24 research outputs found
Speciation generates mosaic genomes in kangaroos
No full textThe iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary relationship within the two genera, Macropus and Wallabia, is controversial: mitochondrial and nuclear genes, and morphological data have produced conflicting scenarios regarding the phylogenetic relationships, which in turn impact the classification and taxonomy. We sequenced and analyzed the genomes of 11 kangaroos to investigate the evolutionary cause of the observed phylogenetic conflict. A multilocus coalescent analysis using ∼14,900 genome fragments, each 10 kb long, significantly resolved the species relationships between and among the sister-genera Macropus and Wallabia. The phylogenomic approach reconstructed the swamp wallaby (Wallabia) as nested inside Macropus, making this genus paraphyletic. However, the phylogenomic analyses indicate multiple conflicting phylogenetic signals in the swamp wallaby genome. This is interpreted as at least one introgression event between the ancestor of the genus Wallabia and a now extinct ghost lineage outside the genus Macropus. Additional phylogenetic signals must therefore be caused by incomplete lineage sorting and/or introgression, but available statistical methods cannot convincingly disentangle the two processes. In addition, the relationships inside the Macropus subgenus M. (Notamacropus) represent a hard polytomy. Thus, the relationships between tammar, red-necked, agile, and parma wallabies remain unresolvable even with whole-genome data. Even if most methods resolve bifurcating trees from genomic data, hard polytomies, incomplete lineage sorting, and introgression complicate the interpretation of the phylogeny and thus taxonomy
DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons)
No full textGenome sequencing and analysis of the model grass Brachypodium distachyon
No full textKirjoittajalista kokonaisuudessaan: Principal investigators John P. Vogel, David F. Garvin, Todd C. Mockler, Jeremy Schmutz, Dan Rokhsar, Michael W. Bevan; DNA sequencing and assembly Kerrie Barry, Susan Lucas, Miranda Harmon-Smith, Kathleen Lail, Hope Tice, Jeremy Schmutz (Leader), Jane Grimwood, Neil McKenzie, Michael W. Bevan; Pseudomolecule assembly and BACend sequencing NaxinHuo, Yong Q.Gu,GerardR. Lazo, OlinD.Anderson, John P. Vogel (Leader), Frank M. You,Ming-Cheng Luo, Jan Dvorak, Jonathan Wright, Melanie Febrer, Michael W. Bevan, Dominika Idziak, Robert Hasterok, David F. Garvin; Transcriptome sequencing and analysis Erika Lindquist, Mei Wang, Samuel E. Fox, Henry D. Priest, Sergei A. Filichkin, Scott A. Givan, Douglas W. Bryant, JeffH.Chang, ToddC.Mockler (Leader), HaiyanWu, Wei Wu, An-Ping Hsia, Patrick S. Schnable, Anantharaman Kalyanaraman, Brad Barbazuk, Todd P.Michael, Samuel P.Hazen, JenniferN. Bragg, Debbie Laudencia-Chingcuanco, John P. Vogel, David F. Garvin, Yiqun Weng, Neil McKenzie, Michael W. Bevan; Gene analysis and annotation Georg Haberer, Manuel Spannagl, Klaus Mayer (Leader), Thomas Rattei, ThereseMitros, Dan Rokhsar, Sang-Jik Lee, Jocelyn K. C. Rose, Lukas A. Mueller, Thomas L. York; Repeats analysis Thomas Wicker (Leader), Jan P. Buchmann, Jaakko Tanskanen, Alan H. Schulman (Leader), Heidrun Gundlach, Jonathan Wright, Michael Bevan, Antonio Costa de Oliveira, Luciano da C. Maia, William Belknap, Yong Q. Gu, Ning Jiang, Jinsheng Lai, Liucun Zhu, JianxinMa, Cheng Sun, Ellen Pritham; Comparative genomics Jerome Salse (Leader), Florent Murat, Michael Abrouk, Georg Haberer, Manuel Spannagl, Klaus Mayer, Remy Bruggmann, Joachim Messing, Frank M. You, Ming-Cheng Luo, Jan Dvorak; Small RNA analysis Noah Fahlgren, Samuel E. Fox, Christopher M. Sullivan, Todd C. Mockler, James C. Carrington, Elisabeth J. Chapman, Greg D.May, Jixian Zhai, Matthias Ganssmann, Sai Guna Ranjan Gurazada, Marcelo German, Blake C. Meyers, Pamela J. Green (Leader); Manual annotation and gene family analysis Jennifer N. Bragg, Ludmila Tyler, Jiajie Wu, Yong Q. Gu, Gerard R. Lazo, Debbie Laudencia-Chingcuanco, James Thomson, John P. Vogel (Leader), Samuel P. Hazen, Shan Chen, Henrik V. Scheller, JesperHarholt, Peter Ulvskov, Samuel E. Fox, Sergei A. Filichkin, Noah Fahlgren, Jeffrey A. Kimbrel, Jeff H. Chang, Christopher M. Sullivan, Elisabeth J. Chapman, James C. Carrington, Todd C. Mockler, Laura E. Bartley, Peijian Cao, Ki-Hong Jung, Manoj K Sharma, Miguel Vega-Sanchez, Pamela Ronald, Christopher D.Dardick, StefanieDe Bodt,Wim Verelst, Dirk Inze, Maren Heese, Arp Schnittger, Xiaohan Yang, Udaya C. Kalluri, GeraldA. Tuskan, ZhihuaHua, Richard D. Vierstra, David F. Garvin, Yu Cui, Shuhong Ouyang, Qixin Sun, Zhiyong Liu, Alper Yilmaz, Erich Grotewold, Richard Sibout, Kian Hematy, Gregory Mouille, Herman Hofte, Todd Michael, JeŽrome Pelloux, Devin O Connor, James Schnable, Scott Rowe, Frank Harmon, Cynthia L. Cass, John C. Sedbrook, Mary E. Byrne, SeanWalsh, Janet Higgins, Michael Bevan, PinghuaLi, ThomasBrutnell, TurgayUnver,Hikmet Budak, Harry Belcram, Mathieu Charles, Boulos Chalhoub, Ivan Baxterv2010okBE
Rolling-circle transposons catalyze genomic innovation in a mammalian lineage
No full text© The Author(s) 2014. cc-by-ncRolling-circle transposons (Helitrons) are a newly discovered group ofmobileDNAwidespread in plant and invertebrate genomes but limited to thebat family Vespertilionidae amongmammals. Little is knownabout thelong-term impact of Helitron activity because the genomeswhere Helitron activity has been extensively studied are predominated by young families. Here,we report a comprehensive catalog of vetted Helitrons from the 7× Myotis lucifugus genome assembly. To estimate the timing of transposition, we scored presence/absence across related vespertilionid genome sequences with estimated divergence times. This analysis revealed that the Helibat family has been a persistent source of genomic innovation throughout the vespertilionid diversification from approximately 30-36 Ma to as recently as approximately 1.8-6 Ma. This is the first report of persistent Helitron transposition over an extended evolutionary timeframe. These findings illustrate that the pattern of Helitron activity is akin to the vertical persistence of LINE retrotransposons in primates and other mammalian lineages. Like retrotransposition in primates, rolling-circle transposition has generated lineage-specific variation and accounts for approximately 110 Mb, approximately 6%of the genome of M. lucifugus. The Helitrons carry a heterogeneous assortment of host sequence including retroposed messenger RNAs, retrotransposons, DNA transposons, as well as introns, exons and regulatory regions (promoters, 50-untranslated regions [UTRs], and 30-UTRs) of which some are evolving in a pattern suggestive of purifying selection. Evidence that Helitrons have contributed putative promoters, exons, splice sites, polyadenylation sites, and microRNA-binding sites to transcripts otherwise conserved across mammals is presented, and the implication of Helitron activity to innovation in these unique mammals is discussed
