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Chaora NS, Khanyile KS, Magwedere K, Pierneef R, Tabit FT, Muchadeyi FC. A 16S Next Generation Sequencing Based Molecular and Bioinformatics Pipeline to Identify Processed Meat Products Contamination and Mislabelling. Animals (Basel) 2022; 12:ani12040416. [PMID: 35203124 PMCID: PMC8868451 DOI: 10.3390/ani12040416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Meat adulteration and fraud encompasses the deliberate fraudulent addition or substitution of proteins of animal or plant origin in edible products primarily for economic gain. The mitochondrial 16S ribosomal (rRNA) gene was used to identify species that are present in pure and processed meat samples. The meat samples were sequenced using an Illumina sequencing platform, and bioinformatics analysis was carried out for species identification. The results indicated that pork was the major contaminant in most of the meat samples. The bioinformatics pipeline demonstrated its specificity through identification of species specific and quantification of the contamination levels across all samples. Food business operators and regulatory sectors can validate this method for food fraud checks and manage any form of mislabeling in the animal or plant protein food ecosystem. Abstract Processed meat is a target in meat adulteration for economic gain. This study demonstrates a molecular and bioinformatics diagnostic pipeline, utilizing the mitochondrial 16S ribosomal RNA (rRNA) gene, to determine processed meat product mislabeling through Next-Generation Sequencing. Nine pure meat samples were collected and artificially mixed at different ratios to verify the specificity and sensitivity of the pipeline. Processed meat products (n = 155), namely, minced meat, biltong, burger patties, and sausages, were collected across South Africa. Sequencing was performed using the Illumina MiSeq sequencing platform. Each sample had paired-end reads with a length of ±300 bp. Quality control and filtering was performed using BBDuk (version 37.90a). Each sample had an average of 134,000 reads aligned to the mitochondrial genomes using BBMap v37.90. All species in the artificial DNA mixtures were detected. Processed meat samples had reads that mapped to the Bos (90% and above) genus, with traces of reads mapping to Sus and Ovis (2–5%) genus. Sausage samples showed the highest level of contamination with 46% of the samples having mixtures of beef, pork, or mutton in one sample. This method can be used to authenticate meat products, investigate, and manage any form of mislabeling.
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Affiliation(s)
- Nyaradzo Stella Chaora
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Rooderpoort 1709, South Africa; (N.S.C.); (F.T.T.)
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (K.S.K.); (R.P.)
| | - Khulekani Sedwell Khanyile
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (K.S.K.); (R.P.)
| | - Kudakwashe Magwedere
- Directorate of Veterinary Public Health, Department of Agriculture, Land Reform and Rural Development, Pretoria 0001, South Africa;
| | - Rian Pierneef
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (K.S.K.); (R.P.)
| | - Frederick Tawi Tabit
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Rooderpoort 1709, South Africa; (N.S.C.); (F.T.T.)
| | - Farai Catherine Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (K.S.K.); (R.P.)
- Correspondence:
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Old JM, Ong OTW, Stannard HJ. Red-tailed phascogales: A review of their biology and importance as model marsupial species. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2020; 335:217-227. [PMID: 33382214 DOI: 10.1002/jez.2438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 11/09/2022]
Abstract
There are many limitations when using traditional laboratory species. Limits on variation, may result in limited outcomes, at both the species and individual level, due to different individuals/species having diverse physiological processes, or differing molecular and genetic mechanisms. By using a variety of model species, we will be able to develop creative solutions to biological problems and identify differences of which we were not previously aware. The laboratory mouse has been a suitable model species for various mammalian studies, however most are bred specifically for laboratory research with limited variability due to selective breeding. Marsupial models offer unique research opportunities compared to eutherian models. We believe that there should be an expansion in marsupial model species, and the introduction of the red-tailed phascogale (Phascogale calura), a dasyurid marsupial, should be one of them. Phascogales are easily managed in captivity, and there are now multiple studies involving their development, reproduction, nutrition, behavior and immune system, which can serve as a baseline for future studies. The addition of the phascogale as a model species will improve future mammalian studies by introducing variability and offer alternate solutions to biological problems, particularly in the areas of genetics, nutrition, immunology, the neuro-endocrine system, and ageing, due to their semelparous reproductive strategy and hence, subsequent predictive physiology. In this review, we provide information based on existing research on red-tailed phascogales to support their inclusion as a model species.
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Affiliation(s)
- Julie M Old
- School of Science, Hawkesbury Campus, Western Sydney University, Penrith, New South Wales, Australia
| | - Oselyne T W Ong
- Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Hayley J Stannard
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
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Molecular cytogenetic map of the central bearded dragon, Pogona vitticeps (Squamata: Agamidae). Chromosome Res 2013; 21:361-74. [PMID: 23703235 DOI: 10.1007/s10577-013-9362-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 04/12/2013] [Accepted: 04/27/2013] [Indexed: 12/20/2022]
Abstract
Reptiles, as the sister group to birds and mammals, are particularly valuable for comparative genomic studies among amniotes. The Australian central bearded dragon (Pogona vitticeps) is being developed as a reptilian model for such comparisons, with whole-genome sequencing near completion. The karyotype consists of 6 pairs of macrochromosomes and 10 pairs microchromosomes (2n = 32), including a female heterogametic ZW sex microchromosome pair. Here, we present a molecular cytogenetic map for P. vitticeps comprising 87 anchor bacterial artificial chromosome clones that together span each macro- and microchromosome. It is the first comprehensive cytogenetic map for any non-avian reptile. We identified an active nucleolus organizer region (NOR) on the sub-telomeric region of 2q by mapping 18S rDNA and Ag-NOR staining. We identified interstitial telomeric sequences in two microchromosome pairs and the W chromosome, indicating that microchromosome fusion has been a mechanism of karyotypic evolution in Australian agamids within the last 21 to 19 million years. Orthology searches against the chicken genome revealed an intrachromosomal rearrangement of P. vitticeps 1q, identified regions orthologous to chicken Z on P. vitticeps 2q, snake Z on P. vitticeps 6q and the autosomal microchromosome pair in P. vitticeps orthologous to turtle Pelodiscus sinensis ZW and lizard Anolis carolinensis XY. This cytogenetic map will be a valuable reference tool for future gene mapping studies and will provide the framework for the work currently underway to physically anchor genome sequences to chromosomes for this model Australian squamate.
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Simmons GS, Young PR, Hanger JJ, Jones K, Clarke D, McKee JJ, Meers J. Prevalence of koala retrovirus in geographically diverse populations in Australia. Aust Vet J 2012; 90:404-9. [PMID: 23004234 DOI: 10.1111/j.1751-0813.2012.00964.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2012] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To determine the prevalence of koala retrovirus (KoRV) in selected koala populations and to estimate proviral copy number in a subset of koalas. METHODS Blood or tissue samples from 708 koalas in Queensland, New South Wales, Victoria and South Australia were tested for KoRV pol provirus gene using standard polymerase chain reaction (PCR), nested PCR and real-time PCR (qPCR). RESULTS Prevalence of KoRV provirus-positive koalas was 100% in four regions of Queensland and New South Wales, 72.2% in mainland Victoria, 26.6% on four Victorian islands and 14.8% on Kangaroo Island, South Australia. Estimated proviral copy number per cell in four groups of koalas from Queensland and Victoria showed marked variation, ranging from a mean of 165 copies per cell in the Queensland group to 1.29 × 10(-4) copies per cell in one group of Victorian koalas. CONCLUSIONS The higher prevalence of KoRV-positive koalas in the north of Australia and high proviral loads in Queensland koalas may indicate KoRV entered and became endogenous in the north and is spreading southwards. It is also possible there are genetic differences between koalas in northern and southern Australia that affect susceptibility to KoRV infection or endogenisation, or that environmental factors affecting transmission in northern states are absent or uncommon in southern regions. Although further studies are required, the finding of proviral copy numbers orders of magnitude lower than what would be expected for the presence of a single copy in every cell for many Victorian animals suggests that KoRV is not endogenous in these animals and likely reflects ongoing exogenous infection.
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Affiliation(s)
- G S Simmons
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia.
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Yu H, Lindsay J, Feng ZP, Frankenberg S, Hu Y, Carone D, Shaw G, Pask AJ, O'Neill R, Papenfuss AT, Renfree MB. Evolution of coding and non-coding genes in HOX clusters of a marsupial. BMC Genomics 2012; 13:251. [PMID: 22708672 PMCID: PMC3541083 DOI: 10.1186/1471-2164-13-251] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 05/22/2012] [Indexed: 12/13/2022] Open
Abstract
Background The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals. Results Here we report a comparative analysis of HOX gene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation of HOX gene sequence and structure and non-protein coding genes including the microRNAs miR-196a, miR-196b, miR-10a and miR-10b and the long non-coding RNAs HOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such as miR-10, miR-414 and miR-464, were found in the tammar HOX clusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammar HOXB and HOXD clusters. Conclusions This study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation of HOX genes to influence the body plan of this marsupial.
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Affiliation(s)
- Hongshi Yu
- ARC Centre of Excellence in Kangaroo Genomics, The University of Melbourne, Melbourne, Victoria 3010, Australia
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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: 1.2] [Reference Citation Analysis] [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] [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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Pan D, Zhang L. An atlas of the speed of copy number changes in animal gene families and its implications. PLoS One 2009; 4:e7342. [PMID: 19851465 PMCID: PMC2761543 DOI: 10.1371/journal.pone.0007342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 08/28/2009] [Indexed: 01/23/2023] Open
Abstract
The notion that gene duplications generating new genes and functions is commonly accepted in evolutionary biology. However, this assumption is more speculative from theory rather than well proven in genome-wide studies. Here, we generated an atlas of the rate of copy number changes (CNCs) in all the gene families of ten animal genomes. We grouped the gene families with similar CNC dynamics into rate pattern groups (RPGs) and annotated their function using a novel bottom-up approach. By comparing CNC rate patterns, we showed that most of the species-specific CNC rates groups are formed by gene duplication rather than gene loss, and most of the changes in rates of CNCs may be the result of adaptive evolution. We also found that the functions of many RPGs match their biological significance well. Our work confirmed the role of gene duplication in generating novel phenotypes, and the results can serve as a guide for researchers to connect the phenotypic features to certain gene duplications.
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Affiliation(s)
- Deng Pan
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
- Program in Genetics, Bioinformatics, and Computational Biology, Blacksburg, Virginia, United States of America
- * E-mail:
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Yu H, Pask AJ, Shaw G, Renfree MB. Comparative analysis of the mammalian WNT4 promoter. BMC Genomics 2009; 10:416. [PMID: 19732466 PMCID: PMC2758904 DOI: 10.1186/1471-2164-10-416] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 09/06/2009] [Indexed: 11/25/2022] Open
Abstract
Background WNT4 is a critical signalling molecule in embryogenesis and homeostasis, but the elements that control its transcriptional regulation are largely unknown. This study uses comparative cross species sequence and functional analyses between humans and a marsupial (the tammar wallaby,Macropus eugenii) to refine the mammalian Wnt4 promoter. Results We have defined a highly conserved 89 bp minimal promoter region in human WNT4 by comparative analysis with the tammar wallaby. There are many conserved transcription factor binding sites in the proximal promoter region, including SP1, MyoD, NFκB and AP2, as well as highly conserved CpG islands within the human, mouse and marsupial promoters, suggesting that DNA methylation may play an important role in WNT4 transcriptional regulation. Conclusion Using a marsupial model, we have been able to provide new information on the transcriptional regulators in the promoter of this essential mammalian developmental gene, WNT4. These transcription factor binding sites and CpG islands are highly conserved in two disparate mammals, and are likely key controlling elements in the regulation of this essential developmental gene.
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Affiliation(s)
- Hongshi Yu
- ARC Centre of Excellence in Kangaroo Genomics, Department of Zoology, The University of Melbourne, Victoria 3010, Australia.
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Wang X, Olp JJ, Miller RD. On the genomics of immunoglobulins in the gray, short-tailed opossum Monodelphis domestica. Immunogenetics 2009; 61:581-96. [PMID: 19609519 PMCID: PMC2880577 DOI: 10.1007/s00251-009-0385-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Accepted: 06/24/2009] [Indexed: 11/30/2022]
Abstract
Annotated maps of the IGH, IGK, and IGL loci in the gray, short-tailed opossum Monodelphis domestica were generated from analyses of the available whole genome sequence for this species. Analyses of their content and organization confirmed a number of previous conclusions based on characterization of complementary DNAs encoding opossum immunoglobulin heavy and light chains and limited genomic analysis, including (a) the predominance of a single immunoglobulin heavy chain variable region (IGHV) subgroup and clan, (b) the presence of a single immunoglobulin (Ig)G subclass, (c) the apparent absence of an IgD, and (d) the general organization and V gene complexity of the IGK and IGL light chain loci. In addition, several unexpected discoveries were made including the presence of a partial V to D, germline-joined IGHV segment, the first germline-joined Ig V gene to be found in a mammal. In addition was the presence of a larger number of IGKV subgroups than had been previously identified. With this report, annotated maps of the major histocompatibility complex, T-cell receptor, and immunoglobulin loci have been completed for M. domestica, the only non-eutherian mammalian species for which this has been accomplished, strengthening the utility of this species as a model organism.
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Affiliation(s)
- Xinxin Wang
- Center for Evolutionary & Theoretical Immunology, Department of Biology, The University of New Mexico, Albuquerque NM 87131 USA, Ph: 1 505 277 2844, Fax: 1 505 277 0304
| | - Jonathan J. Olp
- Center for Evolutionary & Theoretical Immunology, Department of Biology, The University of New Mexico, Albuquerque NM 87131 USA, Ph: 1 505 277 2844, Fax: 1 505 277 0304
| | - Robert D. Miller
- Center for Evolutionary & Theoretical Immunology, Department of Biology, The University of New Mexico, Albuquerque NM 87131 USA, Ph: 1 505 277 2844, Fax: 1 505 277 0304
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Siddle HV, Deakin JE, Coggill P, Hart E, Cheng Y, Wong ESW, 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: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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
| | - 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
| | - Elizabeth Hart
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Yuanyuan Cheng
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | - Emily SW Wong
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, 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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Pan D, Zhang L. Burst of young retrogenes and independent retrogene formation in mammals. PLoS One 2009; 4:e5040. [PMID: 19325906 PMCID: PMC2657826 DOI: 10.1371/journal.pone.0005040] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2008] [Accepted: 02/11/2009] [Indexed: 12/24/2022] Open
Abstract
Retroposition and retrogenes gain increasing attention as recent studies show that they play an important role in human new gene formation. Here we examined the patterns of retrogene distribution in 8 mammalian genomes using 4 non-mammalian genomes as a contrast. There has been a burst of young retrogenes not only in primate lineages as suggested in a recent study, but also in other mammalian lineages. In mammals, most of the retrofamilies (the gene families that have retrogenes) are shared between species. In these shared retrofamilies, 14%–18% of functional retrogenes may have originated independently in multiple mammalian species. Notably, in the independently originated retrogenes, there is an enrichment of ribosome related gene function. In sharp contrast, none of these patterns hold in non-mammals. Our results suggest that the recruitment of the specific L1 retrotransposons in mammals might have been an important evolutionary event for the split of mammals and non-mammals and retroposition continues to be an important active process in shaping the dynamics of mammalian genomes, as compared to being rather inert in non-mammals.
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Affiliation(s)
- Deng Pan
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
- Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, Virginia, United States of America
- * E-mail:
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High levels of genetic variation at MHC class II DBB loci in the tammar wallaby (Macropus eugenii). Immunogenetics 2008; 61:111-8. [PMID: 19082823 DOI: 10.1007/s00251-008-0347-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Accepted: 11/20/2008] [Indexed: 10/21/2022]
Abstract
High levels of MHC diversity are crucial for immunological fitness of populations, with island populations particularly susceptible to loss of genetic diversity. In this study, the level of MHC class II DBB diversity was examined in tammar wallabies (Macropus eugenii) from Kangaroo Island by genotyping class II-linked microsatellite loci and sequencing of DBB genes. Here we show that the tammar wallaby has at least four expressed MHC class II DBB loci and extensive genetic variation in the peptide-binding region of the DBB genes. These results contradict early studies which suggested that wallabies lacked MHC class II diversity and demonstrate that, in spite of the long-term isolation on an offshore island, this population of wallabies has a high level of DBB diversity.
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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: 2.8] [Reference Citation Analysis] [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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15
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Abstract
We have determined the sequence and genomic organization of the genes encoding the cone visual pigment of the platypus (Ornithorhynchus anatinus) and the echidna (Tachyglossus aculeatus), and inferred their spectral properties and evolutionary pathways. We prepared platypus and echidna retinal RNA and used primers of the middle-wave-sensitive (MWS), long-wave-sensitive (LWS), and short-wave sensitive (SWS1) pigments corresponding to coding sequences that are highly conserved among mammals; to PCR amplify the corresponding pigment sequences. Amplification from the retinal RNA revealed the expression of LWS pigment mRNA that is homologous in sequence and spectral properties to the primate LWS visual pigments. However, we were unable to amplify the mammalian SWS1 pigment from these two species, indicating this gene was lost prior to the echidna-platypus divergence (∼21 MYA). Subsequently, when the platypus genome sequence became available, we found an LWS pigment gene in a conserved genomic arrangement that resembles the primate pigment, but, surprisingly we found an adjacent (∼20 kb) SWS2 pigment gene within this conserved genomic arrangement. We obtained the same result after sequencing the echidna genes. The encoded SWS2 pigment is predicted to have a wavelength of maximal absorption of about 440 nm, and is paralogous to SWS pigments typically found in reptiles, birds, and fish but not in mammals. This study suggests the locus control region (LCR) has played an important role in the conservation of photo receptor gene arrays and the control of their spatial and temporal expression in the retina in all mammals. In conclusion, a duplication event of an ancestral cone visual pigment gene, followed by sequence divergence and selection gave rise to the LWS and SWS2 visual pigments. So far, the echidna and platypus are the only mammals that share the gene structure of the LWS-SWS2 pigment gene complex with reptiles, birds and fishes.
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Joss J, Molloy M, Hinds L, Deane E. Proteomic analysis of early lactation milk of the tammar wallaby (Macropus eugenii). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2007; 2:150-64. [DOI: 10.1016/j.cbd.2007.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 02/07/2007] [Accepted: 02/07/2007] [Indexed: 10/23/2022]
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Young LJ, Deane EM. Culture and Stimulation of Tammar Wallaby Lymphocytes. Vet Res Commun 2007; 31:685-701. [PMID: 17245559 DOI: 10.1007/s11259-007-0057-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2006] [Indexed: 10/23/2022]
Abstract
We describe the culture and stimulation of lymphocytes from the model marsupial, the tammar wallaby (Macropus eugenii). We also describe the capacity of tammar wallaby lymphocytes isolated from blood, spleen and lymph nodes to produce soluble immunomodulatory factors. Culture conditions were optimized for mitogen-driven stimulation using the plant lectin phytohaemagglutinin (PHA). Products secreted by stimulated cells were harvested and crudely fractionated before they were added back to freshly isolated lymphocytes. Using the 3-(4,5-dimethylthiazol-2-yl)-2,5 diphenyltetrazolium bromide (MTT) assay, both stimulatory and inhibitory bioactive factors were detected in serum-free supernatants harvested from mitogen-treated peripheral blood mononuclear cells. This paper describes the capacity of leukocytes of the tammar wallaby to respond to mitogenic stimulation and to produce soluble, low-molecular-weight bioactive molecules that possess cytokine-like activity.
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Affiliation(s)
- L J Young
- School of Chemical and Biomedical Sciences, Central Queensland University, Rockhampton, Queensland.
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18
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Renfree MB. Society for Reproductive Biology Founders' Lecture 2006 - life in the pouch: womb with a view. Reprod Fertil Dev 2007; 18:721-34. [PMID: 17032580 DOI: 10.1071/rd06072] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Accepted: 07/11/2006] [Indexed: 12/15/2022] Open
Abstract
Marsupials give birth to an undeveloped altricial young after a relatively short gestation period, but have a long and sophisticated lactation with the young usually developing in a pouch. Their viviparous mode of reproduction trades placentation for lactation, exchanging the umbilical cord for the teat. The special adaptations that marsupials have developed provide us with unique insights into the evolution of all mammalian reproduction. Marsupials hold many mammalian reproductive 'records', for example they have the shortest known gestation but the longest embryonic diapause, the smallest neonate but the longest sperm. They have contributed to our knowledge of many mammalian reproductive events including embryonic diapause and development, birth behaviour, sex determination, sexual differentiation, lactation and seasonal breeding. Because marsupials have been genetically isolated from eutherian mammals for over 125 million years, sequencing of the genome of two marsupial species has made comparative genomic biology an exciting and important new area of investigation. This review will show how the study of marsupials has widened our understanding of mammalian reproduction and development, highlighting some mechanisms that are so fundamental that they are shared by all today's marsupial and eutherian mammals.
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Rapkins RW, Hore T, Smithwick M, Ager E, Pask AJ, Renfree MB, Kohn M, Hameister H, Nicholls RD, Deakin JE, Graves JAM. Recent assembly of an imprinted domain from non-imprinted components. PLoS Genet 2006; 2:e182. [PMID: 17069464 PMCID: PMC1626109 DOI: 10.1371/journal.pgen.0020182] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Accepted: 09/11/2006] [Indexed: 02/02/2023] Open
Abstract
Genomic imprinting, representing parent-specific expression of alleles at a locus, raises many questions about how—and especially why—epigenetic silencing of mammalian genes evolved. We present the first in-depth study of how a human imprinted domain evolved, analyzing a domain containing several imprinted genes that are involved in human disease. Using comparisons of orthologous genes in humans, marsupials, and the platypus, we discovered that the Prader-Willi/Angelman syndrome region on human Chromosome 15q was assembled only recently (105–180 million years ago). This imprinted domain arose after a region bearing UBE3A (Angelman syndrome) fused with an unlinked region bearing SNRPN (Prader-Willi syndrome), which had duplicated from the non-imprinted SNRPB/B′. This region independently acquired several retroposed gene copies and arrays of small nucleolar RNAs from different parts of the genome. In their original configurations, SNRPN and UBE3A are expressed from both alleles, implying that acquisition of imprinting occurred after their rearrangement and required the evolution of a control locus. Thus, the evolution of imprinting in viviparous mammals is ongoing. Humans and other mammals have two copies of the genome. For most genes, both copies are active. However, some genes are active only when they are inherited from the father, others only when inherited from the mother. These “imprinted” genes are clustered in domains that are controlled coordinately. Only mammals show genomic imprinting. It is not understood how or why genes became imprinted during mammalian evolution. The authors used comparisons between humans and the most distantly related mammals, marsupials and monotremes, to discover how one of these imprinted domains evolved. The authors studied an imprinted domain on human Chromosome 15, mutations which cause Prader-Willi and Angelman syndromes (PWS-AS). They discovered that the PWS and AS genes lie on different chromosomes in kangaroos and platypus and are not imprinted. Other imprinted genes in the domain, including the putative control region, are absent from the genome and derived from copies of genes from yet other chromosomes. The arrangement in kangaroos and platypus is present also in the chicken genome, so it must be ancestral. This study concludes that the PWS-AS imprinted region was assembled relatively recently from non-imprinted components that were moved together or copied from all over the genome.
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Affiliation(s)
- Robert W Rapkins
- Australian Research Council Center for Kangaroo Genomics and Research School of Biological Sciences, Australian National University, Canberra, Australia
| | - Tim Hore
- Australian Research Council Center for Kangaroo Genomics and Research School of Biological Sciences, Australian National University, Canberra, Australia
| | - Megan Smithwick
- Department of Genetics, La Trobe University, Melbourne, Australia
| | - Eleanor Ager
- Department of Zoology, University of Melbourne, Melbourne, Australia
| | - Andrew J Pask
- Department of Zoology, University of Melbourne, Melbourne, Australia
| | - Marilyn B Renfree
- Department of Zoology, University of Melbourne, Melbourne, Australia
| | - Matthias Kohn
- Department of Medical Genetics, University of Ulm, Ulm, Germany
| | - Horst Hameister
- Department of Medical Genetics, University of Ulm, Ulm, Germany
| | - Robert D Nicholls
- Department of Pediatrics, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Janine E Deakin
- Australian Research Council Center for Kangaroo Genomics and Research School of Biological Sciences, Australian National University, Canberra, Australia
| | - Jennifer A. Marshall Graves
- Australian Research Council Center for Kangaroo Genomics and Research School of Biological Sciences, Australian National University, Canberra, Australia
- * To whom correspondence should be addressed. E-mail:
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20
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Ambatipudi K, Old J, Guilhaus M, Raftery M, Hinds L, Deane E. Proteomic analysis of the neutrophil proteins of the tammar wallaby (Macropus eugenii). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2006; 1:283-91. [DOI: 10.1016/j.cbd.2006.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2006] [Revised: 04/27/2006] [Accepted: 05/02/2006] [Indexed: 10/24/2022]
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21
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Evaluation of Chemical Derivatisation Methods for Protein Identification using MALDI MS/MS. Int J Pept Res Ther 2006. [DOI: 10.1007/s10989-006-9026-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Belov K, Deakin JE, Papenfuss AT, Baker ML, Melman SD, Siddle HV, Gouin N, Goode DL, Sargeant TJ, Robinson MD, Wakefield MJ, Mahony S, Cross JGR, Benos PV, Samollow PB, Speed TP, Graves JAM, Miller RD. Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol 2006; 4:e46. [PMID: 16435885 PMCID: PMC1351924 DOI: 10.1371/journal.pbio.0040046] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Accepted: 12/12/2005] [Indexed: 11/19/2022] Open
Abstract
The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used the Monodelphis domestica (gray short-tailed opossum) sequence to construct the first map of a marsupial major histocompatibility complex (MHC). The MHC is the most gene-dense region of the mammalian genome and is critical to immunity and reproductive success. The marsupial MHC bridges the phylogenetic gap between the complex MHC of eutherian mammals and the minimal essential MHC of birds. Here we show that the opossum MHC is gene dense and complex, as in humans, but shares more organizational features with non-mammals. The Class I genes have amplified within the Class II region, resulting in a unique Class I/II region. We present a model of the organization of the MHC in ancestral mammals and its elaboration during mammalian evolution. The opossum genome, together with other extant genomes, reveals the existence of an ancestral "immune supercomplex" that contained genes of both types of natural killer receptors together with antigen processing genes and MHC genes.
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Affiliation(s)
- Katherine Belov
- 1Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, The University of Sydney, Camden, Australia
| | - Janine E Deakin
- 2ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, Australia
| | - Anthony T Papenfuss
- 3The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Michelle L Baker
- 4Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Sandra D Melman
- 4Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Hannah V Siddle
- 1Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, The University of Sydney, Camden, Australia
| | - Nicolas Gouin
- 5Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas, United States of America
| | - David L Goode
- 3The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Tobias J Sargeant
- 3The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Mark D Robinson
- 3The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Matthew J Wakefield
- 3The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Shaun Mahony
- 6National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland
| | - Joseph G. R Cross
- 2ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, Australia
| | - Panayiotis V Benos
- 7Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Paul B Samollow
- 8Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Terence P Speed
- 3The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Jennifer A. Marshall Graves
- 2ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, Australia
| | - Robert D Miller
- 4Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
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23
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Koina E, Wakefield MJ, Walcher C, Disteche CM, Whitehead S, Ross M, Marshall Graves JA. Isolation, X location and activity of the marsupial homologue of SLC16A2, an XIST-flanking gene in eutherian mammals. Chromosome Res 2005; 13:687-98. [PMID: 16235118 PMCID: PMC2819140 DOI: 10.1007/s10577-005-1006-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Accepted: 08/08/2005] [Indexed: 10/25/2022]
Abstract
X chromosome inactivation (XCI) achieves dosage compensation between males and females for most X-linked genes in eutherian mammals. It is a whole-chromosome effect under the control of the XIST locus, although some genes escape inactivation. Marsupial XCI differs from the eutherian process, implying fundamental changes in the XCI mechanism during the evolution of the two lineages. There is no direct evidence for the existence of a marsupial XIST homologue. XCI has been studied for only a handful of genes in any marsupial, and none in the model kangaroo Macropus eugenii (the tammar wallaby). We have therefore studied the sequence, location and activity of a gene SLC16A2 (solute carrier, family 16, class A, member 2) that flanks XIST on the human and mouse X chromosomes. A BAC clone containing the marsupial SLC16A2 was mapped to the end of the long arm of the tammar X chromosome and used in RNA FISH experiments to determine whether one or both loci are transcribed in female cells. In male and female cells, only a single signal was found, indicating that the marsupial SLC16A2 gene is silenced on the inactivated X.
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Affiliation(s)
- Edda Koina
- ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia.
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24
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Alsop AE, Miethke P, Rofe R, Koina E, Sankovic N, Deakin JE, Haines H, Rapkins RW, Marshall Graves JA. Characterizing the chromosomes of the Australian model marsupial Macropus eugenii (tammar wallaby). Chromosome Res 2005; 13:627-36. [PMID: 16170627 DOI: 10.1007/s10577-005-0989-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Accepted: 07/05/2005] [Indexed: 11/26/2022]
Abstract
Marsupials occupy a phylogenetic middle ground that is very valuable in genome comparisons of mammal and other vertebrate species. For this reason, whole genome sequencing is being undertaken for two distantly related marsupial species, including the model kangaroo species Macropus eugenii (the tammar wallaby). As a first step towards the molecular characterization of the tammar genome, we present a detailed description of the tammar karyotype, report the development of a set of molecular anchor markers and summarize the comparative mapping data for this species.
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Affiliation(s)
- Amber E Alsop
- ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia.
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25
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Young LJ, Deane EM. Culture and characterisation of peripheral blood monocytes and monocyte-derived adherent cells of the tammar wallaby, Macropus eugenii. Immunol Lett 2005; 96:253-9. [PMID: 15585331 DOI: 10.1016/j.imlet.2004.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2004] [Revised: 08/21/2004] [Accepted: 09/03/2004] [Indexed: 11/18/2022]
Abstract
Monocytes, monocyte-derived adherent cells and dendritic cells all play a role in cellular immunity. In this study, we describe the isolation of monocyte-derived adherent cells and dendritic cells from a model marsupial, the tammar wallaby, Macropus eugenii, and report that in vitro, these cells appear morphologically similar to these cells found in other mammals. The successful culture of marsupial monocyte and dendritic cells was undertaken in serum-free medium which contained lymphocyte conditioned medium as an absolute requirement. This supports the view that similar to cultured dendritic cells from other species reported to date, specific growth factors are required to promote the maturation and differentiation of these cells.
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Affiliation(s)
- L J Young
- School of Chemical and Biomedical Sciences, Central Queensland University, Rockhampton 4702, Qld, Australia
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26
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Ibbotson MR, Price NSC, Crowder NA. On the Division of Cortical Cells Into Simple and Complex Types: A Comparative Viewpoint. J Neurophysiol 2005; 93:3699-702. [PMID: 15659524 DOI: 10.1152/jn.01159.2004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Hubel and Weisel introduced the concept of cells in cat primary visual cortex being partitioned into two categories: simple and complex. Subsequent authors have developed a quantitative measure to distinguish the two cell types based on the ratio between modulated responses at the stimulus frequency ( F1) and unmodulated ( F0) components of the spiking responses to drifting sinusoidal gratings. It has been shown that cells in anesthetized cat and monkey cortex have bimodal distributions of F1/ F0ratios. A clear local minimum or dip exists in the distribution at a ratio close to unity. Here we present a comparison of the distributions of the F1/ F0ratios between cells in the primary visual cortex of the eutherian cat and marsupial Tammar wallaby, Macropus eugenii. This is the first quantitative description of any marsupial cortex using the F1/ F0ratio and follows earlier papers showing that cells in wallaby cortex are tightly oriented and spatial frequency tuned. The results reveal a bimodal distribution in the wallaby F1/ F0ratios that is very similar to that found in the rat, cat, and monkey. Discussion focuses on the mechanisms that could lead to such similar cell distributions in animals with diverse behaviors and phylogenies.
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Affiliation(s)
- M R Ibbotson
- Visual Sciences, Research School of Biological Sciences, Australian National Univ., Canberra, ACT 2601, Australia.
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27
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Premzl M, Delbridge M, Gready JE, Wilson P, Johnson M, Davis J, Kuczek E, Marshall Graves JA. The prion protein gene: identifying regulatory signals using marsupial sequence. Gene 2005; 349:121-34. [PMID: 15777726 DOI: 10.1016/j.gene.2004.11.049] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2004] [Revised: 11/11/2004] [Accepted: 11/26/2004] [Indexed: 11/25/2022]
Abstract
The function of the prion protein gene (PRNP) and its normal product PrP(C) is elusive. We used comparative genomics as a strategy to understand the normal function of PRNP. As the reliability of comparisons increases with the number of species and increased evolutionary distance, we isolated and sequenced a 66.5 kb BAC containing the PRNP gene from a distantly related mammal, the model Australian marsupial Macropus eugenii (tammar wallaby). Marsupials are separated from eutherians such as human and mouse by roughly 180 million years of independent evolution. We found that tammar PRNP, like human PRNP, has two exons. Prion proteins encoded by the tammar wallaby and a distantly related marsupial, Monodelphis domestica (Brazilian opossum) PRNP contain proximal PrP repeats with a distinct, marsupial-specific composition and a variable number. Comparisons of tammar wallaby PRNP with PRNPs from human, mouse, bovine and ovine allowed us to identify non-coding gene regions conserved across the marsupial-eutherian evolutionary distance, which are candidates for regulatory regions. In the PRNP 3' UTR we found a conserved signal for nuclear-specific polyadenylation and the putative cytoplasmic polyadenylation element (CPE), indicating that post-transcriptional control of PRNP mRNA activity is important. Phylogenetic footprinting revealed conserved potential binding sites for the MZF-1 transcription factor in both upstream promoter and intron/intron 1, and for the MEF2, MyT1, Oct-1 and NFAT transcription factors in the intron(s). The presence of a conserved NFAT-binding site and CPE indicates involvement of PrP(C) in signal transduction and synaptic plasticity.
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Affiliation(s)
- Marko Premzl
- Comparative Genomics Group, Research School of Biological Sciences, Australian National University, P.O. Box 475, Canberra, ACT 2601, Australia.
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28
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Abstract
A recent landmark paper demonstrates the unique contribution of marsupials and monotremes to comparative genome analysis, filling an evolutionary gap between the eutherian mammals and more distant vertebrate species. A recent landmark paper demonstrates the unique contribution of marsupials and monotremes to comparative genome analysis, filling an evolutionary gap between the eutherian mammals (including humans) and more distant vertebrate species.
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Affiliation(s)
- Matthew J Wakefield
- Division of Immunology and Genetics, John Curtin School of Medical Research, The Australian National University, Canberra 0200, Australia
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29
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Margulies EH, Maduro VVB, Thomas PJ, Tomkins JP, Amemiya CT, Luo M, Green ED. Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes. Proc Natl Acad Sci U S A 2005; 102:3354-9. [PMID: 15718282 PMCID: PMC549084 DOI: 10.1073/pnas.0408539102] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Indexed: 11/18/2022] Open
Abstract
Sequencing and comparative analyses of genomes from multiple vertebrates are providing insights about the genetic basis for biological diversity. To date, these efforts largely have focused on eutherian mammals, chicken, and fish. In this article, we describe the generation and study of genomic sequences from noneutherian mammals, a group of species occupying unusual phylogenetic positions. A large sequence data set (totaling >5 Mb) was generated for the same orthologous region in three marsupial (North American opossum, South American opossum, and Australian tammar wallaby) and one monotreme (platypus) genomes. These ancient mammalian genomes are characterized by unusual architectural features with respect to G + C and repeat content, as well as compression relative to human. Approximately 14% and 34% of the human sequence forms alignments with the orthologous sequence from platypus and the marsupials, respectively; these numbers are distinctly lower than that observed with nonprimate eutherian mammals (45-70%). The alignable sequences between human and each marsupial species are not completely overlapping (only 80% common to all three species) nor are the platypus-alignable sequences completely contained within the marsupial-alignable sequences. Phylogenetic analysis of synonymous coding positions reveals that platypus has a notably long branch length, with the human-platypus substitution rate being on average 55% greater than that seen with human-marsupial pairs. Finally, analyses of the major mammalian lineages reveal distinct patterns with respect to the common presence of evolutionarily conserved vertebrate sequences. Our results confirm that genomic sequence from noneutherian mammals can contribute uniquely to unraveling the functional and evolutionary histories of the mammalian genome.
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Affiliation(s)
- Elliott H Margulies
- Genome Technology Branch and NISC, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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30
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Margulies EH, Green ED. Detecting highly conserved regions of the human genome by multispecies sequence comparisons. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 68:255-63. [PMID: 15338625 DOI: 10.1101/sqb.2003.68.255] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- E H Margulies
- Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003. [PMCID: PMC2447285 DOI: 10.1002/cfg.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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