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

Marilyn B Renfree12*, Anthony T Papenfuss134*, Janine E Deakin15, James Lindsay6, Thomas Heider6, Katherine Belov17, Willem Rens8, Paul D Waters15, Elizabeth A Pharo2, Geoff Shaw12, Emily SW Wong17, Christophe M Lefèvre9, Kevin R Nicholas9, Yoko Kuroki10, Matthew J Wakefield13, Kyall R Zenger1117, Chenwei Wang17, Malcolm Ferguson-Smith8, Frank W Nicholas7, Danielle Hickford12, Hongshi Yu12, Kirsty R Short12, Hannah V Siddle17, Stephen R Frankenberg12, Keng Yih Chew12, Brandon R Menzies1132, Jessica M Stringer12, Shunsuke Suzuki12, Timothy A Hore114, Margaret L Delbridge15, Amir Mohammadi15, Nanette Y Schneider1152, Yanqiu Hu12, William O'Hara6, Shafagh Al Nadaf15, Chen Wu7, Zhi-Ping Feng163, Benjamin G Cocks17, Jianghui Wang17, Paul Flicek18, Stephen MJ Searle19, Susan Fairley19, Kathryn Beal18, Javier Herrero18, Dawn M Carone206, Yutaka Suzuki21, Sumio Sugano21, Atsushi Toyoda22, Yoshiyuki Sakaki10, Shinji Kondo10, Yuichiro Nishida10, Shoji Tatsumoto10, Ion Mandiou23, Arthur Hsu163, Kaighin A McColl3, Benjamin Lansdell3, George Weinstock24, Elizabeth Kuczek12526, Annette McGrath25, Peter Wilson25, Artem Men25, Mehlika Hazar-Rethinam25, Allison Hall25, John Davis25, David Wood25, Sarah Williams25, Yogi Sundaravadanam25, Donna M Muzny24, Shalini N Jhangiani24, Lora R Lewis24, Margaret B Morgan24, Geoffrey O Okwuonu24, San Juana Ruiz24, Jireh Santibanez24, Lynne Nazareth24, Andrew Cree24, Gerald Fowler24, Christie L Kovar24, Huyen H Dinh24, Vandita Joshi24, Chyn Jing24, Fremiet Lara24, Rebecca Thornton24, Lei Chen24, Jixin Deng24, Yue Liu24, Joshua Y Shen24, Xing-Zhi Song24, Janette Edson25, Carmen Troon25, Daniel Thomas25, Amber Stephens25, Lankesha Yapa25, Tanya Levchenko25, Richard A Gibbs24, Desmond W Cooper128, Terence P Speed13, Asao Fujiyama2227, Jennifer A M Graves15, Rachel J O'Neill6, Andrew J Pask126, Susan M Forrest125 and Kim C Worley24

Author Affiliations

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

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Genome Biology 2011, 12:R81  doi:10.1186/gb-2011-12-8-r81

Published: 19 August 2011

Additional files

Additional file 1:

Supplementary material. Supplementary materials and methods, results and tables [39,42,46,47,58,74,164-192].

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Additional file 2:

Figure S1 - comparison of gene sizes in Monodelphis domestica and Macropus eugenii. One-to-one opossum orthologues of tammar genes located more than 1 kb from the end of a scaffold were downloaded from Ensembl v62. The genomic lengths of the genes are plotted as a scatter plot on the log2 scale. A 1:1 linear relationship between gene sizes is present for genes less than the average scaffold size, suggesting that no major change in genome size has occurred in genic regions. A trend towards larger genes in opossum with log2 length > 15 is driven primarily by incompleteness of tammar genes when the gene size is larger than the average scaffold size.

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Additional file 3:

Figure S2 - analysis of the alignment of transcriptomic reads from different tissues to the tammar genome. (a) Proportion of reads that align to unannotated regions, annotated genes, within 2 kb upstream or downstream of a gene, or fail to align to the tammar genome. (b) Proportion of mapped reads that align to unannotated regions, annotated genes, or within 2 kb upstream or downstream of a gene in the tammar genome.

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Additional file 4:

Figure S3 - Comparative analysis of the mammalian casein locus showing the expansion of the casein locus in mammals. Comparison of the casein locus organization in the platypus, tammar, opossum, cattle, mouse and human genomes. Drawn to scale and aligned on the β-casein gene. Genes are represented by a box with a tail arrow pointing in the direction of gene transcription. Gene models for confirmed genes were generated from mammary gland EST data (platypus and tammar) or retrieved from Ensembl (others) when available. The tammar locus is not fully resolved and sequence scaffolds (indicated by black bars and scaffold numbers) have been aligned with the opossum sequence. Gaps in the tammar genome mainly fall in regions containing a repeated transposon type I in the opossum (black arrows), probably compounding the assembly of the tammar genome. Blank boxes represent putative genes based on similarity, grey boxes represent genes with observed expression. Note the close proximity of α- (CSN1, csna) and β- (CSN2, csnb) casein genes in reverse orientation on the left and the expansion of the region between β- and kappa- (CSN3, csnk) casein on the right. Except for β-casein, all genes are transcribed from left to right. In monotremes, a recent duplication of CSN2 has led to CSN2b, whereas in eutherians, an ancient duplication produced CSN1S2, which has been duplicated in some species to produce CSN1S2b, now a pseudogene in human but not in mouse. In the marsupial locus, there is no casein duplication and the spacing region contains several copies of an invading repetitive element (black arrows), suggesting active rearrangement of this region in the ancient marsupial lineage, probably resulting in the deletion of a putative ancient casein duplicate in the area.

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