Research
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
- † Equal contributors
1 The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
2 Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
3 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
4 Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria 3010, Australia
5 Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
6 Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
7 Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
8 Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge, CB3 0ES, UK
9 Institute for Technology Research and Innovation, Deakin University, Geelong, Victoria, 3214, Australia
10 RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
11 School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia
12 Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria 3010, Australia
13 Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
14 Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge, CB22 3AT, UK
15 Department of Molecular Genetics, German Institute of Human Nutrition, Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
16 Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3010, Australia
17 Biosciences Research Division, Department of Primary Industries, Victoria, 1 Park Drive, Bundoora 3083, Australia
18 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
19 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
20 Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
21 Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8560, Japan
22 National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
23 Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
24 Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
25 Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
26 Westmead Institute for Cancer Research, University of Sydney, Westmead, New South Wales 2145, Australia
27 National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan
28 Department of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
Genome Biology 2011, 12:R81 doi:10.1186/gb-2011-12-8-r81
Published: 19 August 2011Abstract
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.
