilkins MR, Timms P, Belov K. Adaptation and conservation insights from the koala genome. Nat Genet 2018; 50:1102-1111. [PMID: 29967444 PMCID: PMC6197426 DOI: 10.1038/s41588-018-0153-5] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/30/2018] [Indexed: 11/16/2022]
Abstract
The koala, the only extant species of the marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala's ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala's survival in the wild.
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Affiliation(s)
- Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia.
| | - Denis O'Meally
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
- Animal Research Centre, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Zhiliang Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | | | - Simon Y W Ho
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Will J Nash
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
- San Diego Zoo Global, San Diego, CA, USA
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
- UQ Genomics Initiative, University of Queensland, St Lucia, Queensland, Australia
| | - Camilla M Whittington
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Siobhan Dennison
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Emma Peel
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | | | - Rachel J O'Neill
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Don Colgan
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Tonia L Russell
- Ramaciotti Centre for Genomics, University of New South Wales, Kensington, New South Wales, Australia
| | | | - Val Attenbrow
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Jason G Bragg
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Sydney, New South Wales, Australia
| | - Parice A Brandies
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Amanda Yoon-Yee Chong
- Earlham Institute, Norwich Research Park, Norwich, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Federica Di Palma
- Earlham Institute, Norwich Research Park, Norwich, UK
- Department of Biological Sciences, University of East Anglia, Norwich, UK
| | - Zachary Duda
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Kyle M Ewart
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Greta J Frankham
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Amber K Gillett
- Australia Zoo Wildlife Hospital, Beerwah, Queensland, Australia
| | - Merran Govendir
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Takashi Hayakawa
- Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University, Inuyama, Japan
- Japan Monkey Centre, Inuyama, Japan
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
- School of Biological Sciences, Environment Institute, Centre for Applied Conservation Science, and ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew Hobbs
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Clare E Holleley
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Thomas N Heider
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Elizabeth A Jones
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Andrew King
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Danielle Madden
- Animal Research Centre, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Jennifer A Marshall Graves
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
- School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Katrina M Morris
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Linda E Neaves
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Hardip R Patel
- John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia
| | - Adam Polkinghorne
- Animal Research Centre, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Marilyn B Renfree
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Charles Robin
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Ryan Salinas
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Kyriakos Tsangaras
- Department of Translational Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Shafagh A Waters
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Belinda Wright
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
- Ramaciotti Centre for Genomics, University of New South Wales, Kensington, New South Wales, Australia
| | - Peter Timms
- Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
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10
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Abstract
Marsupials typically possess very large, distinctive chromosomes that make them excellent subjects for cytogenetic analysis, and the high level of conservation makes it relatively easy to track chromosome evolution. There are two speciose marsupial families with contrasting rates of karyotypic evolution that could provide insight into the mechanisms driving genome reshuffling and speciation. The family Dasyuridae displays exceptional karyotype conservation with all karyotyped species possessing a 2n = 14 karyotype similar to that predicted for the ancestral marsupial. In contrast, the family Macropodidae has experienced a higher rate of genomic rearrangement and one genus of macropods, the rock-wallabies (Petrogale), has experienced extensive reshuffling. For at least some recently diverged Petrogale species, there is still gene flow despite hybrid fertility issues, making this species group an exceptional model for studying speciation. This review highlights the unique chromosome features of marsupial chromosomes, particularly for these two contrasting families, and the value that a combined cytogenetics, genomics, and epigenomics approach will have for testing models of genome evolution and speciation.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia.
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11
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Taylor RL, Zhang Y, Schöning JP, Deakin JE. Identification of candidate genes for devil facial tumour disease tumourigenesis. Sci Rep 2017; 7:8761. [PMID: 28821767 PMCID: PMC5562891 DOI: 10.1038/s41598-017-08908-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/14/2017] [Indexed: 12/11/2022] Open
Abstract
Devil facial tumour (DFT) disease, a transmissible cancer where the infectious agent is the tumour itself, has caused a dramatic decrease in Tasmanian devil numbers in the wild. The purpose of this study was to take a candidate gene/pathway approach to identify potentially perturbed genes or pathways in DFT. A fusion of chromosome 1 and X is posited as the initial event leading to the development of DFT, with the rearranged chromosome 1 material now stably maintained as the tumour spreads through the population. This hypothesis makes chromosome 1 a prime chromosome on which to search for mutations involved in tumourigenesis. As DFT1 has a Schwann cell origin, we selected genes commonly implicated in tumour pathways in human nerve cancers, or cancers more generally, to determine whether they were rearranged in DFT1, and mapped them using molecular cytogenetics. Many cancer-related genes were rearranged, such as the region containing the tumour suppressor NF2 and a copy gain for ERBB3, a member of the epidermal growth factor receptor family of receptor tyrosine kinases implicated in proliferation and invasion of tumours in humans. Our mapping results have provided strong candidates not previously detected by sequencing DFT1 genomes.
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Affiliation(s)
- Robyn L Taylor
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Yiru Zhang
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Jennifer P Schöning
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.,Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Queensland, 4067, Australia
| | - Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia.
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12
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Deakin JE. Implications of monotreme and marsupial chromosome evolution on sex determination and differentiation. Gen Comp Endocrinol 2017; 244:130-138. [PMID: 26431612 DOI: 10.1016/j.ygcen.2015.09.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/15/2015] [Accepted: 09/26/2015] [Indexed: 12/30/2022]
Abstract
Studies of chromosomes from monotremes and marsupials endemic to Australasia have provided important insight into the evolution of their genomes as well as uncovering fundamental differences in their sex determination/differentiation pathways. Great advances have been made this century into solving the mystery of the complicated sex chromosome system in monotremes. Monotremes possess multiple different X and Y chromosomes and a candidate sex determining gene has been identified. Even greater advancements have been made for marsupials, with reconstruction of the ancestral karyotype enabling the evolutionary history of marsupial chromosomes to be determined. Furthermore, the study of sex chromosomes in intersex marsupials has afforded insight into differences in the sexual differentiation pathway between marsupials and eutherians, together with experiments showing the insensitivity of the mammary glands, pouch and scrotum to exogenous hormones, led to the hypothesis that there is a gene (or genes) on the X chromosome responsible for the development of either pouch or scrotum. This review highlights the major advancements made towards understanding chromosome evolution and how this has impacted on our understanding of sex determination and differentiation in these interesting mammals.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia.
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13
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Potter S, Bragg JG, Blom MPK, Deakin JE, Kirkpatrick M, Eldridge MDB, Moritz C. Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies. Front Genet 2017; 8:10. [PMID: 28265284 PMCID: PMC5301020 DOI: 10.3389/fgene.2017.00010] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/18/2017] [Indexed: 12/24/2022] Open
Abstract
The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.
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Affiliation(s)
- Sally Potter
- Research School of Biology, Australian National University, ActonACT, Australia
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Jason G. Bragg
- National Herbarium of New South Wales, The Royal Botanic Gardens and Domain Trust, SydneyNSW, Australia
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholm, Sweden
| | - Janine E. Deakin
- Institute for Applied Ecology, University of Canberra, BruceACT, Australia
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, AustinTX, USA
| | - Mark D. B. Eldridge
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Craig Moritz
- Research School of Biology, Australian National University, ActonACT, Australia
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14
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Deakin JE, Edwards MJ, Patel H, O'Meally D, Lian J, Stenhouse R, Ryan S, Livernois AM, Azad B, Holleley CE, Li Q, Georges A. Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome. BMC Genomics 2016; 17:447. [PMID: 27286959 PMCID: PMC4902969 DOI: 10.1186/s12864-016-2774-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/25/2016] [Indexed: 12/30/2022] Open
Abstract
Background Squamates (lizards and snakes) are a speciose lineage of reptiles displaying considerable karyotypic diversity, particularly among lizards. Understanding the evolution of this diversity requires comparison of genome organisation between species. Although the genomes of several squamate species have now been sequenced, only the green anole lizard has any sequence anchored to chromosomes. There is only limited gene mapping data available for five other squamates. This makes it difficult to reconstruct the events that have led to extant squamate karyotypic diversity. The purpose of this study was to anchor the recently sequenced central bearded dragon (Pogona vitticeps) genome to chromosomes to trace the evolution of squamate chromosomes. Assigning sequence to sex chromosomes was of particular interest for identifying candidate sex determining genes. Results By using two different approaches to map conserved blocks of genes, we were able to anchor approximately 42 % of the dragon genome sequence to chromosomes. We constructed detailed comparative maps between dragon, anole and chicken genomes, and where possible, made broader comparisons across Squamata using cytogenetic mapping information for five other species. We show that squamate macrochromosomes are relatively well conserved between species, supporting findings from previous molecular cytogenetic studies. Macrochromosome diversity between members of the Toxicofera clade has been generated by intrachromosomal, and a small number of interchromosomal, rearrangements. We reconstructed the ancestral squamate macrochromosomes by drawing upon comparative cytogenetic mapping data from seven squamate species and propose the events leading to the arrangements observed in representative species. In addition, we assigned over 8 Mbp of sequence containing 219 genes to the Z chromosome, providing a list of genes to begin testing as candidate sex determining genes. Conclusions Anchoring of the dragon genome has provided substantial insight into the evolution of squamate genomes, enabling us to reconstruct ancestral macrochromosome arrangements at key positions in the squamate phylogeny, demonstrating that fusions between macrochromosomes or fusions of macrochromosomes and microchromosomes, have played an important role during the evolution of squamate genomes. Assigning sequence to the sex chromosomes has identified NR5A1 as a promising candidate sex determining gene in the dragon. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2774-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia.
| | - Melanie J Edwards
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Hardip Patel
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Jinmin Lian
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Rachael Stenhouse
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Sam Ryan
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Alexandra M Livernois
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Bhumika Azad
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Clare E Holleley
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| | - Qiye Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, 1350, Denmark
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
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15
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Livernois A, Hardy K, Domaschenz R, Papanicolaou A, Georges A, Sarre SD, Rao S, Ezaz T, Deakin JE. Identification of interleukin genes in Pogona vitticeps using a de novo transcriptome assembly from RNA-seq data. Immunogenetics 2016; 68:719-31. [PMID: 27255409 DOI: 10.1007/s00251-016-0922-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/24/2016] [Indexed: 02/07/2023]
Abstract
Interleukins are a group of cytokines with complex immunomodulatory functions that are important for regulating immunity in vertebrate species. Reptiles and mammals last shared a common ancestor more than 350 million years ago, so it is not surprising that low sequence identity has prevented divergent interleukin genes from being identified in the central bearded dragon lizard, Pogona vitticeps, in its genome assembly. To determine the complete nucleotide sequences of key interleukin genes, we constructed full-length transcripts, using the Trinity platform, from short paired-end read RNA sequences from stimulated spleen cells. De novo transcript reconstruction and analysis allowed us to identify interleukin genes that are missing from the published P. vitticeps assembly. Identification of key cytokines in P. vitticeps will provide insight into the essential molecular mechanisms and evolution of interleukin gene families and allow for characterization of the immune response in a lizard for comparison with mammals.
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Affiliation(s)
- Alexandra Livernois
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia
| | - Kristine Hardy
- Discipline of Biomedical Sciences, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, ACT, 2617, Australia
| | - Renae Domaschenz
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - Alexie Papanicolaou
- The Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW, 2751, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia
| | - Stephen D Sarre
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia
| | - Sudha Rao
- Discipline of Biomedical Sciences, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, ACT, 2617, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia
| | - Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia.
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16
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Deakin JE, Kruger-Andrzejewska M. Marsupials as models for understanding the role of chromosome rearrangements in evolution and disease. Chromosoma 2016; 125:633-44. [PMID: 27255308 DOI: 10.1007/s00412-016-0603-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 05/19/2016] [Accepted: 05/23/2016] [Indexed: 12/28/2022]
Abstract
Chromosome rearrangements have been implicated in diseases, such as cancer, and speciation, but it remains unclear whether rearrangements are causal or merely a consequence of these processes. Two marsupial families with very different rates of karyotype evolution provide excellent models in which to study the role of chromosome rearrangements in a disease and evolutionary context. The speciose family Dasyuridae displays remarkable karyotypic conservation, with all species examined to date possessing nearly identical karyotypes. Despite the seemingly high degree of chromosome stability within this family, they appear prone to developing tumours, including transmissible devil facial tumours. In contrast, chromosome rearrangements have been frequent in the evolution of the species-rich family Macropodidae, which displays a high level of karyotypic diversity. In particular, the genus Petrogale (rock-wallabies) displays an extraordinary level of chromosome rearrangement among species. For six parapatric Petrogale species, it appears that speciation has essentially been caught in the act, providing an opportunity to determine whether chromosomal rearrangements are a cause or consequence of speciation in this system. This review highlights the reasons that these two marsupial families are excellent models for testing hypotheses for hotspots of chromosome rearrangement and deciphering the role of chromosome rearrangements in disease and speciation.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia.
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17
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Domaschenz R, Livernois AM, Rao S, Ezaz T, Deakin JE. Immunofluorescent staining reveals hypermethylation of microchromosomes in the central bearded dragon, Pogona vitticeps. Mol Cytogenet 2015; 8:104. [PMID: 26719769 PMCID: PMC4696178 DOI: 10.1186/s13039-015-0208-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/18/2015] [Indexed: 11/18/2022] Open
Abstract
Background Studies of model organisms have demonstrated that DNA cytosine methylation and histone modifications are key regulators of gene expression in biological processes. Comparatively little is known about the presence and distribution of epigenetic marks in non-model amniotes such as non-avian reptiles whose genomes are typically packaged into chromosomes of distinct size classes. Studies of chicken karyotypes have associated the gene-richness and high GC content of microchromosomes with a distinct epigenetic landscape. To determine whether this is likely to be a common feature of amniote microchromosomes, we have analysed the distribution of epigenetic marks using immunofluorescence on metaphase chromosomes of the central bearded dragon (Pogona vitticeps). This study is the first to study the distribution of epigenetic marks on non-avian reptile chromosomes. Results We observed an enrichment of DNA cytosine methylation, active modifications H3K4me2 and H3K4me3, as well as the repressive mark H3K27me3 in telomeric regions on macro and microchromosomes. Microchromosomes were hypermethylated compared to macrochromosomes, as they are in chicken. However, differences between macro- and microchromosomes for histone modifications associated with actively transcribed or repressed DNA were either less distinct or not detectable. Conclusions Hypermethylation of microchromosomes compared to macrochromosomes is a shared feature between P. vitticeps and avian species. The lack of the clear distinction between macro- and microchromosome staining patterns for active and repressive histone modifications makes it difficult to determine at this stage whether microchrosome hypermethylation is correlated with greater gene density as it is in aves, or associated with the greater GC content of P. vitticeps microchromosomes compared to macrochromosomes.
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Affiliation(s)
- Renae Domaschenz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia.,Present address: John Curtin School of Medical Research, The Australian National University, Canberra, ACT Australia
| | | | - Sudha Rao
- Discipline of Biomedical Sciences, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, ACT 2601 Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia
| | - Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia
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18
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Abstract
Platypus (Ornithorhynchus anatinus) holds a unique phylogenetic position at the base of the mammalian lineage due to an amalgamation of mammalian and sauropsid-like features. Here we describe the set of four lamin genes for platypus. Lamins are major components of the nuclear lamina, which constitutes a main component of the nucleoskeleton and is involved in a wide range of nuclear functions. Vertebrate evolution was accompanied by an increase in the number of lamin genes from a single gene in their closest relatives, the tunicates and cephalochordates, to four genes in the vertebrate lineage. Of the four genes the LIII gene is characterized by the presence of two alternatively spliced CaaX-encoding exons. In amphibians and fish LIII is the major lamin protein in oocytes and early embryos. The LIII gene is conserved throughout the vertebrate lineage, with the notable exception of marsupials and placental mammals, which have lost the LIII gene. Here we show that platypus has retained an LIII gene, albeit with a significantly altered structure and with a radically different expression pattern. The platypus LIII gene contains only a single CaaX-encoding exon and the head domain together with coil 1a and part of coil1b of the platypus LIII protein is replaced by a novel short non-helical N-terminus. It is expressed exclusively in the testis. These features resemble those of male germ cell-specific lamins in placental mammals, in particular those of lamin C2. Our data suggest (i) that the specific functions of LIII, which it fulfills in all other vertebrates, is no longer required in mammals and (ii) once it had been freed from these functions has undergone structural alterations and has adopted a new functionality in monotremes.
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Affiliation(s)
- Annette Peter
- Department of Cell Biology, FB2, University of Bremen, P.O. Box 33 04 40, 28334 Bremen, Germany
| | - Shaunak Khandekar
- Cellular and Molecular Pharmacology, Louvain Drug Research Institute, Université catholique de Louvain, avenue E. Mounier 73 bte B1.73.05, B-1200 Brussels, Belgium.
| | - Janine E Deakin
- Research School of Biology, ANU College of Medicine, Biology and Environment, Canberra, Australia.
| | - Reimer Stick
- Department of Cell Biology, FB2, University of Bremen, P.O. Box 33 04 40, 28334 Bremen, Germany.
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19
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Papenfuss AT, Feng ZP, Krasnec K, Deakin JE, Baker ML, Miller RD. Marsupials and monotremes possess a novel family of MHC class I genes that is lost from the eutherian lineage. BMC Genomics 2015; 16:535. [PMID: 26194104 PMCID: PMC4509613 DOI: 10.1186/s12864-015-1745-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/03/2015] [Indexed: 12/11/2022] Open
Abstract
Background Major histocompatibility complex (MHC) class I genes are found in the genomes of all jawed vertebrates. The evolution of this gene family is closely tied to the evolution of the vertebrate genome. Family members are frequently found in four paralogous regions, which were formed in two rounds of genome duplication in the early vertebrates, but in some species class Is have been subject to additional duplication or translocation, creating additional clusters. The gene family is traditionally grouped into two subtypes: classical MHC class I genes that are usually MHC-linked, highly polymorphic, expressed in a broad range of tissues and present endogenously-derived peptides to cytotoxic T-cells; and non-classical MHC class I genes generally have lower polymorphism, may have tissue-specific expression and have evolved to perform immune-related or non-immune functions. As immune genes can evolve rapidly and are subject to different selection pressure, we hypothesised that there may be divergent, as yet unannotated or uncharacterised class I genes. Results Application of a novel method of sensitive genome searching of available vertebrate genome sequences revealed a new, extensive sub-family of divergent MHC class I genes, denoted as UT, which has not previously been characterized. These class I genes are found in both American and Australian marsupials, and in monotremes, at an evolutionary chromosomal breakpoint, but are not present in non-mammalian genomes and have been lost from the eutherian lineage. We show that UT family members are expressed in the thymus of the gray short-tailed opossum and in other immune tissues of several Australian marsupials. Structural homology modelling shows that the proteins encoded by this family are predicted to have an open, though short, antigen-binding groove. Conclusions We have identified a novel sub-family of putatively non-classical MHC class I genes that are specific to marsupials and monotremes. This family was present in the ancestral mammal and is found in extant marsupials and monotremes, but has been lost from the eutherian lineage. The function of this family is as yet unknown, however, their predicted structure may be consistent with presentation of antigens to T-cells. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1745-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Peter MacCallum Cancer Centre, East Melbourne, VIC, 3002, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Zhi-Ping Feng
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Katina Krasnec
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, 87131-0001, USA
| | - Janine E Deakin
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia.,Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Michelle L Baker
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, 87131-0001, USA.,Australian Animal Health Laboratory, CSIRO, East Geelong, VIC, 3219, Australia
| | - Robert D Miller
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, 87131-0001, USA.
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20
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Deakin JE, Delbridge ML, Koina E, Harley N, Alsop AE, Wang C, Patel VS, Graves JAM. Reconstruction of the ancestral marsupial karyotype from comparative gene maps. BMC Evol Biol 2013; 13:258. [PMID: 24261750 PMCID: PMC4222502 DOI: 10.1186/1471-2148-13-258] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 11/19/2013] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n = 14 and 2n = 22 ancestral marsupial karyotype. RESULTS We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n = 14) and therian mammal (2n = 19) karyotypes to be reconstructed. CONCLUSIONS Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n = 14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.
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Affiliation(s)
- Janine E Deakin
- ARC Centre of Excellence for Kangaroo Genomics, Canberra, Australia.
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21
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Abstract
The emergence of a fatal transmissible cancer known as devil facial tumor disease (DFTD) is threatening the iconic Tasmanian devil with extinction in the wild within the next few decades. Since the first report of the disease in 1996, DFTD has spread to over 85% of the devils' distribution and dramatically reduced devil numbers. Research into DFTD has focused on gaining a deeper understanding of the disease on multiple levels, including an accurate assessment of the tissue origin of the tumor, elucidation of how the tumor evades immune detection, and determination of how the tumor is transmitted between individuals and how it is evolving as it spreads through the population. Knowledge gained from these studies has important implications for DFTD management and devil conservation.
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Affiliation(s)
- Hannah S Bender
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
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22
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Livernois AM, Waters SA, Deakin JE, Marshall Graves JA, Waters PD. Independent evolution of transcriptional inactivation on sex chromosomes in birds and mammals. PLoS Genet 2013; 9:e1003635. [PMID: 23874231 PMCID: PMC3715422 DOI: 10.1371/journal.pgen.1003635] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 05/30/2013] [Indexed: 01/09/2023] Open
Abstract
X chromosome inactivation in eutherian mammals has been thought to be tightly controlled, as expected from a mechanism that compensates for the different dosage of X-borne genes in XX females and XY males. However, many X genes escape inactivation in humans, inactivation of the X in marsupials is partial, and the unrelated sex chromosomes of monotreme mammals have incomplete and gene-specific inactivation of X-linked genes. The bird ZW sex chromosome system represents a third independently evolved amniote sex chromosome system with dosage compensation, albeit partial and gene-specific, via an unknown mechanism (i.e. upregulation of the single Z in females, down regulation of one or both Zs in males, or a combination). We used RNA-fluorescent in situ hybridization (RNA-FISH) to demonstrate, on individual fibroblast cells, inactivation of 11 genes on the chicken Z and 28 genes on the X chromosomes of platypus. Each gene displayed a reproducible frequency of 1Z/1X-active and 2Z/2X-active cells in the homogametic sex. Our results indicate that the probability of inactivation is controlled on a gene-by-gene basis (or small domains) on the chicken Z and platypus X chromosomes. This regulatory mechanism must have been exapted independently to the non-homologous sex chromosomes in birds and mammals in response to an over-expressed Z or X in the homogametic sex, highlighting the universal importance that (at least partial) silencing plays in the evolution on amniote dosage compensation and, therefore, the differentiation of sex chromosomes. Dosage compensation is a mechanism that restores the expression of X chromosome genes back to their original level when Y homologues lose function. In placental and marsupial mammals this is achieved by upregulating the single X in males. The carry-through of overexpression to females would result in functional tetraploidy, so there is subsequent inactivation of one X chromosome in the somatic cells of females, leaving males (XY) and females (XX) with a single upregulated X. In contrast, genes on the five platypus (a monotreme mammal) X chromosomes and the chicken Z chromosome (which are orthologous but independently evolved) are expressed globally at a higher level in female platypus and male chicken respectively, indicating partial dosage compensation. Here, for the first time, we provide evidence for inactivation of genes on the chicken Z chromosome in ZZ males, and on all five Xs in female platypus. Our results suggest that the silencing of genes on sex chromosomes has evolved independently in birds and mammals, and is, therefore, a critical step in the pathway to dosage compensate independently evolved amniote sex chromosomes systems.
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Affiliation(s)
- Alexandra M. Livernois
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail: (AML); (PDW)
| | - Shafagh A. Waters
- School of Biotechnology & Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Janine E. Deakin
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jennifer A. Marshall Graves
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
- La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Paul D. Waters
- School of Biotechnology & Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail: (AML); (PDW)
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23
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Nishimoto M, Katano M, Yamagishi T, Hishida T, Kamon M, Suzuki A, Hirasaki M, Nabeshima Y, Nabeshima YI, Katsura Y, Satta Y, Deakin JE, Graves JAM, Kuroki Y, Ono R, Ishino F, Ema M, Takahashi S, Kato H, Okuda A. In vivo function and evolution of the eutherian-specific pluripotency marker UTF1. PLoS One 2013; 8:e68119. [PMID: 23874519 PMCID: PMC3706607 DOI: 10.1371/journal.pone.0068119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 05/24/2013] [Indexed: 11/19/2022] Open
Abstract
Embryogenesis in placental mammals is sustained by exquisite interplay between the embryo proper and placenta. UTF1 is a developmentally regulated gene expressed in both cell lineages. Here, we analyzed the consequence of loss of the UTF1 gene during mouse development. We found that homozygous UTF1 mutant newborn mice were significantly smaller than wild-type or heterozygous mutant mice, suggesting that placental insufficiency caused by the loss of UTF1 expression in extra-embryonic ectodermal cells at least in part contributed to this phenotype. We also found that the effects of loss of UTF1 expression in embryonic stem cells on their pluripotency were very subtle. Genome structure and sequence comparisons revealed that the UTF1 gene exists only in placental mammals. Our analyses of a family of genes with homology to UTF1 revealed a possible mechanism by which placental mammals have evolved the UTF1 genes.
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Affiliation(s)
- Masazumi Nishimoto
- Radioisotope Experimental Laboratory, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Miyuki Katano
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Toshiyuki Yamagishi
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Tomoaki Hishida
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Masayoshi Kamon
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Ayumu Suzuki
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Masataka Hirasaki
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Yoko Nabeshima
- Foundation for Biomedical Research and Innovation, 1-5-4 Minatojima-minamimachi, Chuo-ku, Kobe, Japan
| | - Yo-ichi Nabeshima
- Foundation for Biomedical Research and Innovation, 1-5-4 Minatojima-minamimachi, Chuo-ku, Kobe, Japan
| | - Yukako Katsura
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa, Japan
| | - Janine E. Deakin
- Evolution, Ecology, and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jennifer A. Marshall Graves
- Evolution, Ecology, and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
- La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Yoko Kuroki
- Laboratory for Immunogenomics, RIKEN Research Center for Allergy and Immunology, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Ryuichi Ono
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, Japan
| | - Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, Japan
| | - Masatsugu Ema
- Department of Anatomy and Embryology, Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Hidemasa Kato
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
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24
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Abstract
Marsupial and eutherian mammals inactivate one X chromosome in female somatic cells in what is thought to be a means of compensating for the unbalanced X chromosome dosage between XX females and XY males. The hypothesis of X chromosome inactivation (XCI) was first published by Mary Lyon just over 50 years ago, with the discovery of XCI in marsupials occurring a decade later. However, we are still piecing together the evolutionary origins of this fascinating epigenetic mechanism. From the very first studies on marsupial X inactivation, it was apparent that, although there were some similarities between marsupial and eutherian XCI, there were also some striking differences. For instance, the paternally derived X was found to be preferentially silenced in marsupials, although the silencing was often incomplete, which was in contrast to the random and more tightly controlled inactivation of the X chromosome in eutherians. Many of these earlier studies used isozymes to study the activity of just a few genes in marsupials. The sequencing of several marsupial genomes and the advent of molecular cytogenetic techniques have facilitated more in-depth studies into marsupial X chromosome inactivation and allowed more detailed comparisons of the features of XCI to be made. Several important findings have come from such comparisons, among which is the absence of the XIST gene in marsupials, a non-coding RNA gene with a critical role in eutherian XCI, and the discovery of the marsupial RSX gene, which appears to perform a similar role to XIST. Here I review the history of marsupial XCI studies, the latest advances that have been made and the impact they have had towards unravelling the evolution of XCI in mammals.
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25
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Deakin JE, Cooper DW, Sinclair JJ, Herbert CA, Renfree MB, Wakefield M. Towards an understanding of the genetic basis behind 1080 (sodium fluoroacetate) tolerance and an investigation of the candidate gene ACO2. AUST J ZOOL 2013. [DOI: 10.1071/zo12108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Sodium fluoroacetate, commonly referred to as 1080, is a pesticide heavily used to control vertebrate pests. The development of tolerance to this poison by target species is a critical concern raised by its intensive use. Tolerance to 1080 is common amongst many native vertebrates in south-west Western Australia and is thought to be the result of a long period of coevolution with plant species that produce 1080 in their seeds and flowers. Among those vertebrate species tolerant to 1080 exposure is a subspecies of the tammar wallaby (Macropus eugenii). Tammars from Western Australia are tolerant while the subspecies present on Kangaroo Island is susceptible to 1080 exposure. The availability of genetic and genomic information, combined with a distinct difference in tolerance to 1080 between subspecies, makes the tammar wallaby an ideal species in which to study the genetic basis behind 1080 resistance. To date, research in this area has focussed on a candidate gene approach. Since 1080 inhibits the action of the mitochondrial aconitase enzyme, the aconitase gene ACO2 was considered a prime candidate for involvement in 1080 tolerance. However, sequencing of the full-length ACO2 transcript failed to identify a sequence variant between the two subspecies that would result in an amino acid change in the active site of the enzyme. Future studies will need to take a genome-wide approach to identify the gene(s) responsible for 1080 tolerance.
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26
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Abstract
Extant mammals are divided into sub- and infraclasses that are distinguished by their mode of reproduction. The monotremes lay eggs, the marsupials give birth to altricial young that typically develop in a pouch, and the eutherians have prolonged in utero development, resulting in well developed young at birth. The three groups exhibit what appears to be a nice progression of evolution towards the well developed newborn young of eutherian mammals. However, marsupials do not represent a step in the progression of producing well developed young, but maintain a reproductive strategy that has evolved to prosper in their specific niche. The production of undeveloped young with increased development in the pouch (or counterpart) provides specific advantages to those species living in diverse environments. The evolution of this reproductive strategy provides a clever solution to the uncertain and often adverse conditions encountered by many species, and the survival of the developing young in a pouch containing potentially harmful microorganisms is truly remarkable. In this review, we explore the unique features of the pouch, highlight the research questions that remain unanswered regarding this unique marsupial attribute and discuss the advantages of the marsupial reproductive strategy and the potential role of the pouch in mammalian diversification.
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27
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Tsukamoto K, Deakin JE, Graves JAM, Hashimoto K. Exceptionally high conservation of the MHC class I-related gene, MR1, among mammals. Immunogenetics 2012; 65:115-24. [PMID: 23229473 DOI: 10.1007/s00251-012-0666-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 10/30/2012] [Indexed: 12/31/2022]
Abstract
The major histocompatibility complex (MHC) class I-related gene, MR1, is a non-classical MHC class IA gene and is encoded outside the MHC region. The MR1 is responsible for activation of mucosal-associated invariant T (MAIT) cells expressing semi-invariant T cell receptors in the presence of bacteria, but its ligand has not been identified. A unique characteristic of MR1 is its high evolutionary conservation of the α1 and α2 domains corresponding to the peptide-binding domains of classical MHC class I molecules, showing about 90 % amino acid identity between human and mouse. To clarify the evolutionary history of MR1 and identify more critically conserved residues for the function of MR1, we searched for the MR1 gene using jawed vertebrate genome databases and isolated the MR1 cDNA sequences of marsupials (opossum and wallaby). A comparative genomic analysis indicated that MR1 is only present in placental and marsupial mammals and that the gene organization around MR1 is well conserved among analyzed jawed vertebrates. Moreover, the α1 and α2 domains, especially in amino acid residues presumably shaping a ligand-binding groove, were also highly conserved between placental and marsupial MR1. These findings suggest that the MR1 gene might have been established at its present location in a common ancestor of placental and marsupial mammals and that the shape of the putative ligand-binding groove in MR1 has been maintained, probably for presenting highly conserved component(s) of microbes to MAIT cells.
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Affiliation(s)
- Kentaro Tsukamoto
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
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28
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Bender HS, Murchison EP, Pickett HA, Deakin JE, Strong MA, Conlan C, McMillan DA, Neumann AA, Greider CW, Hannon GJ, Reddel RR, Graves JAM. Extreme telomere length dimorphism in the Tasmanian devil and related marsupials suggests parental control of telomere length. PLoS One 2012; 7:e46195. [PMID: 23049977 PMCID: PMC3458001 DOI: 10.1371/journal.pone.0046195] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 08/27/2012] [Indexed: 01/21/2023] Open
Abstract
Telomeres, specialised structures that protect chromosome ends, play a critical role in preserving chromosome integrity. Telomere dynamics in the Tasmanian devil (Sarcophilus harrisii) are of particular interest in light of the emergence of devil facial tumour disease (DFTD), a transmissible malignancy that causes rapid mortality and threatens the species with extinction. We used fluorescent in situ hybridisation to investigate telomere length in DFTD cells, in healthy Tasmanian devils and in four closely related marsupial species. Here we report that animals in the Order Dasyuromorphia have chromosomes characterised by striking telomere length dimorphism between homologues. Findings in sex chromosomes suggest that telomere length dimorphism may be regulated by events in the parental germlines. Long telomeres on the Y chromosome imply that telomere lengthening occurs during spermatogenesis, whereas telomere diminution occurs during oogenesis. Although found in several somatic cell tissue types, telomere length dimorphism was not found in DFTD cancer cells, which are characterised by uniformly short telomeres. This is, to our knowledge, the first report of naturally occurring telomere length dimorphism in any species and suggests a novel strategy of telomere length control. Comparative studies in five distantly related marsupials and a monotreme indicate that telomere dimorphism evolved at least 50 million years ago.
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Affiliation(s)
- Hannah S Bender
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.
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29
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Abstract
A fatal contagious cancer is driving an entire species to extinction. Comparative genomics will unravel the origin and evolution of devil facial tumor disease (DFTD). The DFTD allograft arose from a Schwann cell in a female Tasmanian devil more than 15 years ago; since then, the tumor has passed through at least 100,000 hosts, evolving and mutating along the way. Tumor genome sequencing and molecular cytogenetic technologies now allow direct comparisons of candidate genes involved in tumorigenesis in human cancers. As a stable transmissible cancer, DFTD provides unique insights into cancer development, progression, and immune evasion and is likely to help increase our understanding of human cancer. In addition, these studies provide hope for discoveries of drug targets or vaccine candidates that will prevent the extinction of this iconic Australian marsupial.
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Affiliation(s)
- Janine E. Deakin
- Research School of Biology, The Australian National University, Canberra 0200, Australia
| | - Katherine Belov
- Faculty of Veterinary Science, University of Sydney, New South Wales 2006, Australia
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30
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Abstract
Marsupial and monotreme mammals fill an important gap in vertebrate phylogeny between reptile-mammal divergence 310 million years ago (mya) and the eutherian (placental) mammal radiation 105 mya. They possess many unique features including their distinctive chromosomes, which in marsupials are typically very large and well conserved between species. In contrast, monotreme genomes are divided into several large chromosomes and many smaller chromosomes, with a complicated sex chromosome system that forms a translocation chain in male meiosis. The application of molecular cytogenetic techniques has greatly advanced our understanding of the evolution of marsupial chromosomes and allowed the reconstruction of the ancestral marsupial karyotype. Chromosome painting and gene mapping have played a vital role in piecing together the puzzle of monotreme karyotypes, particularly their complicated sex chromosome system. Here, we discuss the significant insight into karyotype evolution afforded by the combination of recently sequenced marsupial and monotreme genomes with cytogenetic analysis, which has provided a greater understanding of the events that have shaped not only marsupial and monotreme genomes, but the genomes of all mammals.
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Affiliation(s)
- J E Deakin
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, Australia.
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31
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Edwards MJ, Hinds LA, Deane EM, Deakin JE. A review of complementary mechanisms which protect the developing marsupial pouch young. Dev Comp Immunol 2012; 37:213-220. [PMID: 22504164 DOI: 10.1016/j.dci.2012.03.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 03/26/2012] [Accepted: 03/26/2012] [Indexed: 05/31/2023]
Abstract
Marsupials are born without a functioning adaptive immune system, into a non-sterile environment where they continue to develop. This review examines the extent of exposure of pouch young to microorganisms and describes the protective mechanisms that are complementary to adaptive immunity in the developing young. Complementary protective mechanisms include the role of the innate immune system and maternal protection strategies, such as immune compounds in milk, prenatal transfer of immunoglobulins, antimicrobial compounds secreted in the pouch, and chemical or mechanical cleaning of the pouch and pouch young.
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Affiliation(s)
- M J Edwards
- Research School of Biology, The Australian National University, Canberra, ACT, Australia.
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32
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Deakin JE. Marsupial genome sequences: providing insight into evolution and disease. Scientifica (Cairo) 2012; 2012:543176. [PMID: 24278712 PMCID: PMC3820666 DOI: 10.6064/2012/543176] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 09/26/2012] [Indexed: 05/08/2023]
Abstract
Marsupials (metatherians), with their position in vertebrate phylogeny and their unique biological features, have been studied for many years by a dedicated group of researchers, but it has only been since the sequencing of the first marsupial genome that their value has been more widely recognised. We now have genome sequences for three distantly related marsupial species (the grey short-tailed opossum, the tammar wallaby, and Tasmanian devil), with the promise of many more genomes to be sequenced in the near future, making this a particularly exciting time in marsupial genomics. The emergence of a transmissible cancer, which is obliterating the Tasmanian devil population, has increased the importance of obtaining and analysing marsupial genome sequence for understanding such diseases as well as for conservation efforts. In addition, these genome sequences have facilitated studies aimed at answering questions regarding gene and genome evolution and provided insight into the evolution of epigenetic mechanisms. Here I highlight the major advances in our understanding of evolution and disease, facilitated by marsupial genome projects, and speculate on the future contributions to be made by such sequences.
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Affiliation(s)
- Janine E. Deakin
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
- *Janine E. Deakin:
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33
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Al Nadaf S, Deakin JE, Gilbert C, Robinson TJ, Graves JAM, Waters PD. A cross-species comparison of escape from X inactivation in Eutheria: implications for evolution of X chromosome inactivation. Chromosoma 2011; 121:71-8. [PMID: 21947602 PMCID: PMC3260438 DOI: 10.1007/s00412-011-0343-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 09/12/2011] [Accepted: 09/14/2011] [Indexed: 11/30/2022]
Abstract
Sex chromosome dosage compensation in both eutherian and marsupial mammals is achieved by X chromosome inactivation (XCI)--transcriptional repression that silences one of the two X chromosomes in the somatic cells of females. We recently used RNA fluorescent in situ hybridization (FISH) to show, in individual nuclei, that marsupial X inactivation (in the absence of XIST) occurs on a gene-by-gene basis, and that escape from inactivation is stochastic and independent of gene location. In the absence of similar data from fibroblast cell lines of eutherian representatives, a meaningful comparison is lacking. We therefore used RNA-FISH to examine XCI in fibroblast cell lines obtained from three distantly related eutherian model species: African savannah elephant (Loxodonta africana), mouse (Mus musculus) and human (Homo sapiens). We show that, unlike the orthologous marsupial X, inactivation of the X conserved region (XCR) in eutherians generally is complete. Two-colour RNA-FISH on female human, mouse and elephant interphase nuclei showed that XCR loci have monoallelic expression in almost all nuclei. However, we found that many loci located in the evolutionarily distinct recently added region (XAR) displayed reproducible locus-specific frequencies of nuclei with either one or two active X alleles. We propose that marsupial XCI retains features of an ancient incomplete silencing mechanism that was augmented by the evolution of the XIST gene that progressively stabilized the eutherian XCR. In contrast, the recently added region of the eutherian X displays an incomplete inactivation profile similar to that observed on the evolutionarily distinct marsupial X and the independently evolved monotreme X chromosomes.
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Affiliation(s)
- Shafagh Al Nadaf
- Evolution Ecology and Genetics, Research School of Biology, The Australian National University, ACT 2601, Canberra, Australia.
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34
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Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ESW, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SMJ, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, M Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol 2011; 12:R81. [PMID: 21854559 PMCID: PMC3277949 DOI: 10.1186/gb-2011-12-8-r81] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 07/22/2011] [Accepted: 08/19/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.
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Affiliation(s)
- Marilyn B Renfree
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Anthony T Papenfuss
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Janine E Deakin
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - James Lindsay
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Thomas Heider
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Katherine Belov
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Willem Rens
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge, CB3 0ES, UK
| | - Paul D Waters
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Elizabeth A Pharo
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Geoff Shaw
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Emily SW Wong
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Christophe M Lefèvre
- Institute for Technology Research and Innovation, Deakin University, Geelong, Victoria, 3214, Australia
| | - Kevin R Nicholas
- Institute for Technology Research and Innovation, Deakin University, Geelong, Victoria, 3214, Australia
| | - Yoko Kuroki
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Matthew J Wakefield
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Kyall R Zenger
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
- School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia
| | - Chenwei Wang
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Malcolm Ferguson-Smith
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge, CB3 0ES, UK
| | - Frank W Nicholas
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Danielle Hickford
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Hongshi Yu
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Kirsty R Short
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Hannah V Siddle
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Stephen R Frankenberg
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Keng Yih Chew
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Brandon R Menzies
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
| | - Jessica M Stringer
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Shunsuke Suzuki
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Timothy A Hore
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Margaret L Delbridge
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Amir Mohammadi
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Nanette Y Schneider
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Molecular Genetics, German Institute of Human Nutrition, Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Yanqiu Hu
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - William O'Hara
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Shafagh Al Nadaf
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Chen Wu
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Zhi-Ping Feng
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Benjamin G Cocks
- Biosciences Research Division, Department of Primary Industries, Victoria, 1 Park Drive, Bundoora 3083, Australia
| | - Jianghui Wang
- Biosciences Research Division, Department of Primary Industries, Victoria, 1 Park Drive, Bundoora 3083, Australia
| | - Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stephen MJ Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Susan Fairley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Kathryn Beal
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Javier Herrero
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Dawn M Carone
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8560, Japan
| | - Sumio Sugano
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8560, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yoshiyuki Sakaki
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shinji Kondo
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yuichiro Nishida
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shoji Tatsumoto
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ion Mandiou
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Arthur Hsu
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Kaighin A McColl
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Benjamin Lansdell
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - George Weinstock
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Elizabeth Kuczek
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
- Westmead Institute for Cancer Research, University of Sydney, Westmead, New South Wales 2145, Australia
| | - Annette McGrath
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Peter Wilson
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Artem Men
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mehlika Hazar-Rethinam
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Allison Hall
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - John Davis
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - David Wood
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Sarah Williams
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Yogi Sundaravadanam
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Lora R Lewis
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret B Morgan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Geoffrey O Okwuonu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - San Juana Ruiz
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Jireh Santibanez
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Lynne Nazareth
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew Cree
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Gerald Fowler
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Huyen H Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Vandita Joshi
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Chyn Jing
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Fremiet Lara
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Rebecca Thornton
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Lei Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Jixin Deng
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Yue Liu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Joshua Y Shen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Xing-Zhi Song
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Janette Edson
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Carmen Troon
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Daniel Thomas
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Amber Stephens
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lankesha Yapa
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Tanya Levchenko
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Desmond W Cooper
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Terence P Speed
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Asao Fujiyama
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan
| | - Jennifer A M Graves
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Andrew J Pask
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Susan M Forrest
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
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Wang C, Deakin JE, Rens W, Zenger KR, Belov K, Marshall Graves JA, Nicholas FW. A first-generation integrated tammar wallaby map and its use in creating a tammar wallaby first-generation virtual genome map. BMC Genomics 2011; 12:422. [PMID: 21854555 PMCID: PMC3170641 DOI: 10.1186/1471-2164-12-422] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 08/19/2011] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The limited (2X) coverage of the tammar wallaby (Macropus eugenii) genome sequence dataset currently presents a challenge for assembly and anchoring onto chromosomes. To provide a framework for this assembly, it would be a great advantage to have a dense map of the tammar wallaby genome. However, only limited mapping data are available for this non-model species, comprising a physical map and a linkage map. RESULTS We combined all available tammar wallaby mapping data to create a tammar wallaby integrated map, using the Location DataBase (LDB) strategy. This first-generation integrated map combines all available information from the second-generation tammar wallaby linkage map with 148 loci, and extensive FISH mapping data for 492 loci, especially for genes likely to be located at the ends of wallaby chromosomes or at evolutionary breakpoints inferred from comparative information. For loci whose positions are only approximately known, their location in the integrated map was refined on the basis of comparative information from opossum (Monodelphis domestica) and human. Interpolation of segments from the opossum and human assemblies into the integrated map enabled the subsequent construction of a tammar wallaby first-generation virtual genome map, which comprises 14336 markers, including 13783 genes recruited from opossum and human assemblies. Both maps are freely available at http://compldb.angis.org.au. CONCLUSIONS The first-generation integrated map and the first-generation virtual genome map provide a backbone for the chromosome assembly of the tammar wallaby genome sequence. For example, 78% of the 10257 gene-scaffolds in the Ensembl annotation of the tammar wallaby genome sequence (including 10522 protein-coding genes) can now be given a chromosome location in the tammar wallaby virtual genome map.
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Affiliation(s)
- Chenwei Wang
- Australian Research Council (ARC) Centre of Excellence for Kangaroo Genomics
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | - Janine E Deakin
- Australian Research Council (ARC) Centre of Excellence for Kangaroo Genomics
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Willem Rens
- Department of Veterinary Medicine, University of Cambridge, UK
| | - Kyall R Zenger
- Australian Research Council (ARC) Centre of Excellence for Kangaroo Genomics
- School of Marine & Tropical Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Katherine Belov
- Australian Research Council (ARC) Centre of Excellence for Kangaroo Genomics
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | - Jennifer A Marshall Graves
- Australian Research Council (ARC) Centre of Excellence for Kangaroo Genomics
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Frank W Nicholas
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
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Wang C, Webley L, Wei KJ, Wakefield MJ, Patel HR, Deakin JE, Alsop A, Marshall Graves JA, Cooper DW, Nicholas FW, Zenger KR. A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii). BMC Genet 2011; 12:72. [PMID: 21854616 PMCID: PMC3176194 DOI: 10.1186/1471-2156-12-72] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 08/19/2011] [Indexed: 11/13/2022] Open
Abstract
Background The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. Results A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sex-pooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Conclusions Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first-generation map. It will be a valuable resource for ongoing tammar wallaby genetic research and assembling the genome sequence. The sex-pooled map is available online at http://compldb.angis.org.au/.
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Affiliation(s)
- Chenwei Wang
- Reprogen, Faculty of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia.
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Siddle HV, Deakin JE, Coggill P, Whilming LG, Harrow J, Kaufman J, Beck S, Belov K. The tammar wallaby major histocompatibility complex shows evidence of past genomic instability. BMC Genomics 2011; 12:421. [PMID: 21854592 PMCID: PMC3179965 DOI: 10.1186/1471-2164-12-421] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 08/19/2011] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) is a group of genes with a variety of roles in the innate and adaptive immune responses. MHC genes form a genetically linked cluster in eutherian mammals, an organization that is thought to confer functional and evolutionary advantages to the immune system. The tammar wallaby (Macropus eugenii), an Australian marsupial, provides a unique model for understanding MHC gene evolution, as many of its antigen presenting genes are not linked to the MHC, but are scattered around the genome. RESULTS Here we describe the 'core' tammar wallaby MHC region on chromosome 2q by ordering and sequencing 33 BAC clones, covering over 4.5 MB and containing 129 genes. When compared to the MHC region of the South American opossum, eutherian mammals and non-mammals, the wallaby MHC has a novel gene organization. The wallaby has undergone an expansion of MHC class II genes, which are separated into two clusters by the class III genes. The antigen processing genes have undergone duplication, resulting in two copies of TAP1 and three copies of TAP2. Notably, Kangaroo Endogenous Retroviral Elements are present within the region and may have contributed to the genomic instability. CONCLUSIONS The wallaby MHC has been extensively remodeled since the American and Australian marsupials last shared a common ancestor. The instability is characterized by the movement of antigen presenting genes away from the core MHC, most likely via the presence and activity of retroviral elements. We propose that the movement of class II genes away from the ancestral class II region has allowed this gene family to expand and diversify in the wallaby. The duplication of TAP genes in the wallaby MHC makes this species a unique model organism for studying the relationship between MHC gene organization and function.
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Affiliation(s)
- Hannah V Siddle
- Faculty of Veterinary Science, University of Sydney, NSW 2006, AUSTRALIA
- University of Cambridge, Department of Pathology, Cambridge CB2 1QP, UK
| | - Janine E Deakin
- ARC Centre of Excellence for Kangaroo Genomics, Research School of Biological Sciences, Australian National University, Canberra, ACT 0200, Australia
| | - Penny Coggill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Laurens G Whilming
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jim Kaufman
- University of Cambridge, Department of Pathology, Cambridge CB2 1QP, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Katherine Belov
- Faculty of Veterinary Science, University of Sydney, NSW 2006, AUSTRALIA
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Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ESW, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Patel H, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SMJ, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, M Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol 2011. [PMCID: PMC3334613 DOI: 10.1186/gb-2011-12-12-414] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Al Nadaf S, Waters PD, Koina E, Deakin JE, Jordan KS, Graves JA. Activity map of the tammar X chromosome shows that marsupial X inactivation is incomplete and escape is stochastic. Genome Biol 2010; 11:R122. [PMID: 21182760 PMCID: PMC3046482 DOI: 10.1186/gb-2010-11-12-r122] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 12/08/2010] [Accepted: 12/23/2010] [Indexed: 11/20/2022] Open
Abstract
Background X chromosome inactivation is a spectacular example of epigenetic silencing. In order to deduce how this complex system evolved, we examined X inactivation in a model marsupial, the tammar wallaby (Macropus eugenii). In marsupials, X inactivation is known to be paternal, incomplete and tissue-specific, and occurs in the absence of an XIST orthologue. Results We examined expression of X-borne genes using quantitative PCR, revealing a range of dosage compensation for different loci. To assess the frequency of 1X- or 2X-active fibroblasts, we investigated expression of 32 X-borne genes at the cellular level using RNA-FISH. In female fibroblasts, two-color RNA-FISH showed that genes were coordinately expressed from the same X (active X) in nuclei in which both loci were inactivated. However, loci on the other X escape inactivation independently, with each locus showing a characteristic frequency of 1X-active and 2X-active nuclei, equivalent to stochastic escape. We constructed an activity map of the tammar wallaby inactive X chromosome, which identified no relationship between gene location and extent of inactivation, nor any correlation with the presence or absence of a Y-borne paralog. Conclusions In the tammar wallaby, one X (presumed to be maternal) is expressed in all cells, but genes on the other (paternal) X escape inactivation independently and at characteristic frequencies. The paternal and incomplete X chromosome inactivation in marsupials, with stochastic escape, appears to be quite distinct from the X chromosome inactivation process in eutherians. We find no evidence for a polar spread of inactivation from an X inactivation center.
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Affiliation(s)
- Shafagh Al Nadaf
- Research School of Biology, The Australian National University, Biology Place, Canberra 0200, Australia.
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Patel VS, Ezaz T, Deakin JE, Graves JAM. Globin gene structure in a reptile supports the transpositional model for amniote α- and β-globin gene evolution. Chromosome Res 2010; 18:897-907. [PMID: 21116705 DOI: 10.1007/s10577-010-9164-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 10/20/2010] [Accepted: 10/21/2010] [Indexed: 10/18/2022]
Abstract
The haemoglobin protein, required for oxygen transportation in the body, is encoded by α- and β-globin genes that are arranged in clusters. The transpositional model for the evolution of distinct α-globin and β-globin clusters in amniotes is much simpler than the previously proposed whole genome duplication model. According to this model, all jawed vertebrates share one ancient region containing α- and β-globin genes and several flanking genes in the order MPG-C16orf35-(α-β)-GBY-LUC7L that has been conserved for more than 410 million years, whereas amniotes evolved a distinct β-globin cluster by insertion of a transposed β-globin gene from this ancient region into a cluster of olfactory receptors flanked by CCKBR and RRM1. It could not be determined whether this organisation is conserved in all amniotes because of the paucity of information from non-avian reptiles. To fill in this gap, we examined globin gene organisation in a squamate reptile, the Australian bearded dragon lizard, Pogona vitticeps (Agamidae). We report here that the α-globin cluster (HBK, HBA) is flanked by C16orf35 and GBY and is located on a pair of microchromosomes, whereas the β-globin cluster is flanked by RRM1 on the 3' end and is located on the long arm of chromosome 3. However, the CCKBR gene that flanks the β-globin cluster on the 5' end in other amniotes is located on the short arm of chromosome 5 in P. vitticeps, indicating that a chromosomal break between the β-globin cluster and CCKBR occurred at least in the agamid lineage. Our data from a reptile species provide further evidence to support the transpositional model for the evolution of β-globin gene cluster in amniotes.
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Affiliation(s)
- Vidushi S Patel
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.
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Ho KKK, Deakin JE, Wright ML, Graves JAM, Grützner F. Replication asynchrony and differential condensation of X chromosomes in female platypus (Ornithorhynchus anatinus). Reprod Fertil Dev 2010; 21:952-63. [PMID: 19874719 DOI: 10.1071/rd09099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 09/15/2009] [Indexed: 11/23/2022] Open
Abstract
A common theme in the evolution of sex chromosomes is the massive loss of genes on the sex-specific chromosome (Y or W), leading to a gene imbalance between males (XY) and females (XX) in a male heterogametic species, or between ZZ and ZW in a female heterogametic species. Different mechanisms have evolved to compensate for this difference in dosage of X-borne genes between sexes. In therian mammals, one of the X chromosomes is inactivated, whereas bird dosage compensation is partial and gene-specific. In therian mammals, hallmarks of the inactive X are monoallelic gene expression, late DNA replication and chromatin condensation. Platypuses have five pairs of X chromosomes in females and five X and five Y chromosomes in males. Gene expression analysis suggests a more bird-like partial and gene-specific dosage compensation mechanism. We investigated replication timing and chromosome condensation of three of the five X chromosomes in female platypus. Our data suggest asynchronous replication of X-specific regions on X(1), X(3) and X(5) but show significantly different condensation between homologues for X(3) only, and not for X(1) or X(5). We discuss these results in relation to recent gene expression analysis of X-linked genes, which together give us insights into possible mechanisms of dosage compensation in platypus.
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Affiliation(s)
- Kristen K K Ho
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, Australia
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Sanderson CE, Belov K, Deakin JE. Physical mapping of immune genes in the tammar wallaby (Macropus eugenii). Cytogenet Genome Res 2009; 127:21-5. [PMID: 19940438 DOI: 10.1159/000260372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2009] [Indexed: 11/19/2022] Open
Abstract
The tammar wallaby (Macropus eugenii) is a model marsupial that has recently had its genome sequenced to a depth of 2-fold coverage. Although this is a great resource for comparative genomic studies, information on gene location is essential if this resource is to be used to its full potential. In this study, tammar wallaby bacterial artificial chromosomes (BACs) containing key immune genes were isolated from the tammar wallaby BAC library. BACs containing T cell receptor (TCR) and immunoglobulin (Ig) genes were physically mapped using fluorescence in situ hybridisation (FISH) to tammar wallaby chromosomes. Congruence between the locations of these immune genes in the tammar wallaby genome, with those predicted from chromosome painting data, highlights the conservation of genomic context of these important immune genes in marsupials. The isolation and mapping of these key immune genes in the tammar wallaby will aid in the assembly of the recently sequenced light coverage genome and assignment of sequence to chromosomes.
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Deakin JE, Chaumeil J, Hore TA, Marshall Graves JA. Unravelling the evolutionary origins of X chromosome inactivation in mammals: insights from marsupials and monotremes. Chromosome Res 2009; 17:671-85. [DOI: 10.1007/s10577-009-9058-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Siddle HV, Deakin JE, Coggill P, Hart E, Cheng Y, Wong ES, Harrow J, Beck S, Belov K. MHC-linked and un-linked class I genes in the wallaby. BMC Genomics 2009; 10:310. [PMID: 19602235 PMCID: PMC2719672 DOI: 10.1186/1471-2164-10-310] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 07/14/2009] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND MHC class I antigens are encoded by a rapidly evolving gene family comprising classical and non-classical genes that are found in all vertebrates and involved in diverse immune functions. However, there is a fundamental difference between the organization of class I genes in mammals and non-mammals. Non-mammals have a single classical gene responsible for antigen presentation, which is linked to the antigen processing genes, including TAP. This organization allows co-evolution of advantageous class Ia/TAP haplotypes. In contrast, mammals have multiple classical genes within the MHC, which are separated from the antigen processing genes by class III genes. It has been hypothesized that separation of classical class I genes from antigen processing genes in mammals allowed them to duplicate. We investigated this hypothesis by characterizing the class I genes of the tammar wallaby, a model marsupial that has a novel MHC organization, with class I genes located within the MHC and 10 other chromosomal locations. RESULTS Sequence analysis of 14 BACs containing 15 class I genes revealed that nine class I genes, including one to three classical class I, are not linked to the MHC but are scattered throughout the genome. Kangaroo Endogenous Retroviruses (KERVs) were identified flanking the MHC un-linked class I. The wallaby MHC contains four non-classical class I, interspersed with antigen processing genes. Clear orthologs of non-classical class I are conserved in distant marsupial lineages. CONCLUSION We demonstrate that classical class I genes are not linked to antigen processing genes in the wallaby and provide evidence that retroviral elements were involved in their movement. The presence of retroviral elements most likely facilitated the formation of recombination hotspots and subsequent diversification of class I genes. The classical class I have moved away from antigen processing genes in eutherian mammals and the wallaby independently, but both lineages appear to have benefited from this loss of linkage by increasing the number of classical genes, perhaps enabling response to a wider range of pathogens. The discovery of non-classical orthologs between distantly related marsupial species is unusual for the rapidly evolving class I genes and may indicate an important marsupial specific function.
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Affiliation(s)
- Hannah V Siddle
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia.
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Deakin JE, Koina E, Waters PD, Doherty R, Patel VS, Delbridge ML, Dobson B, Fong J, Hu Y, van den Hurk C, Pask AJ, Shaw G, Smith C, Thompson K, Wakefield MJ, Yu H, Renfree MB, Graves JAM. Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals. Chromosome Res 2008; 16:1159-75. [PMID: 18987984 DOI: 10.1007/s10577-008-1266-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 09/02/2008] [Accepted: 09/02/2008] [Indexed: 01/20/2023]
Abstract
Marsupials are especially valuable for comparative genomic studies of mammals. Two distantly related model marsupials have been sequenced: the South American opossum (Monodelphis domestica) and the tammar wallaby (Macropus eugenii), which last shared a common ancestor about 70 Mya. The six-fold opossum genome sequence has been assembled and assigned to chromosomes with the help of a cytogenetic map. A good cytogenetic map will be even more essential for assembly and anchoring of the two-fold wallaby genome. As a start to generating a physical map of gene locations on wallaby chromosomes, we focused on two chromosomes sharing homology with the human X, wallaby chromosomes X and 5. We devised an efficient strategy for mapping large conserved synteny blocks in non-model mammals, and applied this to generate dense maps of the X and 'neo-X' regions and to determine the arrangement of large conserved synteny blocks on chromosome 5. Comparisons between the wallaby and opossum chromosome maps revealed many rearrangements, highlighting the need for comparative gene mapping between South American and Australian marsupials. Frequent rearrangement of the X, along with the absence of a marsupial XIST gene, suggests that inactivation of the marsupial X chromosome does not depend on a whole-chromosome repression by a control locus.
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Affiliation(s)
- Janine E Deakin
- ARC Centre of Excellence for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia.
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Abstract
CTCF is an essential, ubiquitously expressed DNA-binding protein responsible for insulator function, nuclear architecture, and transcriptional control within vertebrates. The gene CTCF was proposed to have duplicated in early mammals, giving rise to a paralogue called "brother of regulator of imprinted sites" (BORIS or CTCFL) with DNA binding capabilities similar to CTCF, but testis-specific expression in humans and mice. CTCF and BORIS have opposite regulatory effects on human cancer-testis genes, the anti-apoptotic BAG1 gene, the insulin-like growth factor 2/H19 imprint control region (IGF2/H19 ICR), and show mutually exclusive expression in humans and mice, suggesting that they are antagonistic epigenetic regulators. We discovered orthologues of BORIS in at least two reptilian species and found traces of its sequence in the chicken genome, implying that the duplication giving rise to BORIS occurred much earlier than previously thought. We analysed the expression of CTCF and BORIS in a range of amniotes by conventional and quantitative PCR. BORIS, as well as CTCF, was found widely expressed in monotremes (platypus) and reptiles (bearded dragon), suggesting redundancy or cooperation between these genes in a common amniote ancestor. However, we discovered that BORIS expression was gonad-specific in marsupials (tammar wallaby) and eutherians (cattle), implying that a functional change occurred in BORIS during the early evolution of therian mammals. Since therians show imprinting of IGF2 but other vertebrate taxa do not, we speculate that CTCF and BORIS evolved specialised functions along with the evolution of imprinting at this and other loci, coinciding with the restriction of BORIS expression to the germline and potential antagonism with CTCF.
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Affiliation(s)
- Timothy A Hore
- ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia.
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Patel VS, Cooper SJB, Deakin JE, Fulton B, Graves T, Warren WC, Wilson RK, Graves JAM. Platypus globin genes and flanking loci suggest a new insertional model for beta-globin evolution in birds and mammals. BMC Biol 2008; 6:34. [PMID: 18657265 PMCID: PMC2529266 DOI: 10.1186/1741-7007-6-34] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Accepted: 07/25/2008] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Vertebrate alpha (alpha)- and beta (beta)-globin gene families exemplify the way in which genomes evolve to produce functional complexity. From tandem duplication of a single globin locus, the alpha- and beta-globin clusters expanded, and then were separated onto different chromosomes. The previous finding of a fossil beta-globin gene (omega) in the marsupial alpha-cluster, however, suggested that duplication of the alpha-beta cluster onto two chromosomes, followed by lineage-specific gene loss and duplication, produced paralogous alpha- and beta-globin clusters in birds and mammals. Here we analyse genomic data from an egg-laying monotreme mammal, the platypus (Ornithorhynchus anatinus), to explore haemoglobin evolution at the stem of the mammalian radiation. RESULTS The platypus alpha-globin cluster (chromosome 21) contains embryonic and adult alpha- globin genes, a beta-like omega-globin gene, and the GBY globin gene with homology to cytoglobin, arranged as 5'-zeta-zeta'-alphaD-alpha3-alpha2-alpha1-omega-GBY-3'. The platypus beta-globin cluster (chromosome 2) contains single embryonic and adult globin genes arranged as 5'-epsilon-beta-3'. Surprisingly, all of these globin genes were expressed in some adult tissues. Comparison of flanking sequences revealed that all jawed vertebrate alpha-globin clusters are flanked by MPG-C16orf35 and LUC7L, whereas all bird and mammal beta-globin clusters are embedded in olfactory genes. Thus, the mammalian alpha- and beta-globin clusters are orthologous to the bird alpha- and beta-globin clusters respectively. CONCLUSION We propose that alpha- and beta-globin clusters evolved from an ancient MPG-C16orf35-alpha-beta-GBY-LUC7L arrangement 410 million years ago. A copy of the original beta (represented by omega in marsupials and monotremes) was inserted into an array of olfactory genes before the amniote radiation (>315 million years ago), then duplicated and diverged to form orthologous clusters of beta-globin genes with different expression profiles in different lineages.
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Affiliation(s)
- Vidushi S Patel
- The ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia
| | - Steven JB Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, The University of Adelaide, Adelaide, SA 5005, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA 5000, Australia
| | - Janine E Deakin
- The ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia
| | - Bob Fulton
- Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Tina Graves
- Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Wesley C Warren
- Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Richard K Wilson
- Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Jennifer AM Graves
- The ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia
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Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AFA, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ESW, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK. Genome analysis of the platypus reveals unique signatures of evolution. Nature 2008; 453:175-83. [PMID: 18464734 PMCID: PMC2803040 DOI: 10.1038/nature06936] [Citation(s) in RCA: 475] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 03/25/2008] [Indexed: 12/18/2022]
Abstract
We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.
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Affiliation(s)
- Wesley C Warren
- Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.
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Veyrunes F, Waters PD, Miethke P, Rens W, McMillan D, Alsop AE, Grützner F, Deakin JE, Whittington CM, Schatzkamer K, Kremitzki CL, Graves T, Ferguson-Smith MA, Warren W, Marshall Graves JA. Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes. Genome Res 2008; 18:965-73. [PMID: 18463302 DOI: 10.1101/gr.7101908] [Citation(s) in RCA: 218] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In therian mammals (placentals and marsupials), sex is determined by an XX female: XY male system, in which a gene (SRY) on the Y affects male determination. There is no equivalent in other amniotes, although some taxa (notably birds and snakes) have differentiated sex chromosomes. Birds have a ZW female: ZZ male system with no homology with mammal sex chromosomes, in which dosage of a Z-borne gene (possibly DMRT1) affects male determination. As the most basal mammal group, the egg-laying monotremes are ideal for determining how the therian XY system evolved. The platypus has an extraordinary sex chromosome complex, in which five X and five Y chromosomes pair in a translocation chain of alternating X and Y chromosomes. We used physical mapping to identify genes on the pairing regions between adjacent X and Y chromosomes. Most significantly, comparative mapping shows that, contrary to earlier reports, there is no homology between the platypus and therian X chromosomes. Orthologs of genes in the conserved region of the human X (including SOX3, the gene from which SRY evolved) all map to platypus chromosome 6, which therefore represents the ancestral autosome from which the therian X and Y pair derived. Rather, the platypus X chromosomes have substantial homology with the bird Z chromosome (including DMRT1) and to segments syntenic with this region in the human genome. Thus, platypus sex chromosomes have strong homology with bird, but not to therian sex chromosomes, implying that the therian X and Y chromosomes (and the SRY gene) evolved from an autosomal pair after the divergence of monotremes only 166 million years ago. Therefore, the therian X and Y are more than 145 million years younger than previously thought.
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Affiliation(s)
- Frédéric Veyrunes
- Research School of Biological Sciences, Australian National University, Canberra 2601, Australia
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Whittington CM, Papenfuss AT, Bansal P, Torres AM, Wong ESW, Deakin JE, Graves T, Alsop A, Schatzkamer K, Kremitzki C, Ponting CP, Temple-Smith P, Warren WC, Kuchel PW, Belov K. Defensins and the convergent evolution of platypus and reptile venom genes. Genome Res 2008; 18:986-94. [PMID: 18463304 DOI: 10.1101/gr.7149808] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
When the platypus (Ornithorhynchus anatinus) was first discovered, it was thought to be a taxidermist's hoax, as it has a blend of mammalian and reptilian features. It is a most remarkable mammal, not only because it lays eggs but also because it is venomous. Rather than delivering venom through a bite, as do snakes and shrews, male platypuses have venomous spurs on each hind leg. The platypus genome sequence provides a unique opportunity to unravel the evolutionary history of many of these interesting features. While searching the platypus genome for the sequences of antimicrobial defensin genes, we identified three Ornithorhynchus venom defensin-like peptide (OvDLP) genes, which produce the major components of platypus venom. We show that gene duplication and subsequent functional diversification of beta-defensins gave rise to these platypus OvDLPs. The OvDLP genes are located adjacent to the beta-defensins and share similar gene organization and peptide structures. Intriguingly, some species of snakes and lizards also produce venoms containing similar molecules called crotamines and crotamine-like peptides. This led us to trace the evolutionary origins of other components of platypus and reptile venom. Here we show that several venom components have evolved separately in the platypus and reptiles. Convergent evolution has repeatedly selected genes coding for proteins containing specific structural motifs as templates for venom molecules.
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Affiliation(s)
- Camilla M Whittington
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia
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