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      Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation

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      1 , 2 , 3 , 4 , 5 , 5 , 6 , 7 , 5 , 5 , 8 , 8 , 8 , 8 , 2 , 8 , 8 , 2 , 8 , 8 , 9 , 6 , 10 , 1 , 1 , 9 , 11 , 1 , 1 , 2 , 11 , 11 , 11 , 11 , 11 , 11 , 11 , 11 , 11 , 11 , 11 , 11 , 11 , 11 , 11 , 11 , 5 , 5 , 12 , 6 , 2 , 8 , 4 , 12 , 9 , 12 , 2 , 5 , 9 , a , 1 , 2 , 9 , 11
      Nature Communications
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          Abstract

          The colonization of land by plants was a key event in the evolution of life. Here we report the draft genome sequence of the filamentous terrestrial alga Klebsormidium flaccidum (Division Charophyta, Order Klebsormidiales) to elucidate the early transition step from aquatic algae to land plants. Comparison of the genome sequence with that of other algae and land plants demonstrate that K. flaccidum acquired many genes specific to land plants. We demonstrate that K. flaccidum indeed produces several plant hormones and homologues of some of the signalling intermediates required for hormone actions in higher plants. The K. flaccidum genome also encodes a primitive system to protect against the harmful effects of high-intensity light. The presence of these plant-related systems in K. flaccidum suggests that, during evolution, this alga acquired the fundamental machinery required for adaptation to terrestrial environments.

          Abstract

          Plant colonization of land is an important evolutionary event. Here, the authors sequence the genome of a filamentous terrestrial alga and, through a comparative analysis with related algae and land plant species, provide insight into how aquatic algae adapted to terrestrial environments.

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          Most cited references35

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          The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.

          We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.
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            NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

            The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of genomic, transcript and protein sequence records. These records are selected and curated from public sequence archives and represent a significant reduction in redundancy compared to the volume of data archived by the International Nucleotide Sequence Database Collaboration. The database includes over 16 000 organisms, 2.4 × 106 genomic records, 13 × 106 proteins and 2 × 106 RNA records spanning prokaryotes, eukaryotes and viruses (RefSeq release 49, September 2011). The RefSeq database is maintained by a combined approach of automated analyses, collaboration and manual curation to generate an up-to-date representation of the sequence, its features, names and cross-links to related sources of information. We report here on recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline. More information about the resource is available online (see http://www.ncbi.nlm.nih.gov/RefSeq/).
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              A pigment-binding protein essential for regulation of photosynthetic light harvesting.

              Photosynthetic light harvesting in plants is regulated in response to changes in incident light intensity. Absorption of light that exceeds a plant's capacity for fixation of CO2 results in thermal dissipation of excitation energy in the pigment antenna of photosystem II by a poorly understood mechanism. This regulatory process, termed nonphotochemical quenching, maintains the balance between dissipation and utilization of light energy to minimize generation of oxidizing molecules, thereby protecting the plant against photo-oxidative damage. To identify specific proteins that are involved in nonphotochemical quenching, we have isolated mutants of Arabidopsis thaliana that cannot dissipate excess absorbed light energy. Here we show that the gene encoding PsbS, an intrinsic chlorophyll-binding protein of photosystem II, is necessary for nonphotochemical quenching but not for efficient light harvesting and photosynthesis. These results indicate that PsbS may be the site for nonphotochemical quenching, a finding that has implications for the functional evolution of pigment-binding proteins.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Pub. Group
                2041-1723
                28 May 2014
                : 5
                : 3978
                Affiliations
                [1 ]Center for Biological Resources and Informatics, Tokyo Institute of Technology , Yokohama City, Kanagawa 226-8501, Japan
                [2 ]CREST, Japan Science and Technology Agency , Yokohama City, Kanagawa 226-8501, Japan
                [3 ]Section of Microbial Genomics and Ecology, Tokyo Medical and Dental University , 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-0034, Japan
                [4 ]National Institute of Genetics , Yata 1111, Mishima, Shizuoka 411-8540, Japan
                [5 ]Department of Biological Information, Tokyo Institute of Technology , Yokohama City, Kanagawa 226-8501, Japan
                [6 ]Center for Sustainable Resource Science, RIKEN , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
                [7 ]Department of Environmental Life Sciences, Tohoku University , 2-1-1, Katahira, Aoba-ku, Sendai 980-8577, Japan
                [8 ]Graduate School of Arts and Sciences, The University of Tokyo , 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
                [9 ]Earth-Life Science Institute, Tokyo Institute of Technology , 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
                [10 ]Faculty of Science, Shizuoka University , 836 Oya, Suruga-ku, Shizuoka 422-8529, Japan
                [11 ]Department of Biological Sciences, Tokyo Institute of Technology , Yokohama City, Kanagawa 226-8501, Japan
                [12 ]Kazusa DNA Research Institute , 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
                [13 ]Department of Earth and Planetary Sciences, Tokyo Institute of Technology , 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
                Author notes
                Article
                ncomms4978
                10.1038/ncomms4978
                4052687
                24865297
                516f3b1c-7e7f-4c8f-9fc8-68f623643dcc
                Copyright © 2014, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

                This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/

                History
                : 16 March 2014
                : 28 April 2014
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