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

      research-article
      Author(s): 1 , 2 , , 1 , 3 , 4 , ,   1 , 5 , 6 , 6 , 1 , 7 , 8 , 1 , 5 , 2 , 1 , 2 , 1 , 7 , 9 , 9 , 10 , 1 , 3 , 1 , 7 , 11 , 1 , 7 , 8 , 7 , 1 , 2 , 1 , 2 , 12 , 1 , 7 , 1 , 2 , 1 , 2 , 1 , 2 , 13 , 1 , 2 , 1 , 2 , 1 , 14 , 1 , 5 , 1 , 5 , 1 , 2 , 15 , 1 , 2 , 6 , 1 , 5 , 7 , 3 , 16 , 17 , 17 , 18 , 19 ,   19 , 18 , 18 , 6 , 20 , 21 , 21 , 22 , 10 , 10 , 10 , 10 , 23 , 3 , 16 , 3 , 3 , 24 , 1 , 25 , 26 , 25 , 25 , 25 , 25 , 25 , 25 , 25 , 25 , 25 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 24 , 25 , 25 , 25 , 25 , 25 , 25 , 24 , 1 , 28 , 1 , 3 , 22 , 27 , 1 , 5 , 6 , 1 , 2 , 6 , 1 , 25 , 24
      Publication date (Electronic):
      Journal: Genome Biology
      Publisher: BioMed Central

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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.

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          Most cited references143

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          The delayed rise of present-day mammals.

          Olaf Bininda-Emonds, Marcel Cardillo, Kate E. Jones … (2007)
          Did the end-Cretaceous mass extinction event, by eliminating non-avian dinosaurs and most of the existing fauna, trigger the evolutionary radiation of present-day mammals? Here we construct, date and analyse a species-level phylogeny of nearly all extant Mammalia to bring a new perspective to this question. Our analyses of how extant lineages accumulated through time show that net per-lineage diversification rates barely changed across the Cretaceous/Tertiary boundary. Instead, these rates spiked significantly with the origins of the currently recognized placental superorders and orders approximately 93 million years ago, before falling and remaining low until accelerating again throughout the Eocene and Oligocene epochs. Our results show that the phylogenetic 'fuses' leading to the explosion of extant placental orders are not only very much longer than suspected previously, but also challenge the hypothesis that the end-Cretaceous mass extinction event had a major, direct influence on the diversification of today's mammals.
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            Human-mouse alignments with BLASTZ.

            Scott Schwartz, W. Kent, Arian Smit … (2003)
            The Mouse Genome Analysis Consortium aligned the human and mouse genome sequences for a variety of purposes, using alignment programs that suited the various needs. For investigating issues regarding genome evolution, a particularly sensitive method was needed to permit alignment of a large proportion of the neutrally evolving regions. We selected a program called BLASTZ, an independent implementation of the Gapped BLAST algorithm specifically designed for aligning two long genomic sequences. BLASTZ was subsequently modified, both to attain efficiency adequate for aligning entire mammalian genomes and to increase its sensitivity. This work describes BLASTZ, its modifications, the hardware environment on which we run it, and several empirical studies to validate its results.
            Article 0 comments Cited 467 times – based on 0 reviews     Review now
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              Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes.

              Toshiaki Watanabe, Yasushi Totoki, Atsushi Toyoda … (2008)
              RNA interference (RNAi) is a mechanism by which double-stranded RNAs (dsRNAs) suppress specific transcripts in a sequence-dependent manner. dsRNAs are processed by Dicer to 21-24-nucleotide small interfering RNAs (siRNAs) and then incorporated into the argonaute (Ago) proteins. Gene regulation by endogenous siRNAs has been observed only in organisms possessing RNA-dependent RNA polymerase (RdRP). In mammals, where no RdRP activity has been found, biogenesis and function of endogenous siRNAs remain largely unknown. Here we show, using mouse oocytes, that endogenous siRNAs are derived from naturally occurring dsRNAs and have roles in the regulation of gene expression. By means of deep sequencing, we identify a large number of both approximately 25-27-nucleotide Piwi-interacting RNAs (piRNAs) and approximately 21-nucleotide siRNAs corresponding to messenger RNAs or retrotransposons in growing oocytes. piRNAs are bound to Mili and have a role in the regulation of retrotransposons. siRNAs are exclusively mapped to retrotransposons or other genomic regions that produce transcripts capable of forming dsRNA structures. Inverted repeat structures, bidirectional transcription and antisense transcripts from various loci are sources of the dsRNAs. Some precursor transcripts of siRNAs are derived from expressed pseudogenes, indicating that one role of pseudogenes is to adjust the level of the founding source mRNA through RNAi. Loss of Dicer or Ago2 results in decreased levels of siRNAs and increased levels of retrotransposon and protein-coding transcripts complementary to the siRNAs. Thus, the RNAi pathway regulates both protein-coding transcripts and retrotransposons in mouse oocytes. Our results reveal a role for endogenous siRNAs in mammalian oocytes and show that organisms lacking RdRP activity can produce functional endogenous siRNAs from naturally occurring dsRNAs.
              Article 0 comments Cited 343 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2011
                Publication date (Electronic): 19 August 2011
                Volume: 12
                Issue: 8
                Page: R81
                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
                Article
                Publisher ID: gb-2011-12-8-r81
                DOI: 10.1186/gb-2011-12-8-r81
                PMC ID: 3277949
                PubMed ID: 21854559
                SO-VID: a841473c-9ed9-43a2-8bcf-3a4a9c40f8e3
                Copyright © Copyright ©2011 Renfree et al.; licensee BioMed Central Ltd.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 23 May 2011
                Date revision received : 22 July 2011
                Date accepted : 19 August 2011
                Categories
                Subject: Research

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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