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Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes

Identifieur interne : 000A60 ( Main/Exploration ); précédent : 000A59; suivant : 000A61

Assembly 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 :

RBID : PMC:5924527

Abstract

Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta 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 B. retrofracta 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 B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease APOLLO locus, related to apomixis in Boechera, and proposed model of its evolution through the series of duplications. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species.


Url:
DOI: 10.3390/genes9040185
PubMed: 29597328
PubMed Central: 5924527


Affiliations:


Links toward previous steps (curation, corpus...)


Le document en format XML

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<name sortKey="Prasad, Kasavajhala" sort="Prasad, Kasavajhala" uniqKey="Prasad K" first="Kasavajhala" last="Prasad">Kasavajhala Prasad</name>
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<nlm:aff id="af3-genes-09-00185">Department of Biology, Colorado State University, Fort Collins, CO 80523; USA;
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<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>
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<name sortKey="Baskar, R" sort="Baskar, R" uniqKey="Baskar R" first="R." last="Baskar">R. Baskar</name>
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<email>jschmutz@hudsonalpha.org</email>
(J.S.);
<email>dsrokhsar@gmail.com</email>
(D.S.R.)</nlm:aff>
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<name sortKey="Mitchell Olds, Thomas" sort="Mitchell Olds, Thomas" uniqKey="Mitchell Olds T" first="Thomas" last="Mitchell-Olds">Thomas Mitchell-Olds</name>
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<name sortKey="Grossniklaus, Ueli" sort="Grossniklaus, Ueli" uniqKey="Grossniklaus U" first="Ueli" last="Grossniklaus">Ueli Grossniklaus</name>
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<name sortKey="Brukhin, Vladimir" sort="Brukhin, Vladimir" uniqKey="Brukhin V" first="Vladimir" last="Brukhin">Vladimir Brukhin</name>
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<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>
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<nlm:aff id="af10-genes-09-00185">Department of Plant Embryology and Reproductive Biology, Komarov Botanical Institute RAS, 197376 St. Petersburg, Russia</nlm:aff>
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<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>
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<email>eugene.bakin@gmail.com</email>
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<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>
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<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>
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<author>
<name sortKey="Szklarczyk, D" uniqKey="Szklarczyk D">D. Szklarczyk</name>
</author>
<author>
<name sortKey="Forslund, K" uniqKey="Forslund K">K. Forslund</name>
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<author>
<name sortKey="Cook, H" uniqKey="Cook H">H. Cook</name>
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<author>
<name sortKey="Heller, D" uniqKey="Heller D">D. Heller</name>
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<author>
<name sortKey="Walter, M C" uniqKey="Walter M">M.C. Walter</name>
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<author>
<name sortKey="Rattei, T" uniqKey="Rattei T">T. Rattei</name>
</author>
<author>
<name sortKey="Mende, D R" uniqKey="Mende D">D.R. Mende</name>
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</author>
<author>
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<name sortKey="Earl, D" uniqKey="Earl D">D. Earl</name>
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<name sortKey="Haussler, D" uniqKey="Haussler D">D. Haussler</name>
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<li>Russie</li>
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</country>
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<li>Alabama</li>
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<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>
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<name sortKey="Kliver, Sergei" sort="Kliver, Sergei" uniqKey="Kliver S" first="Sergei" last="Kliver">Sergei Kliver</name>
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<name sortKey="Brukhin, Vladimir" sort="Brukhin, Vladimir" uniqKey="Brukhin V" first="Vladimir" last="Brukhin">Vladimir Brukhin</name>
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<name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name>
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</record>

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