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      The Cycas genome and the early evolution of seed plants

      research-article
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      Nature Plants
      Nature Publishing Group UK
      Plant sciences, Evolution

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          Abstract

          Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists.

          Abstract

          The study assembled a chromosome-level genome of Cycas panzhihuaensis, the last major lineage of seed plants for which a high-quality genome assembly was lacking. The study closes an important gap in our understanding of genome structure and evolution in seed plants.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            Trimmomatic: a flexible trimmer for Illumina sequence data

            Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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              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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                Author and article information

                Contributors
                yang.liu0508@gmail.com
                yvpee@psb.vib-ugent.be
                dsoltis@ufl.edu
                gongxun@mail.kib.ac.cn
                liuhuan@genomics.cn
                shouzhouz@szbg.ac.cn
                Journal
                Nat Plants
                Nat Plants
                Nature Plants
                Nature Publishing Group UK (London )
                2055-0278
                18 April 2022
                18 April 2022
                2022
                : 8
                : 4
                : 389-401
                Affiliations
                [1 ]GRID grid.21155.32, ISNI 0000 0001 2034 1839, State Key Laboratory of Agricultural Genomics, , BGI-Shenzhen, ; Shenzhen, China
                [2 ]GRID grid.464438.9, Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, ; Shenzhen, China
                [3 ]GRID grid.32566.34, ISNI 0000 0000 8571 0482, State Key Laboratory of Grassland Agro-Ecosystems, , College of Ecology, Lanzhou University, ; Lanzhou, China
                [4 ]GRID grid.418569.7, ISNI 0000 0001 2166 1076, State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, , Chinese Research Academy of Environmental Sciences, ; Beijing, China
                [5 ]GRID grid.458460.b, ISNI 0000 0004 1764 155X, Key Laboratory for Plant Diversity and Biogeography of East Asia, , Kunming Institute of Botany, Chinese Academy of Sciences, ; Kunming, China
                [6 ]GRID grid.256922.8, ISNI 0000 0000 9139 560X, Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, , Henan University, ; Kaifeng, China
                [7 ]GRID grid.255364.3, ISNI 0000 0001 2191 0423, Department of Biology, , East Carolina University, ; Greenville, NC USA
                [8 ]GRID grid.410625.4, ISNI 0000 0001 2293 4910, College of Biology and Environment, , Nanjing Forestry University, ; Nanjing, China
                [9 ]GRID grid.410726.6, ISNI 0000 0004 1797 8419, College of Life Sciences, , University of Chinese Academy of Sciences, ; Beijing, China
                [10 ]Nanning Botanical Garden, Nanning, China
                [11 ]GRID grid.12981.33, ISNI 0000 0001 2360 039X, School of Life Sciences, , Sun Yat-sen University, ; Guangzhou, China
                [12 ]Sichuan Cycas panzhihuaensis National Nature Reserve, Panzhihua, China
                [13 ]Global Biodiversity Conservancy, Chonburi, Thailand
                [14 ]GRID grid.22935.3f, ISNI 0000 0004 0530 8290, Department of Entomology, , China Agricultural University, ; Beijing, China
                [15 ]GRID grid.63054.34, ISNI 0000 0001 0860 4915, Department of Ecology and Evolutionary Biology, , University of Connecticut, ; Storrs, CT USA
                [16 ]GRID grid.263488.3, ISNI 0000 0001 0472 9649, Guangdong Provincial Key Laboratory for Plant Epigenetics, , Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, ; Shenzhen, China
                [17 ]GRID grid.5170.3, ISNI 0000 0001 2181 8870, Department of Biotechnology and Biomedicine, , Technical University of Denmark, ; Lyngby, Denmark
                [18 ]GRID grid.410727.7, ISNI 0000 0001 0526 1937, Shenzhen Agricultural Genome Research Institute, , Chinese Academy of Agricultural Sciences, ; Shenzhen, China
                [19 ]GRID grid.27871.3b, ISNI 0000 0000 9750 7019, College of Horticulture, Academy for Advanced Interdisciplinary Studies, , Nanjing Agricultural University, ; Nanjing, China
                [20 ]GRID grid.41156.37, ISNI 0000 0001 2314 964X, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, , Nanjing University, ; Nanjing, China
                [21 ]GRID grid.411304.3, ISNI 0000 0001 0376 205X, Chengdu University of Traditional Chinese Medicine, ; Chengdu, China
                [22 ]GRID grid.511033.5, Department of Plant Biotechnology and Bioinformatics, , Ghent University, VIB UGent Center for Plant Systems Biology, ; Gent, Belgium
                [23 ]GRID grid.13402.34, ISNI 0000 0004 1759 700X, College of Agriculture and Biotechnology, , Zhejiang University, ; Hangzhou, China
                [24 ]Hainan Institute of Zhejiang University, Sanya, China
                [25 ]GRID grid.13291.38, ISNI 0000 0001 0807 1581, The College of Life Sciences, , Sichuan University, ; Chengdu, China
                [26 ]GRID grid.256111.0, ISNI 0000 0004 1760 2876, Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, , Fujian Agriculture and Forestry University, ; Fuzhou, China
                [27 ]GRID grid.9227.e, ISNI 0000000119573309, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, , Chinese Academy of Sciences, ; Beijing, China
                [28 ]GRID grid.20561.30, ISNI 0000 0000 9546 5767, College of Life Sciences, , South China Agricultural University, ; Guangzhou, China
                [29 ]GRID grid.507734.2, ISNI 0000 0000 9694 3193, National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, , Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, ; Shanghai, China
                [30 ]GRID grid.5254.6, ISNI 0000 0001 0674 042X, Department of Biology, , University of Copenhagen, ; Copenhagen, Denmark
                [31 ]GRID grid.15276.37, ISNI 0000 0004 1936 8091, Florida Museum of Natural History, , University of Florida, ; Gainesville, FL USA
                [32 ]GRID grid.49697.35, ISNI 0000 0001 2107 2298, Department of Biochemistry, Genetics and Microbiology, , University of Pretoria, ; Pretoria, South Africa
                [33 ]GRID grid.15276.37, ISNI 0000 0004 1936 8091, Department of Biology, , University of Florida, ; Gainesville, FL USA
                Author information
                http://orcid.org/0000-0002-5942-839X
                http://orcid.org/0000-0003-0799-0900
                http://orcid.org/0000-0003-1481-4825
                http://orcid.org/0000-0003-1618-8813
                http://orcid.org/0000-0003-4893-4171
                http://orcid.org/0000-0002-6139-191X
                http://orcid.org/0000-0002-1662-2862
                http://orcid.org/0000-0003-3308-6878
                http://orcid.org/0000-0002-4742-9870
                http://orcid.org/0000-0003-0419-9136
                http://orcid.org/0000-0002-2754-3895
                http://orcid.org/0000-0003-4363-8672
                http://orcid.org/0000-0001-6959-5100
                http://orcid.org/0000-0001-6754-7404
                http://orcid.org/0000-0003-3713-3192
                http://orcid.org/0000-0002-0431-0669
                http://orcid.org/0000-0003-3904-963X
                http://orcid.org/0000-0002-4237-7418
                http://orcid.org/0000-0003-4390-3878
                http://orcid.org/0000-0002-8987-2782
                http://orcid.org/0000-0003-3978-0828
                http://orcid.org/0000-0002-5178-3530
                http://orcid.org/0000-0002-4830-5247
                http://orcid.org/0000-0003-3256-2940
                http://orcid.org/0000-0002-5338-5173
                http://orcid.org/0000-0001-9310-8659
                http://orcid.org/0000-0003-4327-3730
                http://orcid.org/0000-0001-8638-4137
                http://orcid.org/0000-0003-1705-6935
                http://orcid.org/0000-0003-3909-0931
                http://orcid.org/0000-0001-9070-0593
                Article
                1129
                10.1038/s41477-022-01129-7
                9023351
                35437001
                3c890fcb-baef-430d-aa9e-8be10a5971bc
                © The Author(s) 2022

                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
                : 3 September 2021
                : 10 March 2022
                Funding
                Funded by: YVdP acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (No. 833522) and from Ghent University (Methusalem funding, BOF.MET.2021.0005.01)
                Funded by: The National Key R&D Program of China (No. 2019YFC1711000), the Major Science and Technology Projects of Yunnan Province (Digitalization, development and application of biotic resource (No. 860 202002AA100007), and Shenzhen Municipal Government of China (No. JCYJ20151015162041454) to HL
                Funded by: The Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China (No. 2019HJ2096001006)
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                © The Author(s), under exclusive licence to Springer Nature Limited 2022

                plant sciences,evolution
                plant sciences, evolution

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