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    The immune gene repertoire of an important viral reservoir, the Australian black flying fox
    Papenfuss, AT ; Baker, ML ; Feng, Z-P ; Tachedjian, M ; Crameri, G ; Cowled, C ; Ng, J ; Janardhana, V ; Field, HE ; Wang, L-F (BMC, 2012-06-20)
    BACKGROUND: Bats are the natural reservoir host for a range of emerging and re-emerging viruses, including SARS-like coronaviruses, Ebola viruses, henipaviruses and Rabies viruses. However, the mechanisms responsible for the control of viral replication in bats are not understood and there is little information available on any aspect of antiviral immunity in bats. Massively parallel sequencing of the bat transcriptome provides the opportunity for rapid gene discovery. Although the genomes of one megabat and one microbat have now been sequenced to low coverage, no transcriptomic datasets have been reported from any bat species. In this study, we describe the immune transcriptome of the Australian flying fox, Pteropus alecto, providing an important resource for identification of genes involved in a range of activities including antiviral immunity. RESULTS: Towards understanding the adaptations that have allowed bats to coexist with viruses, we have de novo assembled transcriptome sequence from immune tissues and stimulated cells from P. alecto. We identified about 18,600 genes involved in a broad range of activities with the most highly expressed genes involved in cell growth and maintenance, enzyme activity, cellular components and metabolism and energy pathways. 3.5% of the bat transcribed genes corresponded to immune genes and a total of about 500 immune genes were identified, providing an overview of both innate and adaptive immunity. A small proportion of transcripts found no match with annotated sequences in any of the public databases and may represent bat-specific transcripts. CONCLUSIONS: This study represents the first reported bat transcriptome dataset and provides a survey of expressed bat genes that complement existing bat genomic data. In addition, these data provide insight into genes relevant to the antiviral responses of bats, and form a basis for examining the roles of these molecules in immune response to viral infection.
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    Evolution of coding and non-coding genes in HOX clusters of a marsupial
    Yu, H ; Lindsay, J ; Feng, Z-P ; Frankenberg, S ; Hu, Y ; Carone, D ; Shaw, G ; Pask, AJ ; O'Neill, R ; Papenfuss, AT ; Renfree, MB (BMC, 2012-06-18)
    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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    Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer
    Murchison, EP ; Schulz-Trieglaff, OB ; Ning, Z ; Alexandrov, LB ; Bauer, MJ ; Fu, B ; Hims, M ; Ding, Z ; Ivakhno, S ; Stewart, C ; Ng, BL ; Wong, W ; Aken, B ; White, S ; Alsop, A ; Becq, J ; Bignell, GR ; Cheetham, RK ; Cheng, W ; Connor, TR ; Cox, AJ ; Feng, Z-P ; Gu, Y ; Grocock, RJ ; Harris, SR ; Khrebtukova, I ; Kingsbury, Z ; Kowarsky, M ; Kreiss, A ; Luo, S ; Marshall, J ; McBride, DJ ; Murray, L ; Pearse, A-M ; Raine, K ; Rasolonjatovo, I ; Shaw, R ; Tedder, P ; Tregidgo, C ; Vilella, AJ ; Wedge, DC ; Woods, GM ; Gormley, N ; Humphray, S ; Schroth, G ; Smith, G ; Hall, K ; Searle, SMJ ; Carter, NP ; Papenfuss, AT ; Futreal, PA ; Campbell, PJ ; Yang, F ; Bentley, DR ; Evers, DJ ; Stratton, MR (CELL PRESS, 2012-02-17)
    The Tasmanian devil (Sarcophilus harrisii), the largest marsupial carnivore, is endangered due to a transmissible facial cancer spread by direct transfer of living cancer cells through biting. Here we describe the sequencing, assembly, and annotation of the Tasmanian devil genome and whole-genome sequences for two geographically distant subclones of the cancer. Genomic analysis suggests that the cancer first arose from a female Tasmanian devil and that the clone has subsequently genetically diverged during its spread across Tasmania. The devil cancer genome contains more than 17,000 somatic base substitution mutations and bears the imprint of a distinct mutational process. Genotyping of somatic mutations in 104 geographically and temporally distributed Tasmanian devil tumors reveals the pattern of evolution and spread of this parasitic clonal lineage, with evidence of a selective sweep in one geographical area and persistence of parallel lineages in other populations.
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    Marsupials and monotremes possess a novel family of MHC class I genes that is lost from the eutherian lineage
    Papenfuss, AT ; Feng, Z-P ; Krasnec, K ; Deakin, JE ; Baker, ML ; Miller, RD (BMC, 2015-07-22)
    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.
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    Differences in PfEMP1s recognized by antibodies from patients with uncomplicated or severe malaria
    Duffy, MF ; Noviyanti, R ; Tsuboi, T ; Feng, Z-P ; Trianty, L ; Sebayang, BF ; Takashima, E ; Sumardy, F ; Lampah, DA ; Turner, L ; Lavstsen, T ; Fowkes, FJI ; Siba, P ; Rogerson, SJ ; Theander, TG ; Marfurt, J ; Price, RN ; Anstey, NM ; Brown, GV ; Papenfuss, AT (BIOMED CENTRAL LTD, 2016-05-05)
    BACKGROUND: Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) variants are encoded by var genes and mediate pathogenic cytoadhesion and antigenic variation in malaria. PfEMP1s can be broadly divided into three principal groups (A, B and C) and they contain conserved arrangements of functional domains called domain cassettes. Despite their tremendous diversity there is compelling evidence that a restricted subset of PfEMP1s is expressed in severe disease. In this study antibodies from patients with severe and uncomplicated malaria were compared for differences in reactivity with a range of PfEMP1s to determine whether antibodies to particular PfEMP1 domains were associated with severe or uncomplicated malaria. METHODS: Parts of expressed var genes in a severe malaria patient were identified by RNAseq and several of these partial PfEMP1 domains were expressed together with others from laboratory isolates. Antibodies from Papuan patients to these parts of multiple PfEMP1 proteins were measured. RESULTS: Patients with uncomplicated malaria were more likely to have antibodies that recognized PfEMP1 of Group C type and recognized a broader repertoire of group A and B PfEMP1s than patients with severe malaria. CONCLUSION: These data suggest that exposure to a broad range of group A and B PfEMP1s is associated with protection from severe disease in Papua, Indonesia.
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    Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
    Renfree, MB ; Papenfuss, AT ; Deakin, JE ; Lindsay, J ; Heider, T ; Belov, K ; Rens, W ; Waters, PD ; Pharo, EA ; Shaw, G ; Swwong, E ; Lefevre, 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, Z-P ; 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, X-Z ; Edson, J ; Troon, C ; Thomas, D ; Stephens, A ; Yapa, L ; Levchenko, T ; Gibbs, RA ; Cooper, DW ; Speed, TP ; Fujiyama, A ; Graves, JAM ; O'Neill, RJ ; Pask, AJ ; Forrest, SM ; Worley, KC (BMC, 2011-01-01)
    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.