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      The Apostasia genome and the evolution of orchids

      research-article
      1 , 1 , 2 , 3 , 2 , 3 , 4 , 5 , 1 , 6 , 1 , 7 , 2 , 3 , 17 , 1 , 1 , 8 , 9 , 10 , 1 , 9 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 4 , 4 , 5 , 4 , 5 , 9 , 9 , 11 , 12 , 1 , 7 , 13 , 11 , , 6 , , 4 , 5 , 13 , , 2 , 3 , 14 , , 1 , 7 , 15 , 16 ,
      Nature
      Nature Publishing Group UK
      Genome, Speciation

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          Abstract

          WebComparing the whole genome sequence of Apostasia shenzhenica with transcriptome and genome data from five orchid subfamilies permits the reconstruction of an ancestral gene toolkit, providing insight into orchid origins, evolution and diversification.

          Supplementary information

          The online version of this article (doi:10.1038/nature23897) contains supplementary material, which is available to authorized users.

          Orchid origins

          Around 10 per cent of flowering plant species are orchids, with a broad diversity in both morphology and lifestyle. Apostasia is one of the earliest-diverging genera of Orchidaceae. To study the evolution and diversity of Orchidaceae, Zhong-Jian Liu, Yves Van de Peer and colleagues sequenced the genome of Apostasia shenzhenica, a self-pollinating species found in southeast China. The authors also report improved genomes for two species of Epidendroideae, Phalaenopsis equestris and Dendrobium catenatum, as well as transcriptome analysis of representatives of subfamilies of Orchidaceae. Their analyses provide insights into orchid origins, genome evolution, adaptation and diversification.

          Supplementary information

          The online version of this article (doi:10.1038/nature23897) contains supplementary material, which is available to authorized users.

          Abstract

          Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth 1, 2, 3 . Here we report the draft genome sequence of Apostasia shenzhenica 4 , a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.

          Supplementary information

          The online version of this article (doi:10.1038/nature23897) contains supplementary material, which is available to authorized users.

          Related collections

          Most cited references52

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          The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

          The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
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            SMART: recent updates, new developments and status in 2015

            SMART (Simple Modular Architecture Research Tool) is a web resource (http://smart.embl.de/) providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. In the current version, SMART contains manually curated models for more than 1200 protein domains, with ∼200 new models since our last update article. The underlying protein databases were synchronized with UniProt, Ensembl and STRING, bringing the total number of annotated domains and other protein features above 100 million. SMART's ‘Genomic’ mode, which annotates proteins from completely sequenced genomes was greatly expanded and now includes 2031 species, compared to 1133 in the previous release. SMART analysis results pages have been completely redesigned and include links to several new information sources. A new, vector-based display engine has been developed for protein schematics in SMART, which can also be exported as high-resolution bitmap images for easy inclusion into other documents. Taxonomic tree displays in SMART have been significantly improved, and can be easily navigated using the integrated search engine.
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              Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization.

              Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.

                Author and article information

                Contributors
                cmyeh@mail.saitama-u.ac.jp
                luoyb@ibcas.ac.cn
                tsaiwc@mail.ncku.edu.tw
                yves.vandepeer@psb.vib-ugent.be
                liuzj@sinicaorchid.org
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                13 September 2017
                13 September 2017
                2017
                : 549
                : 7672
                : 379-383
                Affiliations
                [1 ]Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114 China
                [2 ]GRID grid.5342.0, ISNI 0000 0001 2069 7798, Department of Plant Biotechnology and Bioinformatics, , Ghent University, ; Gent, 9052 Belgium
                [3 ]GRID grid.11486.3a, ISNI 0000000104788040, VIB Center for Plant Systems Biology, ; Gent, 9052 Belgium
                [4 ]GRID grid.64523.36, ISNI 0000 0004 0532 3255, Orchid Research and Development Center, National Cheng Kung University, ; Tainan, 701 Taiwan
                [5 ]GRID grid.64523.36, ISNI 0000 0004 0532 3255, Department of Life Sciences, , National Cheng Kung University, ; Tainan, 701 Taiwan
                [6 ]GRID grid.435133.3, ISNI 0000 0004 0596 3367, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, ; Beijing, 100093 China
                [7 ]GRID grid.20561.30, ISNI 0000 0000 9546 5767, College of Forestry, South China Agricultural University, ; Guangzhou, 510640 China
                [8 ]GRID grid.472041.4, ISNI 0000 0000 9914 1911, Technology Center, Taisei Corporation, Nase-cho 344-1, Totsuka-ku, ; Yokohama, 245-0051 Kanagawa Japan
                [9 ]GRID grid.208504.b, ISNI 0000 0001 2230 7538, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, ; Higashi 1-1-1, Tsukuba, 305-8562 Ibaraki Japan
                [10 ]PubBio-Tech Services Corporation, Wuhan, 430070 China
                [11 ]GRID grid.263023.6, ISNI 0000 0001 0703 3735, Graduate School of Science and Engineering, Saitama University, ; 255 Shimo-Okubo, Sakura-ku, 338-8570 Saitama Japan
                [12 ]GRID grid.416835.d, ISNI 0000 0001 2222 0432, NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, ; Tsukuba, 305-8519 Ibaraki Japan
                [13 ]GRID grid.64523.36, ISNI 0000 0004 0532 3255, Institute of Tropical Plant Sciences, National Cheng Kung University, ; Tainan, 701 Taiwan
                [14 ]Department of Genetics, Genomics Research Institute, Pretoria, 0028 South Africa
                [15 ]GRID grid.256111.0, ISNI 0000 0004 1760 2876, College of Landscape Architecture, Fujian Agriculture and Forestry University, ; Fuzhou, 350002 China
                [16 ]GRID grid.12527.33, ISNI 0000 0001 0662 3178, The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, ; Shenzhen, 518055 China
                [17 ]GRID grid.28665.3f, ISNI 0000 0001 2287 1366, Present Address: Biotechnology Center in Southern Taiwan, , Agricultural Biotechnology Research Center, Academia Sinica, ; 741 Tainan, Taiwan
                Article
                BFnature23897
                10.1038/nature23897
                7416622
                28902843
                7b2479d0-55d1-4fd2-98f4-a3338cb4302d
                © The Author(s) 2017

                This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) licence. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons licence, users will need to obtain permission from the licence holder to reproduce the material. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 6 June 2016
                : 7 August 2017
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                © Springer Nature Limited 2017

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