PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-7 (7)
 

Clipboard (0)
None

Select a Filter Below

Journals
Year of Publication
Document Types
1.  Immunome database for marsupials and monotremes 
BMC Immunology  2011;12:48.
Background
To understand the evolutionary origins of our own immune system, we need to characterise the immune system of our distant relatives, the marsupials and monotremes. The recent sequencing of the genomes of two marsupials (opossum and tammar wallaby) and a monotreme (platypus) provides an opportunity to characterise the immune gene repertoires of these model organisms. This was required as many genes involved in immunity evolve rapidly and fail to be detected by automated gene annotation pipelines.
Description
We have developed a database of immune genes from the tammar wallaby, red-necked wallaby, northern brown bandicoot, brush-tail possum, opossum, echidna and platypus. The resource contains 2,235 newly identified sequences and 3,197 sequences which had been described previously. This comprehensive dataset was built from a variety of sources, including EST projects and expert-curated gene predictions generated through a variety of methods including chained-BLAST and sensitive HMMER searches. To facilitate systems-based research we have grouped sequences based on broad Gene Ontology categories as well as by specific functional immune groups. Sequences can be extracted by keyword, gene name, protein domain and organism name. Users can also search the database using BLAST.
Conclusion
The Immunome Database for Marsupials and Monotremes (IDMM) is a comprehensive database of all known marsupial and monotreme immune genes. It provides a single point of reference for genomic and transcriptomic datasets. Data from other marsupial and monotreme species will be added to the database as it become available. This resource will be utilized by marsupial and monotreme immunologists as well as researchers interested in the evolution of mammalian immunity.
doi:10.1186/1471-2172-12-48
PMCID: PMC3173380  PMID: 21854560
2.  Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby 
BMC Genomics  2011;12:420.
Background
The thymus plays a critical role in the development and maturation of T-cells. Humans have a single thoracic thymus and presence of a second thymus is considered an anomaly. However, many vertebrates have multiple thymuses. The tammar wallaby has two thymuses: a thoracic thymus (typically found in all mammals) and a dominant cervical thymus. Researchers have known about the presence of the two wallaby thymuses since the 1800s, but no genome-wide research has been carried out into possible functional differences between the two thymic tissues. Here, we used pyrosequencing to compare the transcriptomes of a cervical and thoracic thymus from a single 178 day old tammar wallaby.
Results
We show that both the tammar thoracic and the cervical thymuses displayed gene expression profiles consistent with roles in T-cell development. Both thymuses expressed genes that mediate distinct phases of T-cells differentiation, including the initial commitment of blood stem cells to the T-lineage, the generation of T-cell receptor diversity and development of thymic epithelial cells. Crucial immune genes, such as chemokines were also present. Comparable patterns of expression of non-coding RNAs were seen. 67 genes differentially expressed between the two thymuses were detected, and the possible significance of these results are discussed.
Conclusion
This is the first study comparing the transcriptomes of two thymuses from a single individual. Our finding supports that both thymuses are functionally equivalent and drive T-cell development. These results are an important first step in the understanding of the genetic processes that govern marsupial immunity, and also allow us to begin to trace the evolution of the mammalian immune system.
doi:10.1186/1471-2164-12-420
PMCID: PMC3173455  PMID: 21854594
3.  Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development 
Renfree, Marilyn B | Papenfuss, Anthony T | Deakin, Janine E | Lindsay, James | Heider, Thomas | Belov, Katherine | Rens, Willem | Waters, Paul D | Pharo, Elizabeth A | Shaw, Geoff | Wong, Emily SW | Lefèvre, Christophe M | Nicholas, Kevin R | Kuroki, Yoko | Wakefield, Matthew J | Zenger, Kyall R | Wang, Chenwei | Ferguson-Smith, Malcolm | Nicholas, Frank W | Hickford, Danielle | Yu, Hongshi | Short, Kirsty R | Siddle, Hannah V | Frankenberg, Stephen R | Chew, Keng Yih | Menzies, Brandon R | Stringer, Jessica M | Suzuki, Shunsuke | Hore, Timothy A | Delbridge, Margaret L | Mohammadi, Amir | Schneider, Nanette Y | Hu, Yanqiu | O'Hara, William | Al Nadaf, Shafagh | Wu, Chen | Feng, Zhi-Ping | Cocks, Benjamin G | Wang, Jianghui | Flicek, Paul | Searle, Stephen MJ | Fairley, Susan | Beal, Kathryn | Herrero, Javier | Carone, Dawn M | Suzuki, Yutaka | Sugano, Sumio | Toyoda, Atsushi | Sakaki, Yoshiyuki | Kondo, Shinji | Nishida, Yuichiro | Tatsumoto, Shoji | Mandiou, Ion | Hsu, Arthur | McColl, Kaighin A | Lansdell, Benjamin | Weinstock, George | Kuczek, Elizabeth | McGrath, Annette | Wilson, Peter | Men, Artem | Hazar-Rethinam, Mehlika | Hall, Allison | Davis, John | Wood, David | Williams, Sarah | Sundaravadanam, Yogi | Muzny, Donna M | Jhangiani, Shalini N | Lewis, Lora R | Morgan, Margaret B | Okwuonu, Geoffrey O | Ruiz, San Juana | Santibanez, Jireh | Nazareth, Lynne | Cree, Andrew | Fowler, Gerald | Kovar, Christie L | Dinh, Huyen H | Joshi, Vandita | Jing, Chyn | Lara, Fremiet | Thornton, Rebecca | Chen, Lei | Deng, Jixin | Liu, Yue | Shen, Joshua Y | Song, Xing-Zhi | Edson, Janette | Troon, Carmen | Thomas, Daniel | Stephens, Amber | Yapa, Lankesha | Levchenko, Tanya | Gibbs, Richard A | Cooper, Desmond W | Speed, Terence P | Fujiyama, Asao | M Graves, Jennifer A | O'Neill, Rachel J | Pask, Andrew J | Forrest, Susan M | Worley, Kim C
Genome Biology  2011;12(8):R81.
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.
doi:10.1186/gb-2011-12-8-r81
PMCID: PMC3277949  PMID: 21854559
4.  Novel venom gene discovery in the platypus 
Genome Biology  2010;11(9):R95.
Background
To date, few peptides in the complex mixture of platypus venom have been identified and sequenced, in part due to the limited amounts of platypus venom available to study. We have constructed and sequenced a cDNA library from an active platypus venom gland to identify the remaining components.
Results
We identified 83 novel putative platypus venom genes from 13 toxin families, which are homologous to known toxins from a wide range of vertebrates (fish, reptiles, insectivores) and invertebrates (spiders, sea anemones, starfish). A number of these are expressed in tissues other than the venom gland, and at least three of these families (those with homology to toxins from distant invertebrates) may play non-toxin roles. Thus, further functional testing is required to confirm venom activity. However, the presence of similar putative toxins in such widely divergent species provides further evidence for the hypothesis that there are certain protein families that are selected preferentially during evolution to become venom peptides. We have also used homology with known proteins to speculate on the contributions of each venom component to the symptoms of platypus envenomation.
Conclusions
This study represents a step towards fully characterizing the first mammal venom transcriptome. We have found similarities between putative platypus toxins and those of a number of unrelated species, providing insight into the evolution of mammalian venom.
doi:10.1186/gb-2010-11-9-r95
PMCID: PMC2965387  PMID: 20920228
5.  MHC-linked and un-linked class I genes in the wallaby 
BMC Genomics  2009;10:310.
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.
doi:10.1186/1471-2164-10-310
PMCID: PMC2719672  PMID: 19602235
6.  In silico identification of opossum cytokine genes suggests the complexity of the marsupial immune system rivals that of eutherian mammals 
Immunome Research  2006;2:4.
Background
Cytokines are small proteins that regulate immunity in vertebrate species. Marsupial and eutherian mammals last shared a common ancestor more than 180 million years ago, so it is not surprising that attempts to isolate many key marsupial cytokines using traditional laboratory techniques have been unsuccessful. This paucity of molecular data has led some authors to suggest that the marsupial immune system is 'primitive' and not on par with the sophisticated immune system of eutherian (placental) mammals.
Results
The sequencing of the first marsupial genome has allowed us to identify highly divergent immune genes. We used gene prediction methods that incorporate the identification of gene location using BLAST, SYNTENY + BLAST and HMMER to identify 23 key marsupial immune genes, including IFN-γ, IL-2, IL-4, IL-6, IL-12 and IL-13, in the genome of the grey short-tailed opossum (Monodelphis domestica). Many of these genes were not predicted in the publicly available automated annotations.
Conclusion
The power of this approach was demonstrated by the identification of orthologous cytokines between marsupials and eutherians that share only 30% identity at the amino acid level. Furthermore, the presence of key immunological genes suggests that marsupials do indeed possess a sophisticated immune system, whose function may parallel that of eutherian mammals.
doi:10.1186/1745-7580-2-4
PMCID: PMC1660534  PMID: 17094811
7.  Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development 
Renfree, Marilyn B | Papenfuss, Anthony T | Deakin, Janine E | Lindsay, James | Heider, Thomas | Belov, Katherine | Rens, Willem | Waters, Paul D | Pharo, Elizabeth A | Shaw, Geoff | Wong, Emily SW | Lefèvre, Christophe M | Nicholas, Kevin R | Kuroki, Yoko | Wakefield, Matthew J | Zenger, Kyall R | Wang, Chenwei | Ferguson-Smith, Malcolm | Nicholas, Frank W | Hickford, Danielle | Yu, Hongshi | Short, Kirsty R | Siddle, Hannah V | Frankenberg, Stephen R | Chew, Keng Y | Menzies, Brandon R | Stringer, Jessica M | Suzuki, Shunsuke | Hore, Timothy A | Delbridge, Margaret L | Patel, Hardip | Mohammadi, Amir | Schneider, Nanette Y | Hu, Yanqiu | O'Hara, William | Al Nadaf, Shafagh | Wu, Chen | Feng, Zhi-Ping | Cocks, Benjamin G | Wang, Jianghui | Flicek, Paul | Searle, Stephen MJ | Fairley, Susan | Beal, Kathryn | Herrero, Javier | Carone, Dawn M | Suzuki, Yutaka | Sugano, Sumio | Toyoda, Atsushi | Sakaki, Yoshiyuki | Kondo, Shinji | Nishida, Yuichiro | Tatsumoto, Shoji | Mandiou, Ion | Hsu, Arthur | McColl, Kaighin A | Lansdell, Benjamin | Weinstock, George | Kuczek, Elizabeth | McGrath, Annette | Wilson, Peter | Men, Artem | Hazar-Rethinam, Mehlika | Hall, Allison | Davis, John | Wood, David | Williams, Sarah | Sundaravadanam, Yogi | Muzny, Donna M | Jhangiani, Shalini N | Lewis, Lora R | Morgan, Margaret B | Okwuonu, Geoffrey O | Ruiz, San J | Santibanez, Jireh | Nazareth, Lynne | Cree, Andrew | Fowler, Gerald | Kovar, Christie L | Dinh, Huyen H | Joshi, Vandita | Jing, Chyn | Lara, Fremiet | Thornton, Rebecca | Chen, Lei | Deng, Jixin | Liu, Yue | Shen, Joshua Y | Song, Xing-Zhi | Edson, Janette | Troon, Carmen | Thomas, Daniel | Stephens, Amber | Yapa, Lankesha | Levchenko, Tanya | Gibbs, Richard A | Cooper, Desmond W | Speed, Terence P | Fujiyama, Asao | M Graves, Jennifer A | O'Neill, Rachel J | Pask, Andrew J | Forrest, Susan M | Worley, Kim C
Genome Biology  2011;12(12):414.
doi:10.1186/gb-2011-12-12-414
PMCID: PMC3334613

Results 1-7 (7)