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      Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae

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          Abstract

          Sex chromosomes in plants and animals and fungal mating-type chromosomes often show exceptional genome features, with extensive suppression of homologous recombination and cytological differentiation between members of the diploid chromosome pair. Despite strong interest in the genetics of these chromosomes, their large regions of suppressed recombination often are enriched in transposable elements and therefore can be challenging to assemble. Here we show that the latest improvements of the PacBio sequencing yield assembly of the whole genome of the anther-smut fungus, Microbotryum lychnidis-dioicae (the pathogenic fungus causing anther-smut disease of Silene latifolia), into finished chromosomes or chromosome arms, even for the repeat-rich mating-type chromosomes and centromeres. Suppressed recombination of the mating-type chromosomes is revealed to span nearly 90% of their lengths, with extreme levels of rearrangements, transposable element accumulation, and differentiation between the two mating types. We observed no correlation between allelic divergence and physical position in the nonrecombining regions of the mating-type chromosomes. This may result from gene conversion or from rearrangements of ancient evolutionary strata, i.e., successive steps of suppressed recombination. Centromeres were found to be composed mainly of copia-like transposable elements and to possess specific minisatellite repeats identical between the different chromosomes. We also identified subtelomeric motifs. In addition, extensive signs of degeneration were detected in the nonrecombining regions in the form of transposable element accumulation and of hundreds of gene losses on each mating-type chromosome. Furthermore, our study highlights the potential of the latest breakthrough PacBio chemistry to resolve complex genome architectures.

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          Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration.

          The human Y chromosome is intriguing not only because it harbours the master-switch gene that determines gender but also because of its unusual evolutionary history. The Y chromosome evolved from an autosome, and its evolution has been characterized by massive gene decay. Recent whole-genome and transcriptome analyses of Y chromosomes in humans and other primates, in Drosophila species and in plants have shed light on the current gene content of the Y chromosome, its origins and its long-term fate. Furthermore, comparative analysis of young and old Y chromosomes has given further insights into the evolutionary and molecular forces triggering Y-chromosome degeneration and into the evolutionary destiny of the Y chromosome.
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            The Ectocarpus genome and the independent evolution of multicellularity in brown algae.

            Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further.
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                Author and article information

                Journal
                Genetics
                Genetics
                genetics
                genetics
                genetics
                Genetics
                Genetics Society of America
                0016-6731
                1943-2631
                August 2015
                03 June 2015
                03 June 2015
                : 200
                : 4
                : 1275-1284
                Affiliations
                [* ]Ecologie, Systématique et Evolution, Univ Paris-Sud, 91405 Orsay, France
                []Centre National de la Recherche Scientifique, F-91405 Orsay, France
                []Department of Biology, Amherst College, Amherst, Massachusetts 02142
                [§ ]INRA, Laboratoire des Interactions Plantes-Microorganismes, 31326 Castanet-Tolosan, France
                [** ]Centre National de la Recherche Scientifique, Laboratoire des Interactions Plantes-Microorganismes, 31326 Castanet-Tolosan, France
                [†† ]Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, Kentucky 40292
                [‡‡ ]Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
                [§§ ]Institut de Génétique et Microbiologie, Université Paris-Sud, F-91405 Orsay cedex, France
                Author notes
                [1]

                These authors contributed equally to this work.

                [2 ]Corresponding author: Laboratoire Ecologie, Systématique et Evolution, Bâtiment 360, Université de Paris-Sud, 91405 Orsay cedex, France. E-mail: tatiana.giraud@ 123456u-psud.fr
                Author information
                http://orcid.org/0000-0002-2456-5968
                http://orcid.org/0000-0002-5778-960X
                Article
                177709
                10.1534/genetics.115.177709
                4574255
                26044594
                a0fe9074-b1b7-411d-96cf-7e780e6c6f0e
                Copyright © 2015 by the Genetics Society of America

                Available freely online through the author-supported open access option.

                History
                : 02 May 2015
                : 02 June 2015
                Page count
                Pages: 10
                Categories
                Investigations
                Population and Evolutionary Genetics

                Genetics
                microbotryum violaceum,finished genome assembly,intratetrad mating,mat,basidiomycete,selfing,bipolarity

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