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      The asparagus genome sheds light on the origin and evolution of a young Y chromosome

      research-article
      1 , 25 , 2 , 3 , 1 , 4 , 1 , 5 , 6 , 7 , 26 , 8 , 9 , 10 , 11 , 1 , 12 , 10 , 27 , 8 , 10 , 8 , 10 , 13 , 1 , 14 , 15 , 3 , 3 , 3 , 3 , 3 , 2 , 2 , 16 , 17 , 18 , 19 , 20 , 21 , 21 , 8 , 10 , 16 , 17 , 13 , 4 , 5 , 7 , 22 , 3 , 23 , 24 , , 1 , , 2 ,
      Nature Communications
      Nature Publishing Group UK

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          Abstract

          Sex chromosomes evolved from autosomes many times across the eukaryote phylogeny. Several models have been proposed to explain this transition, some involving male and female sterility mutations linked in a region of suppressed recombination between X and Y (or Z/ W, U/ V) chromosomes. Comparative and experimental analysis of a reference genome assembly for a double haploid YY male garden asparagus ( Asparagus officinalis L.) individual implicates separate but linked genes as responsible for sex determination. Dioecy has evolved recently within Asparagus and sex chromosomes are cytogenetically identical with the Y, harboring a megabase segment that is missing from the X. We show that deletion of this entire region results in a male-to-female conversion, whereas loss of a single suppressor of female development drives male-to-hermaphrodite conversion. A single copy anther-specific gene with a male sterile Arabidopsis knockout phenotype is also in the Y-specific region, supporting a two-gene model for sex chromosome evolution.

          Abstract

          Several models have been proposed to explain the emergence of sex chromosomes. Here, through comparative genomics and mutant analysis, Harkess et al. show that linked but separate genes on the Y chromosome are responsible for sex determination in Asparagus, supporting a two-gene model for sex chromosome evolution.

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          Most cited references63

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            • Article: found
            Is Open Access

            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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              BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

              Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.

                Author and article information

                Contributors
                yinye@genomics.cn
                jleebensmack@uga.edu
                genebksh@hotmail.com
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                2 November 2017
                2 November 2017
                2017
                : 8
                : 1279
                Affiliations
                [1 ]ISNI 0000 0004 1936 738X, GRID grid.213876.9, Department of Plant Biology, , University of Georgia, ; Athens, GA 30602 USA
                [2 ]ISNI 0000 0000 9885 0994, GRID grid.464380.d, Institute of Vegetables and Flowers, , Jiangxi Academy of Agricultural Sciences, ; 330200 Nanchang, China
                [3 ]ISNI 0000 0001 2034 1839, GRID grid.21155.32, BGI Genomics, , BGI-Shenzhen, ; Shenzhen, 518083 China
                [4 ]Limgroup B.V., 5961 NV Horst, The Netherlands
                [5 ]ISNI 0000000122070761, GRID grid.11567.34, Dipartimento AGRARIA, , Università Mediterranea degli Studi di Reggio Calabria, ; 89124 Reggio Calabria, Italy
                [6 ]ISNI 0000 0001 1940 4177, GRID grid.5326.2, Institute of Biosciences and BioResources, Division of Palermo, , National Research Council, ; 90129 Palermo, Italy
                [7 ]Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Research Unit for Vegetable Crops, 26836 Montanaso Lombardo, Lodi Italy
                [8 ]ISNI 0000 0004 0466 6352, GRID grid.34424.35, Donald Danforth Plant Science Center, ; St. Louis, MO 63132 USA
                [9 ]ISNI 0000 0001 0727 7545, GRID grid.411015.0, Department of Biological Sciences, , University of Alabama, ; Tuscaloosa, Alabama 35487 USA
                [10 ]ISNI 0000 0001 0454 4791, GRID grid.33489.35, Department of Plant and Soil Science, , University of Delaware, ; Newark, DE 19711 USA
                [11 ]ISNI 0000 0004 1760 2876, GRID grid.256111.0, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), , Fujian Agriculture and Forestry University, ; Fuzhou, Fujian 350002 China
                [12 ]Green Acres Life Science, De Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
                [13 ]ISNI 0000000119573309, GRID grid.9227.e, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, , Chinese Academy of Sciences, ; Beijing, China
                [14 ]GRID grid.425691.d, KWS SAAT AG, ; 37574 Einbeck, Germany
                [15 ]ISNI 0000 0001 2248 6943, GRID grid.69566.3a, Graduate School of Life Sciences, , Tohoku University, ; Katahira 2-1-1, Aoba-ku, Sendai 980-8577 Japan
                [16 ]ISNI 0000 0000 9835 1415, GRID grid.453499.6, Institute of Tropical Bioscience and Biotechnology, , Chinese Academy of Tropical Agricultural Sciences, ; Haikou, 571101 China
                [17 ]Environment and Plant Protection Research Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, 571101 China
                [18 ]GRID grid.410696.c, College of Agriculture and Biotechnology, , Yunnan Agricultural University, ; Kunming, 650201 China
                [19 ]ISNI 0000 0001 2162 3504, GRID grid.134936.a, Division of Biological Sciences, , University of Missouri, ; Columbia, MO 65211 USA
                [20 ]ISNI 0000 0004 1790 4137, GRID grid.35155.37, College of Life Science and Technology, , Huazhong Agricultural University, ; Wuhan, Hubei 430070 China
                [21 ]ISNI 0000 0001 2168 186X, GRID grid.134563.6, Arizona Genomics Institute, , School of Plant Sciences and Department of Ecology and Evolutionary Biology, ; Tucson, AZ 85750 USA
                [22 ]Blumen Group S.p.A., Piacenza, 29122 Italy
                [23 ]ISNI 0000 0000 9247 7930, GRID grid.30055.33, School of Life Science and Biotechnology, , Dalian University of Technology, ; Dalian, China
                [24 ]ISNI 0000 0001 0674 042X, GRID grid.5254.6, Laboratory of Genomics and Molecular Biomedicine, Department of Biology, , University of Copenhagen, ; Universitesparken 13, Copenhagen, 2100 Denmark
                [25 ]ISNI 0000 0004 0466 6352, GRID grid.34424.35, Donald Danforth Plant Science Center, ; St. Louis, MO 63132 USA
                [26 ]Bayer, Via Ghiarone 2, 40019 Sant’Agata Bolognese, Italy
                [27 ]ISNI 0000 0001 0944 049X, GRID grid.9723.f, Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen and Rice Science Center, , Kasetsart University, ; Kamphaeng Saen, Nakhon Pathom 73140 Thailand
                Author information
                http://orcid.org/0000-0003-4095-9569
                http://orcid.org/0000-0002-9091-306X
                http://orcid.org/0000-0002-3460-8570
                http://orcid.org/0000-0001-9682-2639
                http://orcid.org/0000-0001-6633-6226
                http://orcid.org/0000-0003-3436-6097
                http://orcid.org/0000-0002-0034-0510
                http://orcid.org/0000-0001-5201-5413
                http://orcid.org/0000-0003-4811-2231
                Article
                1064
                10.1038/s41467-017-01064-8
                5665984
                29093472
                ddcded47-1e28-4047-9bd5-5d011094441c
                © The Author(s) 2017

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 11 August 2016
                : 16 August 2017
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