Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
Authors: Renfree Marilyn B , Papenfuss Anthony T , Deakin Janine E , Lindsay James , Heider Thomas , Belov Katherine , Rens Willem , Waters Paul D , Pharo Elizabeth A , Shaw Geoff , Wong Emily SW , Lefèvre Christophe M , Nicholas Kevin R , Kuroki Yoko , Wakefield Matthew J , Zenger Kyall R , Wang Chenwei , Ferguson-Smith Malcolm , Nicholas Frank W , Hickford Danielle , Yu Hongshi , Short Kirsty R , Siddle Hannah V , Frankenberg Stephen R , Chew Keng Yih , Menzies Brandon R , Stringer Jessica M , Suzuki Shunsuke , Hore Timothy A , Delbridge Margaret L , Mohammadi Amir , Schneider Nanette Y , Hu Yanqiu , O'Hara William , Al Nadaf Shafagh , Wu Chen , Feng Zhi-Ping , Cocks Benjamin G , Wang Jianghui , Flicek Paul , Searle Stephen MJ , Fairley Susan , Beal Kathryn , Herrero Javier , Carone Dawn M , Suzuki Yutaka , Sugano Sumio , Toyoda Atsushi , Sakaki Yoshiyuki , Kondo Shinji , Nishida Yuichiro , Tatsumoto Shoji , Mandiou Ion , Hsu Arthur , McColl Kaighin A , Lansdell Benjamin , Weinstock George , Kuczek Elizabeth , McGrath Annette , Wilson Peter , Men Artem , Hazar-Rethinam Mehlika , Hall Allison , Davis John , Wood David , Williams Sarah , Sundaravadanam Yogi , Muzny Donna M , Jhangiani Shalini N , Lewis Lora R , Morgan Margaret B , Okwuonu Geoffrey O , Ruiz San Juana , Santibanez Jireh , Nazareth Lynne , Cree Andrew , Fowler Gerald , Kovar Christie L , Dinh Huyen H , Joshi Vandita , Jing Chyn , Lara Fremiet , Thornton Rebecca , Chen Lei , Deng Jixin , Liu Yue , Shen Joshua Y , Song Xing-Zhi , Edson Janette , Troon Carmen , Thomas Daniel , Stephens Amber , Yapa Lankesha , Levchenko Tanya , Gibbs Richard A , Cooper Desmond W , Speed Terence P , Fujiyama Asao , M Graves Jennifer A , O'Neill Rachel J , Pask Andrew J , Forrest Susan M , Worley Kim C 
Published: August 2011

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.