RiTE database: a resource database for genus-wide rice genomics and evolutionary biology
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Auteurs : Dario Copetti [États-Unis] ; Jianwei Zhang [États-Unis] ; Moaine El Baidouri [France, États-Unis] ; Dongying Gao [États-Unis] ; Jun Wang [États-Unis] ; Elena Barghini [Italie] ; Rosa M. Cossu [Italie] ; Angelina Angelova ; Carlos E. Maldonado L. [États-Unis] ; Stefan Roffler [Suisse] ; Hajime Ohyanagi ; Thomas Wicker [Suisse] ; Chuanzhu Fan [États-Unis] ; Andrea Zuccolo [Italie] ; Mingsheng Chen [République populaire de Chine] ; Antonio Costa De Oliveira [Brésil] ; Bin Han [République populaire de Chine] ; Robert Henry ; Yue-Ie Hsing [Taïwan] ; Nori Kurata ; Wen Wang ; Scott A. Jackson [États-Unis] ; Olivier Panaud [France] ; Rod A. Wing [États-Unis]Source :
- BMC Genomics [ 1471-2164 ] ; 2015.
Abstract
Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size.
Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus
This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of
The online version of this article (doi:10.1186/s12864-015-1762-3) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-015-1762-3
PubMed: 26194356
PubMed Central: 4508813
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Dario Copetti<affiliation><nlm:aff id="Aff2">International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna Philippines</nlm:aff><wicri:noCountry code="subfield">Laguna Philippines</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff8">School of Life Sciences, Heriot-Watt University, Edinburgh, EH14 4AS Scotland</nlm:aff><wicri:noCountry code="subfield">EH14 4AS Scotland</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff10">Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540 Japan</nlm:aff><wicri:noCountry code="subfield">Shizuoka 411-8540 Japan</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff14">Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia</nlm:aff><wicri:noCountry code="subfield">QLD 4072 Australia</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff10">Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540 Japan</nlm:aff><wicri:noCountry code="subfield">Shizuoka 411-8540 Japan</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff16">State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223 China</nlm:aff><wicri:noCountry code="subfield">Yunnan 650223 China</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna Philippines</nlm:aff><wicri:noCountry code="subfield">Laguna Philippines</wicri:noCountry></affiliation>Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">RiTE database: a resource database for genus-wide rice genomics and evolutionary biology</title><author><name sortKey="Copetti, Dario" sort="Copetti, Dario" uniqKey="Copetti D" first="Dario" last="Copetti">Dario Copetti</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ 85721 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Arizona</region></placeName><wicri:cityArea>Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson</wicri:cityArea></affiliation><affiliation><nlm:aff id="Aff2">International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna Philippines</nlm:aff><wicri:noCountry code="subfield">Laguna Philippines</wicri:noCountry></affiliation></author><author><name sortKey="Zhang, Jianwei" sort="Zhang, Jianwei" uniqKey="Zhang J" first="Jianwei" last="Zhang">Jianwei Zhang</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ 85721 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Arizona</region></placeName><wicri:cityArea>Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson</wicri:cityArea></affiliation></author><author><name sortKey="El Baidouri, Moaine" sort="El Baidouri, Moaine" uniqKey="El Baidouri M" first="Moaine" last="El Baidouri">Moaine El Baidouri</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860 Perpignan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860 Perpignan</wicri:regionArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff4">Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Gao, Dongying" sort="Gao, Dongying" uniqKey="Gao D" first="Dongying" last="Gao">Dongying Gao</name><affiliation wicri:level="2"><nlm:aff id="Aff4">Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation wicri:level="2"><nlm:aff id="Aff5">Department of Biological Sciences, Wayne State University, Detroit, MI 48202 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Michigan</region></placeName><wicri:cityArea>Department of Biological Sciences, Wayne State University, Detroit</wicri:cityArea></affiliation></author><author><name sortKey="Barghini, Elena" sort="Barghini, Elena" uniqKey="Barghini E" first="Elena" last="Barghini">Elena Barghini</name><affiliation wicri:level="1"><nlm:aff id="Aff6">Department of Agriculture, Food, and Environment, University of Pisa, 56124 Pisa, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Agriculture, Food, and Environment, University of Pisa, 56124 Pisa</wicri:regionArea></affiliation></author><author><name sortKey="Cossu, Rosa M" sort="Cossu, Rosa M" uniqKey="Cossu R" first="Rosa M." last="Cossu">Rosa M. Cossu</name><affiliation wicri:level="1"><nlm:aff id="Aff7">Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa</wicri:regionArea></affiliation></author><author><name sortKey="Angelova, Angelina" sort="Angelova, Angelina" uniqKey="Angelova A" first="Angelina" last="Angelova">Angelina Angelova</name><affiliation><nlm:aff id="Aff8">School of Life Sciences, Heriot-Watt University, Edinburgh, EH14 4AS Scotland</nlm:aff><wicri:noCountry code="subfield">EH14 4AS Scotland</wicri:noCountry></affiliation></author><author><name sortKey="Maldonado L, Carlos E" sort="Maldonado L, Carlos E" uniqKey="Maldonado L C" first="Carlos E." last="Maldonado L.">Carlos E. Maldonado L.</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ 85721 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Arizona</region></placeName><wicri:cityArea>Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson</wicri:cityArea></affiliation></author><author><name sortKey="Roffler, Stefan" sort="Roffler, Stefan" uniqKey="Roffler S" first="Stefan" last="Roffler">Stefan Roffler</name><affiliation wicri:level="1"><nlm:aff id="Aff9">Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008 Zürich</wicri:regionArea></affiliation></author><author><name sortKey="Ohyanagi, Hajime" sort="Ohyanagi, Hajime" uniqKey="Ohyanagi H" first="Hajime" last="Ohyanagi">Hajime Ohyanagi</name><affiliation><nlm:aff id="Aff10">Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540 Japan</nlm:aff><wicri:noCountry code="subfield">Shizuoka 411-8540 Japan</wicri:noCountry></affiliation></author><author><name sortKey="Wicker, Thomas" sort="Wicker, Thomas" uniqKey="Wicker T" first="Thomas" last="Wicker">Thomas Wicker</name><affiliation wicri:level="1"><nlm:aff id="Aff9">Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008 Zürich</wicri:regionArea></affiliation></author><author><name sortKey="Fan, Chuanzhu" sort="Fan, Chuanzhu" uniqKey="Fan C" first="Chuanzhu" last="Fan">Chuanzhu Fan</name><affiliation wicri:level="2"><nlm:aff id="Aff5">Department of Biological Sciences, Wayne State University, Detroit, MI 48202 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Michigan</region></placeName><wicri:cityArea>Department of Biological Sciences, Wayne State University, Detroit</wicri:cityArea></affiliation></author><author><name sortKey="Zuccolo, Andrea" sort="Zuccolo, Andrea" uniqKey="Zuccolo A" first="Andrea" last="Zuccolo">Andrea Zuccolo</name><affiliation wicri:level="1"><nlm:aff id="Aff7">Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa</wicri:regionArea></affiliation></author><author><name sortKey="Chen, Mingsheng" sort="Chen, Mingsheng" uniqKey="Chen M" first="Mingsheng" last="Chen">Mingsheng Chen</name><affiliation wicri:level="1"><nlm:aff id="Aff11">State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing, 100101 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Costa De Oliveira, Antonio" sort="Costa De Oliveira, Antonio" uniqKey="Costa De Oliveira A" first="Antonio" last="Costa De Oliveira">Antonio Costa De Oliveira</name><affiliation wicri:level="1"><nlm:aff id="Aff12">Plant Genomics and Breeding Center, Federal University of Pelotas, Pelotas-RS, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Plant Genomics and Breeding Center, Federal University of Pelotas, Pelotas-RS</wicri:regionArea></affiliation></author><author><name sortKey="Han, Bin" sort="Han, Bin" uniqKey="Han B" first="Bin" last="Han">Bin Han</name><affiliation wicri:level="1"><nlm:aff id="Aff13">National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Beijing, 100029 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Henry, Robert" sort="Henry, Robert" uniqKey="Henry R" first="Robert" last="Henry">Robert Henry</name><affiliation><nlm:aff id="Aff14">Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia</nlm:aff><wicri:noCountry code="subfield">QLD 4072 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Hsing, Yue Ie" sort="Hsing, Yue Ie" uniqKey="Hsing Y" first="Yue-Ie" last="Hsing">Yue-Ie Hsing</name><affiliation wicri:level="1"><nlm:aff id="Aff15">Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei</wicri:regionArea></affiliation></author><author><name sortKey="Kurata, Nori" sort="Kurata, Nori" uniqKey="Kurata N" first="Nori" last="Kurata">Nori Kurata</name><affiliation><nlm:aff id="Aff10">Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540 Japan</nlm:aff><wicri:noCountry code="subfield">Shizuoka 411-8540 Japan</wicri:noCountry></affiliation></author><author><name sortKey="Wang, Wen" sort="Wang, Wen" uniqKey="Wang W" first="Wen" last="Wang">Wen Wang</name><affiliation><nlm:aff id="Aff16">State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223 China</nlm:aff><wicri:noCountry code="subfield">Yunnan 650223 China</wicri:noCountry></affiliation></author><author><name sortKey="Jackson, Scott A" sort="Jackson, Scott A" uniqKey="Jackson S" first="Scott A." last="Jackson">Scott A. Jackson</name><affiliation wicri:level="2"><nlm:aff id="Aff4">Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Panaud, Olivier" sort="Panaud, Olivier" uniqKey="Panaud O" first="Olivier" last="Panaud">Olivier Panaud</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860 Perpignan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860 Perpignan</wicri:regionArea></affiliation></author><author><name sortKey="Wing, Rod A" sort="Wing, Rod A" uniqKey="Wing R" first="Rod A." last="Wing">Rod A. Wing</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ 85721 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Arizona</region></placeName><wicri:cityArea>Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson</wicri:cityArea></affiliation><affiliation><nlm:aff id="Aff2">International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna Philippines</nlm:aff><wicri:noCountry code="subfield">Laguna Philippines</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26194356</idno><idno type="pmc">4508813</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4508813</idno><idno type="RBID">PMC:4508813</idno><idno type="doi">10.1186/s12864-015-1762-3</idno><date when="2015">2015</date><idno 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Tucson</wicri:cityArea></affiliation><affiliation><nlm:aff id="Aff2">International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna Philippines</nlm:aff><wicri:noCountry code="subfield">Laguna Philippines</wicri:noCountry></affiliation></author><author><name sortKey="Zhang, Jianwei" sort="Zhang, Jianwei" uniqKey="Zhang J" first="Jianwei" last="Zhang">Jianwei Zhang</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ 85721 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Arizona</region></placeName><wicri:cityArea>Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson</wicri:cityArea></affiliation></author><author><name sortKey="El Baidouri, Moaine" sort="El Baidouri, Moaine" uniqKey="El Baidouri M" first="Moaine" last="El Baidouri">Moaine El Baidouri</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860 Perpignan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860 Perpignan</wicri:regionArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff4">Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Gao, Dongying" sort="Gao, Dongying" uniqKey="Gao D" first="Dongying" last="Gao">Dongying Gao</name><affiliation wicri:level="2"><nlm:aff id="Aff4">Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation wicri:level="2"><nlm:aff id="Aff5">Department of Biological Sciences, Wayne State University, Detroit, MI 48202 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Michigan</region></placeName><wicri:cityArea>Department of Biological Sciences, Wayne State University, Detroit</wicri:cityArea></affiliation></author><author><name sortKey="Barghini, Elena" sort="Barghini, Elena" uniqKey="Barghini E" first="Elena" last="Barghini">Elena Barghini</name><affiliation wicri:level="1"><nlm:aff id="Aff6">Department of Agriculture, Food, and Environment, University of Pisa, 56124 Pisa, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Agriculture, Food, and Environment, University of Pisa, 56124 Pisa</wicri:regionArea></affiliation></author><author><name sortKey="Cossu, Rosa M" sort="Cossu, Rosa M" uniqKey="Cossu R" first="Rosa M." last="Cossu">Rosa M. Cossu</name><affiliation wicri:level="1"><nlm:aff id="Aff7">Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa</wicri:regionArea></affiliation></author><author><name sortKey="Angelova, Angelina" sort="Angelova, Angelina" uniqKey="Angelova A" first="Angelina" last="Angelova">Angelina Angelova</name><affiliation><nlm:aff id="Aff8">School of Life Sciences, Heriot-Watt University, Edinburgh, EH14 4AS Scotland</nlm:aff><wicri:noCountry code="subfield">EH14 4AS Scotland</wicri:noCountry></affiliation></author><author><name sortKey="Maldonado L, Carlos E" sort="Maldonado L, Carlos E" uniqKey="Maldonado L C" first="Carlos E." last="Maldonado L.">Carlos E. Maldonado L.</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ 85721 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Arizona</region></placeName><wicri:cityArea>Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson</wicri:cityArea></affiliation></author><author><name sortKey="Roffler, Stefan" sort="Roffler, Stefan" uniqKey="Roffler S" first="Stefan" last="Roffler">Stefan Roffler</name><affiliation wicri:level="1"><nlm:aff id="Aff9">Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008 Zürich</wicri:regionArea></affiliation></author><author><name sortKey="Ohyanagi, Hajime" sort="Ohyanagi, Hajime" uniqKey="Ohyanagi H" first="Hajime" last="Ohyanagi">Hajime Ohyanagi</name><affiliation><nlm:aff id="Aff10">Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540 Japan</nlm:aff><wicri:noCountry code="subfield">Shizuoka 411-8540 Japan</wicri:noCountry></affiliation></author><author><name sortKey="Wicker, Thomas" sort="Wicker, Thomas" uniqKey="Wicker T" first="Thomas" last="Wicker">Thomas Wicker</name><affiliation wicri:level="1"><nlm:aff id="Aff9">Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008 Zürich</wicri:regionArea></affiliation></author><author><name sortKey="Fan, Chuanzhu" sort="Fan, Chuanzhu" uniqKey="Fan C" first="Chuanzhu" last="Fan">Chuanzhu Fan</name><affiliation wicri:level="2"><nlm:aff id="Aff5">Department of Biological Sciences, Wayne State University, Detroit, MI 48202 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Michigan</region></placeName><wicri:cityArea>Department of Biological Sciences, Wayne State University, Detroit</wicri:cityArea></affiliation></author><author><name sortKey="Zuccolo, Andrea" sort="Zuccolo, Andrea" uniqKey="Zuccolo A" first="Andrea" last="Zuccolo">Andrea Zuccolo</name><affiliation wicri:level="1"><nlm:aff id="Aff7">Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa</wicri:regionArea></affiliation></author><author><name sortKey="Chen, Mingsheng" sort="Chen, Mingsheng" uniqKey="Chen M" first="Mingsheng" last="Chen">Mingsheng Chen</name><affiliation wicri:level="1"><nlm:aff id="Aff11">State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing, 100101 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Costa De Oliveira, Antonio" sort="Costa De Oliveira, Antonio" uniqKey="Costa De Oliveira A" first="Antonio" last="Costa De Oliveira">Antonio Costa De Oliveira</name><affiliation wicri:level="1"><nlm:aff id="Aff12">Plant Genomics and Breeding Center, Federal University of Pelotas, Pelotas-RS, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Plant Genomics and Breeding Center, Federal University of Pelotas, Pelotas-RS</wicri:regionArea></affiliation></author><author><name sortKey="Han, Bin" sort="Han, Bin" uniqKey="Han B" first="Bin" last="Han">Bin Han</name><affiliation wicri:level="1"><nlm:aff id="Aff13">National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Beijing, 100029 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Henry, Robert" sort="Henry, Robert" uniqKey="Henry R" first="Robert" last="Henry">Robert Henry</name><affiliation><nlm:aff id="Aff14">Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia</nlm:aff><wicri:noCountry code="subfield">QLD 4072 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Hsing, Yue Ie" sort="Hsing, Yue Ie" uniqKey="Hsing Y" first="Yue-Ie" last="Hsing">Yue-Ie Hsing</name><affiliation wicri:level="1"><nlm:aff id="Aff15">Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 11529 Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei</wicri:regionArea></affiliation></author><author><name sortKey="Kurata, Nori" sort="Kurata, Nori" uniqKey="Kurata N" first="Nori" last="Kurata">Nori Kurata</name><affiliation><nlm:aff id="Aff10">Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540 Japan</nlm:aff><wicri:noCountry code="subfield">Shizuoka 411-8540 Japan</wicri:noCountry></affiliation></author><author><name sortKey="Wang, Wen" sort="Wang, Wen" uniqKey="Wang W" first="Wen" last="Wang">Wen Wang</name><affiliation><nlm:aff id="Aff16">State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223 China</nlm:aff><wicri:noCountry code="subfield">Yunnan 650223 China</wicri:noCountry></affiliation></author><author><name sortKey="Jackson, Scott A" sort="Jackson, Scott A" uniqKey="Jackson S" first="Scott A." last="Jackson">Scott A. Jackson</name><affiliation wicri:level="2"><nlm:aff id="Aff4">Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Géorgie (États-Unis)</region></placeName><wicri:cityArea>Center for Applied Genetic Technologies, University of Georgia, Athens</wicri:cityArea></affiliation></author><author><name sortKey="Panaud, Olivier" sort="Panaud, Olivier" uniqKey="Panaud O" first="Olivier" last="Panaud">Olivier Panaud</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860 Perpignan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860 Perpignan</wicri:regionArea></affiliation></author><author><name sortKey="Wing, Rod A" sort="Wing, Rod A" uniqKey="Wing R" first="Rod A." last="Wing">Rod A. Wing</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ 85721 United States</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Arizona</region></placeName><wicri:cityArea>Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson</wicri:cityArea></affiliation><affiliation><nlm:aff id="Aff2">International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna Philippines</nlm:aff><wicri:noCountry code="subfield">Laguna Philippines</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size.</p></sec><sec><title>Results</title><p>Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus <italic>Oryza</italic> and the closely-related out-group <italic>Leersia perrieri</italic>. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies.</p></sec><sec><title>Conclusions</title><p>This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of <italic>Oryza</italic> diversity.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-015-1762-3) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bergman, Cm" uniqKey="Bergman C">CM Bergman</name></author><author><name sortKey="Quesneville, H" uniqKey="Quesneville H">H Quesneville</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saha, S" uniqKey="Saha S">S Saha</name></author><author><name sortKey="Bridges, S" uniqKey="Bridges S">S Bridges</name></author><author><name sortKey="Magbanua, Zv" uniqKey="Magbanua Z">ZV Magbanua</name></author><author><name sortKey="Peterson, Dg" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Genomics</journal-id><journal-id journal-id-type="iso-abbrev">BMC Genomics</journal-id><journal-title-group><journal-title>BMC Genomics</journal-title></journal-title-group><issn pub-type="epub">1471-2164</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26194356</article-id><article-id pub-id-type="pmc">4508813</article-id><article-id pub-id-type="publisher-id">1762</article-id><article-id pub-id-type="doi">10.1186/s12864-015-1762-3</article-id><article-categories><subj-group subj-group-type="heading"><subject>Methodology Article</subject></subj-group></article-categories><title-group><article-title>RiTE database: a resource database for genus-wide rice genomics and evolutionary biology</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Copetti</surname><given-names>Dario</given-names></name><address><email>dcopetti@email.arizona.edu</email></address><xref ref-type="aff" rid="Aff1"></xref><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Jianwei</given-names></name><address><email>zhangjw@email.arizona.edu</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>El Baidouri</surname><given-names>Moaine</given-names></name><address><email>moaine.elbaidouri@gmail.com</email></address><xref ref-type="aff" rid="Aff3"></xref><xref ref-type="aff" rid="Aff4"></xref></contrib><contrib contrib-type="author"><name><surname>Gao</surname><given-names>Dongying</given-names></name><address><email>dgao@uga.edu</email></address><xref ref-type="aff" rid="Aff4"></xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Jun</given-names></name><address><email>wangj@wayne.edu</email></address><xref ref-type="aff" rid="Aff5"></xref></contrib><contrib contrib-type="author"><name><surname>Barghini</surname><given-names>Elena</given-names></name><address><email>elena.barghini@gmail.com</email></address><xref ref-type="aff" rid="Aff6"></xref></contrib><contrib contrib-type="author"><name><surname>Cossu</surname><given-names>Rosa M.</given-names></name><address><email>rosa.cossu@gmail.com</email></address><xref ref-type="aff" rid="Aff7"></xref></contrib><contrib contrib-type="author"><name><surname>Angelova</surname><given-names>Angelina</given-names></name><address><email>angelova@email.arizona.edu</email></address><xref ref-type="aff" rid="Aff8"></xref></contrib><contrib contrib-type="author"><name><surname>Maldonado L.</surname><given-names>Carlos E.</given-names></name><address><email>ceml@email.arizona.edu</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Roffler</surname><given-names>Stefan</given-names></name><address><email>stefan.roffler@access.uzh.ch</email></address><xref ref-type="aff" rid="Aff9"></xref></contrib><contrib contrib-type="author"><name><surname>Ohyanagi</surname><given-names>Hajime</given-names></name><address><email>hohyanag@nig.ac.jp</email></address><xref ref-type="aff" rid="Aff10"></xref></contrib><contrib contrib-type="author"><name><surname>Wicker</surname><given-names>Thomas</given-names></name><address><email>wicker@botinst.uzh.ch</email></address><xref ref-type="aff" rid="Aff9"></xref></contrib><contrib contrib-type="author"><name><surname>Fan</surname><given-names>Chuanzhu</given-names></name><address><email>cfan@wayne.edu</email></address><xref ref-type="aff" rid="Aff5"></xref></contrib><contrib contrib-type="author"><name><surname>Zuccolo</surname><given-names>Andrea</given-names></name><address><email>a.zuccolo@sssup.it</email></address><xref ref-type="aff" rid="Aff7"></xref></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Mingsheng</given-names></name><address><email>mschen@genetics.ac.cn</email></address><xref ref-type="aff" rid="Aff11"></xref></contrib><contrib contrib-type="author"><name><surname>Costa de Oliveira</surname><given-names>Antonio</given-names></name><address><email>antonio.oliveira@pq.cnpq.br</email></address><xref ref-type="aff" rid="Aff12"></xref></contrib><contrib contrib-type="author"><name><surname>Han</surname><given-names>Bin</given-names></name><address><email>bhan@ncgr.ac.cn</email></address><xref ref-type="aff" rid="Aff13"></xref></contrib><contrib contrib-type="author"><name><surname>Henry</surname><given-names>Robert</given-names></name><address><email>robert.henry@uq.edu.au</email></address><xref ref-type="aff" rid="Aff14"></xref></contrib><contrib contrib-type="author"><name><surname>Hsing</surname><given-names>Yue-ie</given-names></name><address><email>bohsing@gate.sinica.edu.tw</email></address><xref ref-type="aff" rid="Aff15"></xref></contrib><contrib contrib-type="author"><name><surname>Kurata</surname><given-names>Nori</given-names></name><address><email>nkurata@nig.ac.jp</email></address><xref ref-type="aff" rid="Aff10"></xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Wen</given-names></name><address><email>wwang@mail.kiz.ac.cn</email></address><xref ref-type="aff" rid="Aff16"></xref></contrib><contrib contrib-type="author"><name><surname>Jackson</surname><given-names>Scott A.</given-names></name><address><email>sjackson@uga.edu</email></address><xref ref-type="aff" rid="Aff4"></xref></contrib><contrib contrib-type="author"><name><surname>Panaud</surname><given-names>Olivier</given-names></name><address><email>panaud@univ-perp.fr</email></address><xref ref-type="aff" rid="Aff3"></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Wing</surname><given-names>Rod A.</given-names></name><address><phone>+1 (520) 626 9595</phone><email>rwing@email.arizona.edu</email></address><xref ref-type="aff" rid="Aff1"></xref><xref ref-type="aff" rid="Aff2"></xref></contrib><aff id="Aff1"><label></label>Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ 85721 United States</aff><aff id="Aff2"><label></label>International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna Philippines</aff><aff id="Aff3"><label></label>Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860 Perpignan, France</aff><aff id="Aff4"><label></label>Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 United States</aff><aff id="Aff5"><label></label>Department of Biological Sciences, Wayne State University, Detroit, MI 48202 United States</aff><aff id="Aff6"><label></label>Department of Agriculture, Food, and Environment, University of Pisa, 56124 Pisa, Italy</aff><aff id="Aff7"><label></label>Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy</aff><aff id="Aff8"><label></label>School of Life Sciences, Heriot-Watt University, Edinburgh, EH14 4AS Scotland</aff><aff id="Aff9"><label></label>Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland</aff><aff id="Aff10"><label></label>Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540 Japan</aff><aff id="Aff11"><label></label>State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing, 100101 China</aff><aff id="Aff12"><label></label>Plant Genomics and Breeding Center, Federal University of Pelotas, Pelotas-RS, Brazil</aff><aff id="Aff13"><label></label>National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Beijing, 100029 China</aff><aff id="Aff14"><label></label>Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia</aff><aff id="Aff15"><label></label>Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 11529 Taiwan</aff><aff id="Aff16"><label></label>State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223 China</aff></contrib-group><pub-date pub-type="epub"><day>22</day><month>7</month><year>2015</year></pub-date><pub-date pub-type="pmc-release"><day>22</day><month>7</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>16</volume><issue>1</issue><elocation-id>538</elocation-id><history><date date-type="received"><day>11</day><month>3</month><year>2015</year></date><date date-type="accepted"><day>9</day><month>7</month><year>2015</year></date></history><permissions><copyright-statement>© Copetti et al. 2015</copyright-statement><license license-type="open-access"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0">http://creativecommons.org/licenses/by/4.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><abstract id="Abs1"><sec><title>Background</title><p>Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size.</p></sec><sec><title>Results</title><p>Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus <italic>Oryza</italic> and the closely-related out-group <italic>Leersia perrieri</italic>. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies.</p></sec><sec><title>Conclusions</title><p>This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of <italic>Oryza</italic> diversity.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-015-1762-3) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>Rice</kwd><kwd><italic>Oryza</italic></kwd><kwd>Transposable elements</kwd><kwd>Repeats</kwd><kwd>Genome</kwd><kwd>RiTE-db</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2015</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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