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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 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.