@article{Renfree2011, 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.}, author = {Renfree, Marilyn B. and Mb, Renfree and Papenfuss, Anthony T. and Je, Deakin and Deakin, Janine E. and Lindsay, James and Pd, Waters and Kr, Nicholas and Heider, Thomas and Belov, Katherine and Rens, Willem and Waters, Paul D. and Mj, Wakefield and Pharo, Elizabeth A. and Shaw, Geoff and Wong, Emily Sw W. and Kr, Zenger and Lefevre, Christophe M. and Nicholas, Kevin R. and Toyoda,Atsushi, and Kr, Short and Wakefield, Matthew J. and Zenger, Kyall R. and Hv, Siddle and Wang, Chenwei and Sr, Frankenberg and Ferguson-Smith, Malcolm and Nicholas, Frank W. and Kuroki, Yuko and Hickford, Danielle and Ky, Chew and Yu, Hongshi and Short, Kirsty R. and Jm, Stringer and Siddle, Hannah V. and Ta, Hore and Frankenberg, Stephen R. and Chew, Keng Yih and Menzies, Brandon R. and Ml, Delbridge and Stringer, Jessica M. and Suzuki, Shunsuke and Hore, Timothy A. and Delbridge, Margaret L. and Ny, Schneider and Patel, Hardip R. and Mohammadi, Amir and Schneider, Nanette Y. and Sm, Searle and Hu, Yanqiu and Nadaf, Shafagh Al and O'Hara, William and Wu, Chen and Al Nadaf, Shafagh and Ka, McColl and Feng, Zhi-Ping and Cocks, Benjamin G. and Wang, Jianghui and Sn, Jhangiani and Flicek, Paul and Searle, Stephen Mj J. and Fairley, Susan and Beal, Kathryn and Herrero, Javier and Suzuki, Yutaka and Carone, Dawn M. and Lef?vre, Christophe M. and Sugano, Sumio and Toyoda, Atsushi and Sakaki, Yoshiyuki and Lr, Lewis and Kondo, Shinji and Nishida, Yuichiro and Tatsumoto, Shoji and Mb, Morgan and Mandiou, Ion and Wood, Dav and Hsu, Arthur and McColl, Kaighin A. and Lansdell, Benjamin and Sj, Ruiz and Weinstock, George and Kuczek, Elizabeth and Hh, Dinh and McGrath, Annette and Wilson, Peter and Men, Artem and Jy, Shen and Ra, Gibbs and Hall, Allison and Tp, Speed and Davis, John and Williams, Sarah and Ja, M. Graves and Sundaravadanam, Yogi and Muzny, Donna M. and Rj, O'Neill and Jhangiani, Shalini N. and Hazar-Rethinam, Mehlike and Sm, Forrest and Lewis, Lora R. and Kc, Worley and Morgan, Margaret B. and Okwuonu, Geoffrey O. and At, Papenfuss and Ruiz, San Juana and Santibanez, Jireh and Nazareth, Lynne and Cree, Andrew and Ea, Pharo and Fowler, Gerald and Kovar, Christie L. and Dinh, Huyen H. and Es, Wong and Joshi, Vandita and Jing, Chyn and Lara, Fremiet and Cm, Lef?vre and Thornton, Rebecca and Fw, Nicholas and Chen, Lei and Br, Menzies and Deng, Jixin and Liu, Yue and Shen, Joshua Y. and Song, Xing-Zhi and Edson, Janette and Bg, Cocks and Troon, Carmen and Thomas, Daniel and Dm, Carone and Stephens, Amber and Yapa, Lankesha and Dm, Muzny and Levchenko, Tanya and Go, Okwuonu and Gibbs, Richard A. and Cooper, Desmond W. and Speed, Terence P. and Cl, Kovar and Fujiyama, Asao and M. Graves, Jennifer A. and O'Neill, Rachel J. and Graves, Jennifer A. M. and Pask, Andrew J. and Dw, Cooper and Aj, Pask and Forrest, Susan M. and Worley, Kim C.}, doi = {10.1186/gb-2011-12-8-r81}, journal = {Genome Biology}, month = {jan}, pages = {R81}, title = {Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development}, url = {http://dx.doi.org/10.1186/gb-2011-12-8-r81}, volume = {12}, year = {2011} }