Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes
Identifieur interne : 000635 ( Pmc/Checkpoint ); précédent : 000634; suivant : 000636Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes
Auteurs : Sergei Kliver [Russie] ; Mike Rayko ; Alexey Komissarov ; Evgeny Bakin ; Daria Zhernakova ; Kasavajhala Prasad ; Catherine Rushworth ; R. Baskar ; Dmitry Smetanin ; Jeremy Schmutz [États-Unis] ; Daniel S. Rokhsar ; Thomas Mitchell-Olds ; Ueli Grossniklaus ; Vladimir Brukhin [Russie]Source :
- Genes [ 2073-4425 ] ; 2018.
Abstract
Closely related to the model plant
Url:
DOI: 10.3390/genes9040185
PubMed: 29597328
PubMed Central: 5924527
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
PMC:5924527Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Assembly of the <italic>Boechera retrofracta</italic> Genome and Evolutionary Analysis of Apomixis-Associated Genes</title><author><name sortKey="Kliver, Sergei" sort="Kliver, Sergei" uniqKey="Kliver S" first="Sergei" last="Kliver">Sergei Kliver</name><affiliation><nlm:aff id="af1-genes-09-00185">Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia;<email>mahajrod@gmail.com</email> (S.K.);<email>mikerayko@gmail.com</email> (M.R.);<email>ad3002@gmail.com</email> (A.K.);<email>eugene.bakin@gmail.com</email> (E.B.);<email>dashzhernakova@gmail.com</email> (D.Z.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-genes-09-00185">All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 St. Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 St. Petersburg</wicri:regionArea><wicri:noRegion>196608 St. Petersburg</wicri:noRegion></affiliation></author><author><name sortKey="Rayko, Mike" sort="Rayko, Mike" uniqKey="Rayko M" first="Mike" last="Rayko">Mike Rayko</name><affiliation><nlm:aff id="af1-genes-09-00185">Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia;<email>mahajrod@gmail.com</email> (S.K.);<email>mikerayko@gmail.com</email> (M.R.);<email>ad3002@gmail.com</email> (A.K.);<email>eugene.bakin@gmail.com</email> (E.B.);<email>dashzhernakova@gmail.com</email> (D.Z.)</nlm:aff></affiliation></author><author><name sortKey="Komissarov, Alexey" sort="Komissarov, Alexey" uniqKey="Komissarov A" first="Alexey" last="Komissarov">Alexey Komissarov</name><affiliation><nlm:aff id="af1-genes-09-00185">Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia;<email>mahajrod@gmail.com</email> (S.K.);<email>mikerayko@gmail.com</email> (M.R.);<email>ad3002@gmail.com</email> (A.K.);<email>eugene.bakin@gmail.com</email> (E.B.);<email>dashzhernakova@gmail.com</email> (D.Z.)</nlm:aff></affiliation></author><author><name sortKey="Bakin, Evgeny" sort="Bakin, Evgeny" uniqKey="Bakin E" first="Evgeny" last="Bakin">Evgeny Bakin</name><affiliation><nlm:aff id="af1-genes-09-00185">Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia;<email>mahajrod@gmail.com</email> (S.K.);<email>mikerayko@gmail.com</email> (M.R.);<email>ad3002@gmail.com</email> (A.K.);<email>eugene.bakin@gmail.com</email> (E.B.);<email>dashzhernakova@gmail.com</email> (D.Z.)</nlm:aff></affiliation></author><author><name sortKey="Zhernakova, Daria" sort="Zhernakova, Daria" uniqKey="Zhernakova D" first="Daria" last="Zhernakova">Daria Zhernakova</name><affiliation><nlm:aff id="af1-genes-09-00185">Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia;<email>mahajrod@gmail.com</email> (S.K.);<email>mikerayko@gmail.com</email> (M.R.);<email>ad3002@gmail.com</email> (A.K.);<email>eugene.bakin@gmail.com</email> (E.B.);<email>dashzhernakova@gmail.com</email> (D.Z.)</nlm:aff></affiliation></author><author><name sortKey="Prasad, Kasavajhala" sort="Prasad, Kasavajhala" uniqKey="Prasad K" first="Kasavajhala" last="Prasad">Kasavajhala Prasad</name><affiliation><nlm:aff id="af3-genes-09-00185">Department of Biology, Colorado State University, Fort Collins, CO 80523; USA;<email>kasavajhalaprasad@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Rushworth, Catherine" sort="Rushworth, Catherine" uniqKey="Rushworth C" first="Catherine" last="Rushworth">Catherine Rushworth</name><affiliation><nlm:aff id="af4-genes-09-00185">University and Jepson Herbaria, University of California, Berkeley, NC 94720; USA;<email>crushworth@berkeley.edu</email></nlm:aff></affiliation></author><author><name sortKey="Baskar, R" sort="Baskar, R" uniqKey="Baskar R" first="R." last="Baskar">R. Baskar</name><affiliation><nlm:aff id="af5-genes-09-00185">Department of Biotechnology, Indian Institute of Technology. Sardar Patel road, 600036 Chennai, India;<email>rbaskar@iitm.ac.in</email></nlm:aff></affiliation></author><author><name sortKey="Smetanin, Dmitry" sort="Smetanin, Dmitry" uniqKey="Smetanin D" first="Dmitry" last="Smetanin">Dmitry Smetanin</name><affiliation><nlm:aff id="af6-genes-09-00185">Department of Plant and Microbial Biology Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich; Switzerland;<email>dmitry.smetanin@botinst.uzh.ch</email> (D.S.);<email>grossnik@botinst.uzh.ch</email> (U.G.)</nlm:aff></affiliation></author><author><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><affiliation><nlm:aff id="af7-genes-09-00185">Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; USA;<email>jschmutz@hudsonalpha.org</email> (J.S.);<email>dsrokhsar@gmail.com</email> (D.S.R.)</nlm:aff></affiliation><affiliation wicri:level="2"><nlm:aff id="af8-genes-09-00185">HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806; USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Alabama</region></placeName><wicri:cityArea>HudsonAlpha Institute of Biotechnology, Huntsville</wicri:cityArea></affiliation></author><author><name sortKey="Rokhsar, Daniel S" sort="Rokhsar, Daniel S" uniqKey="Rokhsar D" first="Daniel S." last="Rokhsar">Daniel S. Rokhsar</name><affiliation><nlm:aff id="af7-genes-09-00185">Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; USA;<email>jschmutz@hudsonalpha.org</email> (J.S.);<email>dsrokhsar@gmail.com</email> (D.S.R.)</nlm:aff></affiliation></author><author><name sortKey="Mitchell Olds, Thomas" sort="Mitchell Olds, Thomas" uniqKey="Mitchell Olds T" first="Thomas" last="Mitchell-Olds">Thomas Mitchell-Olds</name><affiliation><nlm:aff id="af9-genes-09-00185">Department of Biology, Duke University, Durham, NC 27708-0338; USA;<email>tmo1@duke.edu</email></nlm:aff></affiliation></author><author><name sortKey="Grossniklaus, Ueli" sort="Grossniklaus, Ueli" uniqKey="Grossniklaus U" first="Ueli" last="Grossniklaus">Ueli Grossniklaus</name><affiliation><nlm:aff id="af6-genes-09-00185">Department of Plant and Microbial Biology Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich; Switzerland;<email>dmitry.smetanin@botinst.uzh.ch</email> (D.S.);<email>grossnik@botinst.uzh.ch</email> (U.G.)</nlm:aff></affiliation></author><author><name sortKey="Brukhin, Vladimir" sort="Brukhin, Vladimir" uniqKey="Brukhin V" first="Vladimir" last="Brukhin">Vladimir Brukhin</name><affiliation><nlm:aff id="af1-genes-09-00185">Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia;<email>mahajrod@gmail.com</email> (S.K.);<email>mikerayko@gmail.com</email> (M.R.);<email>ad3002@gmail.com</email> (A.K.);<email>eugene.bakin@gmail.com</email> (E.B.);<email>dashzhernakova@gmail.com</email> (D.Z.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af10-genes-09-00185">Department of Plant Embryology and Reproductive Biology, Komarov Botanical Institute RAS, 197376 St. Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Department of Plant Embryology and Reproductive Biology, Komarov Botanical Institute RAS, 197376 St. Petersburg</wicri:regionArea><wicri:noRegion>197376 St. Petersburg</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">29597328</idno><idno type="pmc">5924527</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5924527</idno><idno type="RBID">PMC:5924527</idno><idno type="doi">10.3390/genes9040185</idno><date when="2018">2018</date><idno type="wicri:Area/Pmc/Corpus">000C93</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000C93</idno><idno type="wicri:Area/Pmc/Curation">000C93</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000C93</idno><idno type="wicri:Area/Pmc/Checkpoint">000635</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000635</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Assembly of the <italic>Boechera retrofracta</italic> Genome and Evolutionary Analysis of Apomixis-Associated Genes</title><author><name sortKey="Kliver, Sergei" sort="Kliver, Sergei" uniqKey="Kliver S" first="Sergei" last="Kliver">Sergei Kliver</name><affiliation><nlm:aff id="af1-genes-09-00185">Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia;<email>mahajrod@gmail.com</email> (S.K.);<email>mikerayko@gmail.com</email> (M.R.);<email>ad3002@gmail.com</email> (A.K.);<email>eugene.bakin@gmail.com</email> (E.B.);<email>dashzhernakova@gmail.com</email> (D.Z.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-genes-09-00185">All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 St. Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 St. Petersburg</wicri:regionArea><wicri:noRegion>196608 St. Petersburg</wicri:noRegion></affiliation></author><author><name sortKey="Rayko, Mike" sort="Rayko, Mike" uniqKey="Rayko M" first="Mike" last="Rayko">Mike Rayko</name><affiliation><nlm:aff id="af1-genes-09-00185">Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia;<email>mahajrod@gmail.com</email> (S.K.);<email>mikerayko@gmail.com</email> (M.R.);<email>ad3002@gmail.com</email> (A.K.);<email>eugene.bakin@gmail.com</email> (E.B.);<email>dashzhernakova@gmail.com</email> (D.Z.)</nlm:aff></affiliation></author><author><name sortKey="Komissarov, Alexey" sort="Komissarov, Alexey" uniqKey="Komissarov A" first="Alexey" last="Komissarov">Alexey Komissarov</name><affiliation><nlm:aff id="af1-genes-09-00185">Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia;<email>mahajrod@gmail.com</email> (S.K.);<email>mikerayko@gmail.com</email> (M.R.);<email>ad3002@gmail.com</email> (A.K.);<email>eugene.bakin@gmail.com</email> (E.B.);<email>dashzhernakova@gmail.com</email> (D.Z.)</nlm:aff></affiliation></author><author><name sortKey="Bakin, Evgeny" sort="Bakin, Evgeny" uniqKey="Bakin E" first="Evgeny" last="Bakin">Evgeny Bakin</name><affiliation><nlm:aff id="af1-genes-09-00185">Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia;<email>mahajrod@gmail.com</email> (S.K.);<email>mikerayko@gmail.com</email> (M.R.);<email>ad3002@gmail.com</email> (A.K.);<email>eugene.bakin@gmail.com</email> (E.B.);<email>dashzhernakova@gmail.com</email> (D.Z.)</nlm:aff></affiliation></author><author><name sortKey="Zhernakova, Daria" sort="Zhernakova, Daria" uniqKey="Zhernakova D" first="Daria" last="Zhernakova">Daria Zhernakova</name><affiliation><nlm:aff id="af1-genes-09-00185">Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia;<email>mahajrod@gmail.com</email> (S.K.);<email>mikerayko@gmail.com</email> (M.R.);<email>ad3002@gmail.com</email> (A.K.);<email>eugene.bakin@gmail.com</email> (E.B.);<email>dashzhernakova@gmail.com</email> (D.Z.)</nlm:aff></affiliation></author><author><name sortKey="Prasad, Kasavajhala" sort="Prasad, Kasavajhala" uniqKey="Prasad K" first="Kasavajhala" last="Prasad">Kasavajhala Prasad</name><affiliation><nlm:aff id="af3-genes-09-00185">Department of Biology, Colorado State University, Fort Collins, CO 80523; USA;<email>kasavajhalaprasad@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Rushworth, Catherine" sort="Rushworth, Catherine" uniqKey="Rushworth C" first="Catherine" last="Rushworth">Catherine Rushworth</name><affiliation><nlm:aff id="af4-genes-09-00185">University and Jepson Herbaria, University of California, Berkeley, NC 94720; USA;<email>crushworth@berkeley.edu</email></nlm:aff></affiliation></author><author><name sortKey="Baskar, R" sort="Baskar, R" uniqKey="Baskar R" first="R." last="Baskar">R. Baskar</name><affiliation><nlm:aff id="af5-genes-09-00185">Department of Biotechnology, Indian Institute of Technology. Sardar Patel road, 600036 Chennai, India;<email>rbaskar@iitm.ac.in</email></nlm:aff></affiliation></author><author><name sortKey="Smetanin, Dmitry" sort="Smetanin, Dmitry" uniqKey="Smetanin D" first="Dmitry" last="Smetanin">Dmitry Smetanin</name><affiliation><nlm:aff id="af6-genes-09-00185">Department of Plant and Microbial Biology Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich; Switzerland;<email>dmitry.smetanin@botinst.uzh.ch</email> (D.S.);<email>grossnik@botinst.uzh.ch</email> (U.G.)</nlm:aff></affiliation></author><author><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><affiliation><nlm:aff id="af7-genes-09-00185">Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; USA;<email>jschmutz@hudsonalpha.org</email> (J.S.);<email>dsrokhsar@gmail.com</email> (D.S.R.)</nlm:aff></affiliation><affiliation wicri:level="2"><nlm:aff id="af8-genes-09-00185">HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806; USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Alabama</region></placeName><wicri:cityArea>HudsonAlpha Institute of Biotechnology, Huntsville</wicri:cityArea></affiliation></author><author><name sortKey="Rokhsar, Daniel S" sort="Rokhsar, Daniel S" uniqKey="Rokhsar D" first="Daniel S." last="Rokhsar">Daniel S. Rokhsar</name><affiliation><nlm:aff id="af7-genes-09-00185">Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; USA;<email>jschmutz@hudsonalpha.org</email> (J.S.);<email>dsrokhsar@gmail.com</email> (D.S.R.)</nlm:aff></affiliation></author><author><name sortKey="Mitchell Olds, Thomas" sort="Mitchell Olds, Thomas" uniqKey="Mitchell Olds T" first="Thomas" last="Mitchell-Olds">Thomas Mitchell-Olds</name><affiliation><nlm:aff id="af9-genes-09-00185">Department of Biology, Duke University, Durham, NC 27708-0338; USA;<email>tmo1@duke.edu</email></nlm:aff></affiliation></author><author><name sortKey="Grossniklaus, Ueli" sort="Grossniklaus, Ueli" uniqKey="Grossniklaus U" first="Ueli" last="Grossniklaus">Ueli Grossniklaus</name><affiliation><nlm:aff id="af6-genes-09-00185">Department of Plant and Microbial Biology Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich; Switzerland;<email>dmitry.smetanin@botinst.uzh.ch</email> (D.S.);<email>grossnik@botinst.uzh.ch</email> (U.G.)</nlm:aff></affiliation></author><author><name sortKey="Brukhin, Vladimir" sort="Brukhin, Vladimir" uniqKey="Brukhin V" first="Vladimir" last="Brukhin">Vladimir Brukhin</name><affiliation><nlm:aff id="af1-genes-09-00185">Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia;<email>mahajrod@gmail.com</email> (S.K.);<email>mikerayko@gmail.com</email> (M.R.);<email>ad3002@gmail.com</email> (A.K.);<email>eugene.bakin@gmail.com</email> (E.B.);<email>dashzhernakova@gmail.com</email> (D.Z.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af10-genes-09-00185">Department of Plant Embryology and Reproductive Biology, Komarov Botanical Institute RAS, 197376 St. Petersburg, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Department of Plant Embryology and Reproductive Biology, Komarov Botanical Institute RAS, 197376 St. Petersburg</wicri:regionArea><wicri:noRegion>197376 St. Petersburg</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genes</title><idno type="eISSN">2073-4425</idno><imprint><date when="2018">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Closely related to the model plant <italic>Arabidopsis thaliana</italic>, the genus <italic>Boechera</italic> is known to contain both sexual and apomictic species or accessions. <italic>Boechera retrofracta</italic> is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. Here we report the de novo assembly of the <italic>B. retrofracta</italic> genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a hybrid approach that combines homology-based and de novo methods 27,048 protein-coding genes were predicted. Also repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were annotated. Finally, genes of <italic>B. retrofracta</italic> and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease <italic>APOLLO</italic> locus, related to apomixis in <italic>Boechera</italic>, and proposed model of its evolution through the series of duplications. An assembled genome of <italic>B. retrofracta</italic> will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species<italic>.</italic></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Sharbel, T F" uniqKey="Sharbel T">T.F. Sharbel</name></author><author><name sortKey="Mitchell Olds, T" uniqKey="Mitchell Olds T">T. Mitchell-Olds</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schranz, M E" uniqKey="Schranz M">M.E. Schranz</name></author><author><name sortKey="Dobes, C" uniqKey="Dobes C">C. Dobes</name></author><author><name sortKey="Koch, M A" uniqKey="Koch M">M.A. Koch</name></author><author><name sortKey="Mitchell Olds, T" uniqKey="Mitchell Olds T">T. Mitchell-Olds</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Naumova, T N" uniqKey="Naumova T">T.N. Naumova</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Aliyu, O M" uniqKey="Aliyu O">O.M. Aliyu</name></author><author><name sortKey="Schranz, M E" uniqKey="Schranz M">M.E. Schranz</name></author><author><name sortKey="Sharbel, T F" uniqKey="Sharbel T">T.F. Sharbel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Koltunow, A M" uniqKey="Koltunow A">A.M. Koltunow</name></author><author><name sortKey="Grossniklaus, U" uniqKey="Grossniklaus U">U. Grossniklaus</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rodriguez Leal, D" uniqKey="Rodriguez Leal D">D. Rodríguez-Leal</name></author><author><name sortKey="Vielle Calzada, J P" uniqKey="Vielle Calzada J">J.P. Vielle-Calzada</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brukhin, V" uniqKey="Brukhin V">V. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Genes (Basel)</journal-id><journal-id journal-id-type="iso-abbrev">Genes (Basel)</journal-id><journal-id journal-id-type="publisher-id">genes</journal-id><journal-title-group><journal-title>Genes</journal-title></journal-title-group><issn pub-type="epub">2073-4425</issn><publisher><publisher-name>MDPI</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">29597328</article-id><article-id pub-id-type="pmc">5924527</article-id><article-id pub-id-type="doi">10.3390/genes9040185</article-id><article-id pub-id-type="publisher-id">genes-09-00185</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Assembly of the <italic>Boechera retrofracta</italic> Genome and Evolutionary Analysis of Apomixis-Associated Genes</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Kliver</surname><given-names>Sergei</given-names></name><xref ref-type="aff" rid="af1-genes-09-00185">1</xref><xref ref-type="aff" rid="af2-genes-09-00185">2</xref></contrib><contrib contrib-type="author"><name><surname>Rayko</surname><given-names>Mike</given-names></name><xref ref-type="aff" rid="af1-genes-09-00185">1</xref></contrib><contrib contrib-type="author"><name><surname>Komissarov</surname><given-names>Alexey</given-names></name><xref ref-type="aff" rid="af1-genes-09-00185">1</xref></contrib><contrib contrib-type="author"><name><surname>Bakin</surname><given-names>Evgeny</given-names></name><xref ref-type="aff" rid="af1-genes-09-00185">1</xref></contrib><contrib contrib-type="author"><name><surname>Zhernakova</surname><given-names>Daria</given-names></name><xref ref-type="aff" rid="af1-genes-09-00185">1</xref></contrib><contrib contrib-type="author"><name><surname>Prasad</surname><given-names>Kasavajhala</given-names></name><xref ref-type="aff" rid="af3-genes-09-00185">3</xref></contrib><contrib contrib-type="author"><name><surname>Rushworth</surname><given-names>Catherine</given-names></name><xref ref-type="aff" rid="af4-genes-09-00185">4</xref></contrib><contrib contrib-type="author"><name><surname>Baskar</surname><given-names>R.</given-names></name><xref ref-type="aff" rid="af5-genes-09-00185">5</xref></contrib><contrib contrib-type="author"><name><surname>Smetanin</surname><given-names>Dmitry</given-names></name><xref ref-type="aff" rid="af6-genes-09-00185">6</xref></contrib><contrib contrib-type="author"><name><surname>Schmutz</surname><given-names>Jeremy</given-names></name><xref ref-type="aff" rid="af7-genes-09-00185">7</xref><xref ref-type="aff" rid="af8-genes-09-00185">8</xref></contrib><contrib contrib-type="author"><name><surname>Rokhsar</surname><given-names>Daniel S.</given-names></name><xref ref-type="aff" rid="af7-genes-09-00185">7</xref></contrib><contrib contrib-type="author"><name><surname>Mitchell-Olds</surname><given-names>Thomas</given-names></name><xref ref-type="aff" rid="af9-genes-09-00185">9</xref></contrib><contrib contrib-type="author"><name><surname>Grossniklaus</surname><given-names>Ueli</given-names></name><xref ref-type="aff" rid="af6-genes-09-00185">6</xref></contrib><contrib contrib-type="author"><name><surname>Brukhin</surname><given-names>Vladimir</given-names></name><xref ref-type="aff" rid="af1-genes-09-00185">1</xref><xref ref-type="aff" rid="af10-genes-09-00185">10</xref><xref rid="c1-genes-09-00185" ref-type="corresp">*</xref></contrib></contrib-group><aff id="af1-genes-09-00185"><label>1</label>Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia;<email>mahajrod@gmail.com</email> (S.K.);<email>mikerayko@gmail.com</email> (M.R.);<email>ad3002@gmail.com</email> (A.K.);<email>eugene.bakin@gmail.com</email> (E.B.);<email>dashzhernakova@gmail.com</email> (D.Z.)</aff><aff id="af2-genes-09-00185"><label>2</label>All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 St. Petersburg, Russia</aff><aff id="af3-genes-09-00185"><label>3</label>Department of Biology, Colorado State University, Fort Collins, CO 80523; USA;<email>kasavajhalaprasad@gmail.com</email></aff><aff id="af4-genes-09-00185"><label>4</label>University and Jepson Herbaria, University of California, Berkeley, NC 94720; USA;<email>crushworth@berkeley.edu</email></aff><aff id="af5-genes-09-00185"><label>5</label>Department of Biotechnology, Indian Institute of Technology. Sardar Patel road, 600036 Chennai, India;<email>rbaskar@iitm.ac.in</email></aff><aff id="af6-genes-09-00185"><label>6</label>Department of Plant and Microbial Biology Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich; Switzerland;<email>dmitry.smetanin@botinst.uzh.ch</email> (D.S.);<email>grossnik@botinst.uzh.ch</email> (U.G.)</aff><aff id="af7-genes-09-00185"><label>7</label>Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; USA;<email>jschmutz@hudsonalpha.org</email> (J.S.);<email>dsrokhsar@gmail.com</email> (D.S.R.)</aff><aff id="af8-genes-09-00185"><label>8</label>HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806; USA</aff><aff id="af9-genes-09-00185"><label>9</label>Department of Biology, Duke University, Durham, NC 27708-0338; USA;<email>tmo1@duke.edu</email></aff><aff id="af10-genes-09-00185"><label>10</label>Department of Plant Embryology and Reproductive Biology, Komarov Botanical Institute RAS, 197376 St. Petersburg, Russia</aff><author-notes><corresp id="c1-genes-09-00185"><label>*</label>Correspondence: <email>vbrukhin@gmail.com</email>; Tel.: +7-965-046-5605</corresp></author-notes><pub-date pub-type="epub"><day>28</day><month>3</month><year>2018</year></pub-date><pub-date pub-type="collection"><month>4</month><year>2018</year></pub-date><volume>9</volume><issue>4</issue><elocation-id>185</elocation-id><history><date date-type="received"><day>14</day><month>2</month><year>2018</year></date><date date-type="accepted"><day>22</day><month>3</month><year>2018</year></date></history><permissions><copyright-statement>© 2018 by the authors.</copyright-statement><copyright-year>2018</copyright-year><license license-type="open-access"><license-p>Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) 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>).</license-p></license></permissions><abstract><p>Closely related to the model plant <italic>Arabidopsis thaliana</italic>, the genus <italic>Boechera</italic> is known to contain both sexual and apomictic species or accessions. <italic>Boechera retrofracta</italic> is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. Here we report the de novo assembly of the <italic>B. retrofracta</italic> genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a hybrid approach that combines homology-based and de novo methods 27,048 protein-coding genes were predicted. Also repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were annotated. Finally, genes of <italic>B. retrofracta</italic> and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease <italic>APOLLO</italic> locus, related to apomixis in <italic>Boechera</italic>, and proposed model of its evolution through the series of duplications. An assembled genome of <italic>B. retrofracta</italic> will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species<italic>.</italic></p></abstract><kwd-group><kwd><italic>Boechera</italic></kwd><kwd>Brassicaceae</kwd><kwd>genome</kwd><kwd>assembly</kwd><kwd>annotation</kwd><kwd>apomixis</kwd></kwd-group></article-meta></front><floats-group><fig id="genes-09-00185-f001" orientation="portrait" position="float"><label>Figure 1</label><caption><p>Plant (<bold>a</bold>) and flower (<bold>b</bold>) of <italic>Boechera retrofracta</italic>.</p></caption><graphic xlink:href="genes-09-00185-g001"></graphic></fig><fig id="genes-09-00185-f002" orientation="portrait" position="float"><label>Figure 2</label><caption><p>Distribution of 23-mers for PE LIB400 library. Only one major peak at 371× coverage is present, however there are detectable duplications and triplications at 737× and 1120× coverage (upper plot, Y axis is on a logarithmic scale).</p></caption><graphic xlink:href="genes-09-00185-g002"></graphic></fig><fig id="genes-09-00185-f003" orientation="portrait" position="float"><label>Figure 3</label><caption><p>Phylogenetic tree of seven Brassicaceae species used for analysis. Maximum likelihood tree was reconstructed by RAxML using 8959 single copy orthologs and was tested with 1000 bootstrap replicates. Numbers near nodes represent corresponding bootstrap support.</p></caption><graphic xlink:href="genes-09-00185-g003"></graphic></fig><fig id="genes-09-00185-f004" orientation="portrait" position="float"><label>Figure 4</label><caption><p>Phylogenetic tree of the isoforms of <italic>APOLLO</italic> locus (exonuclease NEN) in seven species of interest and alleles of <italic>APOLLO</italic> locus of apomictic <italic>Boechera</italic> species from Corral et al (2013) [<xref rid="B56-genes-09-00185" ref-type="bibr">56</xref>]. Sequences of <italic>Populus trichocarpa</italic>, <italic>Vitus vinifera</italic> and <italic>Glycine max</italic> were used as outgroup. The clade related to the <italic>APOLLO</italic> locus is shown in green, with apo-alleles shown in red. Numbers near nodes represent corresponding bootstrap support.</p></caption><graphic xlink:href="genes-09-00185-g004"></graphic></fig><table-wrap id="genes-09-00185-t001" orientation="portrait" position="float"><object-id pub-id-type="pii">genes-09-00185-t001_Table 1</object-id><label>Table 1</label><caption><p>General statistics for all stages of the assembly pipeline.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Parameter</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Contigs</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Extended Contigs</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Raw Scaffolds</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Intermediate Scaffolfs</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Gap Closed Scaffolds</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Final Scaffolds</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1">Longest contig</td><td align="center" valign="middle" rowspan="1" colspan="1">791,985</td><td align="center" valign="middle" rowspan="1" colspan="1">792,340</td><td align="center" valign="middle" rowspan="1" colspan="1">8,101,256</td><td align="center" valign="middle" rowspan="1" colspan="1">9,045,706</td><td align="center" valign="middle" rowspan="1" colspan="1">9,049,080</td><td align="center" valign="middle" rowspan="1" colspan="1">9,049,080</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Ns</td><td align="center" valign="middle" rowspan="1" colspan="1">28,100</td><td align="center" valign="middle" rowspan="1" colspan="1">28,100</td><td align="center" valign="middle" rowspan="1" colspan="1">11,890,519</td><td align="center" valign="middle" rowspan="1" colspan="1">16,366,994</td><td align="center" valign="middle" rowspan="1" colspan="1">12,409,189</td><td align="center" valign="middle" rowspan="1" colspan="1">12,409,189</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Total length</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">225,649 216</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">226,402,628</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">236,469,041</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">240,945,496</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">241,014,839</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">222,253,471</td></tr></tbody></table></table-wrap><table-wrap id="genes-09-00185-t002" orientation="portrait" position="float"><object-id pub-id-type="pii">genes-09-00185-t002_Table 2</object-id><label>Table 2</label><caption><p>N50 values for all stages of the assembly pipeline and several different cutoffs for minimal scaffold length.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Scaffold Length Cutoff</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Contigs</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Extended Contigs</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Raw Scaffolds</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Intermediate Scaffolfs</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Gap Closed Scaffolds</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Final Scaffolds</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1">all</td><td align="center" valign="middle" rowspan="1" colspan="1">85,286</td><td align="center" valign="middle" rowspan="1" colspan="1">84,648</td><td align="center" valign="middle" rowspan="1" colspan="1">1,256,534</td><td align="center" valign="middle" rowspan="1" colspan="1">1,898,006</td><td align="center" valign="middle" rowspan="1" colspan="1">1,898,985</td><td align="center" valign="middle" rowspan="1" colspan="1">2,297,899</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">≥100</td><td align="center" valign="middle" rowspan="1" colspan="1">85,286</td><td align="center" valign="middle" rowspan="1" colspan="1">84,648</td><td align="center" valign="middle" rowspan="1" colspan="1">1,256,534</td><td align="center" valign="middle" rowspan="1" colspan="1">1,898,006</td><td align="center" valign="middle" rowspan="1" colspan="1">1,898,985</td><td align="center" valign="middle" rowspan="1" colspan="1">2,297,899</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">≥250</td><td align="center" valign="middle" rowspan="1" colspan="1">101,388</td><td align="center" valign="middle" rowspan="1" colspan="1">100,393</td><td align="center" valign="middle" rowspan="1" colspan="1">1,442,421</td><td align="center" valign="middle" rowspan="1" colspan="1">2,296,484</td><td align="center" valign="middle" rowspan="1" colspan="1">2,297,899</td><td align="center" valign="middle" rowspan="1" colspan="1">2,297,899</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">≥500</td><td align="center" valign="middle" rowspan="1" colspan="1">115,732</td><td align="center" valign="middle" rowspan="1" colspan="1">115,486</td><td align="center" valign="middle" rowspan="1" colspan="1">1,538,795</td><td align="center" valign="middle" rowspan="1" colspan="1">2,678,857</td><td align="center" valign="middle" rowspan="1" colspan="1">2,680,941</td><td align="center" valign="middle" rowspan="1" colspan="1">2,680,941</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">≥1000</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">122,300</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">121,678</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">1,704,064</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2,678,857</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2,680,941</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2,680,941</td></tr></tbody></table></table-wrap><table-wrap id="genes-09-00185-t003" orientation="portrait" position="float"><object-id pub-id-type="pii">genes-09-00185-t003_Table 3</object-id><label>Table 3</label><caption><p>Repeats found by RepeatMasker.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Class</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Number of Elements</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Total Length (bp)</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Fraction of Assembly (%)</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1">SINEs</td><td align="center" valign="middle" rowspan="1" colspan="1">577</td><td align="center" valign="middle" rowspan="1" colspan="1">125,298</td><td align="center" valign="middle" rowspan="1" colspan="1">0.06</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">LINEs</td><td align="center" valign="middle" rowspan="1" colspan="1">7075</td><td align="center" valign="middle" rowspan="1" colspan="1">4,351,241</td><td align="center" valign="middle" rowspan="1" colspan="1">1.96</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">LTR elements</td><td align="center" valign="middle" rowspan="1" colspan="1">51,040</td><td align="center" valign="middle" rowspan="1" colspan="1">40,608,195</td><td align="center" valign="middle" rowspan="1" colspan="1">18.27</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">DNA elements</td><td align="center" valign="middle" rowspan="1" colspan="1">31,638</td><td align="center" valign="middle" rowspan="1" colspan="1">12,868,684</td><td align="center" valign="middle" rowspan="1" colspan="1">5.79</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Unclassified</td><td align="center" valign="middle" rowspan="1" colspan="1">82,693</td><td align="center" valign="middle" rowspan="1" colspan="1">24,363,135</td><td align="center" valign="middle" rowspan="1" colspan="1">10.96</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Total interspersed repeats</td><td align="center" valign="middle" rowspan="1" colspan="1">-</td><td align="center" valign="middle" rowspan="1" colspan="1">82,316,553</td><td align="center" valign="middle" rowspan="1" colspan="1">37.04</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Small RNA</td><td align="center" valign="middle" rowspan="1" colspan="1">5461</td><td align="center" valign="middle" rowspan="1" colspan="1">1,599,354</td><td align="center" valign="middle" rowspan="1" colspan="1">0.72</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Satellites</td><td align="center" valign="middle" rowspan="1" colspan="1">1541</td><td align="center" valign="middle" rowspan="1" colspan="1">573,026</td><td align="center" valign="middle" rowspan="1" colspan="1">0.26</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Simple repeats</td><td align="center" valign="middle" rowspan="1" colspan="1">2044</td><td align="center" valign="middle" rowspan="1" colspan="1">363,642</td><td align="center" valign="middle" rowspan="1" colspan="1">0.16</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Low complexity</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">56</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">7456</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">0</td></tr></tbody></table></table-wrap><table-wrap id="genes-09-00185-t004" orientation="portrait" position="float"><object-id pub-id-type="pii">genes-09-00185-t004_Table 4</object-id><label>Table 4</label><caption><p>Results of repeat masking performed by three different tools: RepeatMasker [<xref rid="B32-genes-09-00185" ref-type="bibr">32</xref>], TRF [<xref rid="B34-genes-09-00185" ref-type="bibr">34</xref>], WindowMasker [<xref rid="B35-genes-09-00185" ref-type="bibr">35</xref>].</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Tool</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Number of Repeats</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Total Length (Mbp)</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1">RepeatMasker</td><td align="center" valign="middle" rowspan="1" colspan="1">173,023</td><td align="center" valign="middle" rowspan="1" colspan="1">82.31</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">TRF</td><td align="center" valign="middle" rowspan="1" colspan="1">100,593</td><td align="center" valign="middle" rowspan="1" colspan="1">17.41</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Windowmasker</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">1,104,650</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">64.20</td></tr></tbody></table></table-wrap><table-wrap id="genes-09-00185-t005" orientation="portrait" position="float"><object-id pub-id-type="pii">genes-09-00185-t005_Table 5</object-id><label>Table 5</label><caption><p>Annotated transfer RNAs (tRNAs).</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">tRNA Type</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Number</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1">tRNAs decoding standard 20 AA</td><td align="center" valign="middle" rowspan="1" colspan="1">1126</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Selenocysteine tRNAs (TCA)</td><td align="center" valign="middle" rowspan="1" colspan="1">0</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Possible suppressor tRNAs (CTA,TTA)</td><td align="center" valign="middle" rowspan="1" colspan="1">3</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">tRNAs with undetermined isotypes</td><td align="center" valign="middle" rowspan="1" colspan="1">5</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Resolution of Brassicaceae Phylogeny Using Nuclear Genes<break></break>Uncovers Nested Radiations and Supports Convergent<break></break>Morphological Evolution Predicted pseudogenes</td><td align="center" valign="middle" rowspan="1" colspan="1">32</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Total tRNAs</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">1166</td></tr></tbody></table></table-wrap><table-wrap id="genes-09-00185-t006" orientation="portrait" position="float"><object-id pub-id-type="pii">genes-09-00185-t006_Table 6</object-id><label>Table 6</label><caption><p>Annotated ribosomal RNAs (rRNAs).</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">rRNA</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Complete (≥80% of Expected Length)</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Partial (<80% of Expected Length)</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1">5.8S</td><td align="center" valign="middle" rowspan="1" colspan="1">178</td><td align="center" valign="middle" rowspan="1" colspan="1">53</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">5S</td><td align="center" valign="middle" rowspan="1" colspan="1">601</td><td align="center" valign="middle" rowspan="1" colspan="1">104</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">28S</td><td align="center" valign="middle" rowspan="1" colspan="1">0</td><td align="center" valign="middle" rowspan="1" colspan="1">1782</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">18S</td><td align="center" valign="middle" rowspan="1" colspan="1">1</td><td align="center" valign="middle" rowspan="1" colspan="1">1458</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">12S</td><td align="center" valign="middle" rowspan="1" colspan="1">0</td><td align="center" valign="middle" rowspan="1" colspan="1">173</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">16S</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">0</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">607</td></tr></tbody></table></table-wrap><table-wrap id="genes-09-00185-t007" orientation="portrait" position="float"><object-id pub-id-type="pii">genes-09-00185-t007_Table 7</object-id><label>Table 7</label><caption><p>Comparison of genome characteristics of <italic>Boechera retrofracta</italic> with previously sequenced <italic>Boechera stricta</italic> and <italic>Arabidopsis thaliana</italic> genomes. Source for <italic>B.retrofracta</italic>—this paper, <italic>B.stricta</italic>, <italic>Arabidopsis lyrata</italic> and <italic>A.thaliana</italic>—Phytozome v12.1 database [<xref rid="B57-genes-09-00185" ref-type="bibr">57</xref>].</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1"></th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1"><italic>Boechera retrofracta</italic></th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1"><italic>Boechera stricta</italic> v.1.2</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1"><italic>Arabidopsis lyrata</italic> v2.1</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic> TAIR10</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1">Total length</td><td align="center" valign="middle" rowspan="1" colspan="1">227 M</td><td align="center" valign="middle" rowspan="1" colspan="1">184 M</td><td align="center" valign="middle" rowspan="1" colspan="1">207 Mb</td><td align="center" valign="middle" rowspan="1" colspan="1">135 Mb</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Chromosomes</td><td align="center" valign="middle" rowspan="1" colspan="1"><italic>n</italic> = 7</td><td align="center" valign="middle" rowspan="1" colspan="1"><italic>n</italic> = 7</td><td align="center" valign="middle" rowspan="1" colspan="1"><italic>n</italic> = 8</td><td align="center" valign="middle" rowspan="1" colspan="1"><italic>n</italic> = 5</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">Protein-coding loci </td><td align="center" valign="middle" rowspan="1" colspan="1">27,048</td><td align="center" valign="middle" rowspan="1" colspan="1">27,416</td><td align="center" valign="middle" rowspan="1" colspan="1">31,073</td><td align="center" valign="middle" rowspan="1" colspan="1">27,416</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Transcripts</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">28,269</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">29,812</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">33,132</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">35,386</td></tr></tbody></table></table-wrap></floats-group></pmc><affiliations><list><country><li>Russie</li><li>États-Unis</li></country><region><li>Alabama</li></region></list><tree><noCountry><name sortKey="Bakin, Evgeny" sort="Bakin, Evgeny" uniqKey="Bakin E" first="Evgeny" last="Bakin">Evgeny Bakin</name><name sortKey="Baskar, R" sort="Baskar, R" uniqKey="Baskar R" first="R." last="Baskar">R. Baskar</name><name sortKey="Grossniklaus, Ueli" sort="Grossniklaus, Ueli" uniqKey="Grossniklaus U" first="Ueli" last="Grossniklaus">Ueli Grossniklaus</name><name sortKey="Komissarov, Alexey" sort="Komissarov, Alexey" uniqKey="Komissarov A" first="Alexey" last="Komissarov">Alexey Komissarov</name><name sortKey="Mitchell Olds, Thomas" sort="Mitchell Olds, Thomas" uniqKey="Mitchell Olds T" first="Thomas" last="Mitchell-Olds">Thomas Mitchell-Olds</name><name sortKey="Prasad, Kasavajhala" sort="Prasad, Kasavajhala" uniqKey="Prasad K" first="Kasavajhala" last="Prasad">Kasavajhala Prasad</name><name sortKey="Rayko, Mike" sort="Rayko, Mike" uniqKey="Rayko M" first="Mike" last="Rayko">Mike Rayko</name><name sortKey="Rokhsar, Daniel S" sort="Rokhsar, Daniel S" uniqKey="Rokhsar D" first="Daniel S." last="Rokhsar">Daniel S. Rokhsar</name><name sortKey="Rushworth, Catherine" sort="Rushworth, Catherine" uniqKey="Rushworth C" first="Catherine" last="Rushworth">Catherine Rushworth</name><name sortKey="Smetanin, Dmitry" sort="Smetanin, Dmitry" uniqKey="Smetanin D" first="Dmitry" last="Smetanin">Dmitry Smetanin</name><name sortKey="Zhernakova, Daria" sort="Zhernakova, Daria" uniqKey="Zhernakova D" first="Daria" last="Zhernakova">Daria Zhernakova</name></noCountry><country name="Russie"><noRegion><name sortKey="Kliver, Sergei" sort="Kliver, Sergei" uniqKey="Kliver S" first="Sergei" last="Kliver">Sergei Kliver</name></noRegion><name sortKey="Brukhin, Vladimir" sort="Brukhin, Vladimir" uniqKey="Brukhin V" first="Vladimir" last="Brukhin">Vladimir Brukhin</name></country><country name="États-Unis"><region name="Alabama"><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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