Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

M. B. Renfree, Anthony Papenfuss, Janine DEAKIN, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul Waters, Elizabeth Pharo, Geoff Shaw, Emily Wong, Christophe Lefevre, Kevin R. Nicholas, Yoko Kuroki, Matthew Wakefield, Kyall Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank Nicholas, Danielle Hickford & 83 others Hongshi Yu, Kirsty R. Short, Hannah Siddle, Stephen Frankenberg, Keng Chew, Brandon Menzies, Jessica Stringer, Shunsuke Suzuki, Timothy Hore, Margaret L. Delbridge, Amir Mohammadi, Nanette Schneider, Yanqiu Hu, William O'Hara, Shafagh Nadaf, Chen Wu, Zhi-Ping Feng, Benjamin Cocks, Jianghui Wang, Paul Flicek, Stephen Searle, Susan Fairley, Kathryn Beal, Javier Herrero, Dawn Carone, Yutaka Suzuki, Sumio Sugano, Atsushi Toyoda, Yoshiyuki Sakaki, Shinji Kondo, Yuichiro Nishida, Shoji Tatsumoto, Ion Mandiou, Arthur Hsu, Kaighin McColl, Benjamin Lansdell, George Weinstock, Elizabeth Kuczek, Annette McGrath, Peter Wilson, Artem Men, Mehlika Hazar-Rethinam, Allison Hall, John Davis, David Wood, Sarah Williams, Yogi Sundaravadanam, Donna Muzny, Shalini Jhangiani, Lora Lewis, Margaret Morgan, Geoffrey Okwuonu, San Ruiz, Jireh Santibanez, Lynne Nazareth, Andrew Cree, Gerald Fowler, Christie Kovar, Huyen Dinh, Vandita Joshi, Chyn Jing, Fremiet Lara, Rebecca Thornton, Lei Chen, Jixin Deng, Yue Liu, Joshua Shen, Xing-Zhi Song, Janette Edson, Carmen Troon, Daniel Thomas, Amber Stephens, Lankesha Yapa, Tanya Levchenko, Richard A. Gibbs, Desmond Cooper, Terence Speed, Asao Fujiyama, Jennifer A Marshall Graves, Rachel O’Neill, Andrew Pask, Susan Forrest, Kim Worley

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Abstract

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.
Original languageEnglish
Pages (from-to)1-25
Number of pages25
JournalGenome Biology
Volume12:R81
DOIs
Publication statusPublished - 2011
Externally publishedYes

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