The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure
Identifieur interne : 000002 ( Pmc/Curation ); précédent : 000001; suivant : 000003The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure
Auteurs : Sateesh Kagale [Canada] ; Chushin Koh [Canada] ; John Nixon [Canada] ; Venkatesh Bollina [Canada] ; Wayne E. Clarke [Canada] ; Reetu Tuteja [Irlande (pays)] ; Charles Spillane [Irlande (pays)] ; Stephen J. Robinson [Canada] ; Matthew G. Links [Canada] ; Carling Clarke [Canada] ; Erin E. Higgins [Canada] ; Terry Huebert [Canada] ; Andrew G. Sharpe [Canada] ; Isobel A. P. Parkin [Canada]Source :
- Nature Communications [ 2041-1723 ] ; 2014.
Abstract
Url:
DOI: 10.1038/ncomms4706
PubMed: 24759634
PubMed Central: 4015329
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The emerging biofuel crop <italic>Camelina sativa</italic> retains a highly undifferentiated hexaploid genome structure</title><author><name sortKey="Kagale, Sateesh" sort="Kagale, Sateesh" uniqKey="Kagale S" first="Sateesh" last="Kagale">Sateesh Kagale</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a2"><institution>National Research Council Canada</institution>, 110 Gymnasium Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0W9</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Koh, Chushin" sort="Koh, Chushin" uniqKey="Koh C" first="Chushin" last="Koh">Chushin Koh</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>National Research Council Canada</institution>, 110 Gymnasium Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0W9</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Nixon, John" sort="Nixon, John" uniqKey="Nixon J" first="John" last="Nixon">John Nixon</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Bollina, Venkatesh" sort="Bollina, Venkatesh" uniqKey="Bollina V" first="Venkatesh" last="Bollina">Venkatesh Bollina</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Clarke, Wayne E" sort="Clarke, Wayne E" uniqKey="Clarke W" first="Wayne E." last="Clarke">Wayne E. 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Robinson</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Links, Matthew G" sort="Links, Matthew G" uniqKey="Links M" first="Matthew G." last="Links">Matthew G. Links</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Clarke, Carling" sort="Clarke, Carling" uniqKey="Clarke C" first="Carling" last="Clarke">Carling Clarke</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>National Research Council Canada</institution>, 110 Gymnasium Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0W9</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Higgins, Erin E" sort="Higgins, Erin E" uniqKey="Higgins E" first="Erin E." last="Higgins">Erin E. Higgins</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Huebert, Terry" sort="Huebert, Terry" uniqKey="Huebert T" first="Terry" last="Huebert">Terry Huebert</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Sharpe, Andrew G" sort="Sharpe, Andrew G" uniqKey="Sharpe A" first="Andrew G." last="Sharpe">Andrew G. Sharpe</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>National Research Council Canada</institution>, 110 Gymnasium Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0W9</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Parkin, Isobel A P" sort="Parkin, Isobel A P" uniqKey="Parkin I" first="Isobel A. P." last="Parkin">Isobel A. P. Parkin</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24759634</idno><idno type="pmc">4015329</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015329</idno><idno type="RBID">PMC:4015329</idno><idno type="doi">10.1038/ncomms4706</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000002</idno><idno type="wicri:Area/Pmc/Curation">000002</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The emerging biofuel crop <italic>Camelina sativa</italic> retains a highly undifferentiated hexaploid genome structure</title><author><name sortKey="Kagale, Sateesh" sort="Kagale, Sateesh" uniqKey="Kagale S" first="Sateesh" last="Kagale">Sateesh Kagale</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a2"><institution>National Research Council Canada</institution>, 110 Gymnasium Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0W9</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Koh, Chushin" sort="Koh, Chushin" uniqKey="Koh C" first="Chushin" last="Koh">Chushin Koh</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>National Research Council Canada</institution>, 110 Gymnasium Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0W9</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Nixon, John" sort="Nixon, John" uniqKey="Nixon J" first="John" last="Nixon">John Nixon</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Bollina, Venkatesh" sort="Bollina, Venkatesh" uniqKey="Bollina V" first="Venkatesh" last="Bollina">Venkatesh Bollina</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Clarke, Wayne E" sort="Clarke, Wayne E" uniqKey="Clarke W" first="Wayne E." last="Clarke">Wayne E. Clarke</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Tuteja, Reetu" sort="Tuteja, Reetu" uniqKey="Tuteja R" first="Reetu" last="Tuteja">Reetu Tuteja</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>Plant and AgriBiosciences Centre (PABC), School of Natural Sciences, National University of Ireland Galway</institution>, Galway,<country>Ireland</country></nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Spillane, Charles" sort="Spillane, Charles" uniqKey="Spillane C" first="Charles" last="Spillane">Charles Spillane</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>Plant and AgriBiosciences Centre (PABC), School of Natural Sciences, National University of Ireland Galway</institution>, Galway,<country>Ireland</country></nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Robinson, Stephen J" sort="Robinson, Stephen J" uniqKey="Robinson S" first="Stephen J." last="Robinson">Stephen J. Robinson</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Links, Matthew G" sort="Links, Matthew G" uniqKey="Links M" first="Matthew G." last="Links">Matthew G. Links</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Clarke, Carling" sort="Clarke, Carling" uniqKey="Clarke C" first="Carling" last="Clarke">Carling Clarke</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>National Research Council Canada</institution>, 110 Gymnasium Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0W9</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Higgins, Erin E" sort="Higgins, Erin E" uniqKey="Higgins E" first="Erin E." last="Higgins">Erin E. Higgins</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Huebert, Terry" sort="Huebert, Terry" uniqKey="Huebert T" first="Terry" last="Huebert">Terry Huebert</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Sharpe, Andrew G" sort="Sharpe, Andrew G" uniqKey="Sharpe A" first="Andrew G." last="Sharpe">Andrew G. Sharpe</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>National Research Council Canada</institution>, 110 Gymnasium Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0W9</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Parkin, Isobel A P" sort="Parkin, Isobel A P" uniqKey="Parkin I" first="Isobel A. P." last="Parkin">Isobel A. P. Parkin</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Nature Communications</title><idno type="eISSN">2041-1723</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>Camelina sativa</italic> is an oilseed with desirable agronomic and oil-quality attributes for a viable industrial oil platform crop. Here we generate the first chromosome-scale high-quality reference genome sequence for <italic>C. sativa</italic> and annotated 89,418 protein-coding genes, representing a whole-genome triplication event relative to the crucifer model <italic>Arabidopsis thaliana</italic>. <italic>C. sativa</italic> represents the first crop species to be sequenced from lineage I of the Brassicaceae. The well-preserved hexaploid genome structure of <italic>C. sativa</italic> surprisingly mirrors those of economically important amphidiploid <italic>Brassica</italic> crop species from lineage II as well as wheat and cotton. The three genomes of <italic>C. sativa</italic> show no evidence of fractionation bias and limited expression-level bias, both characteristics commonly associated with polyploid evolution. The highly undifferentiated polyploid genome of <italic>C. sativa</italic> presents significant consequences for breeding and genetic manipulation of this industrial oil crop.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Gehringer, A" uniqKey="Gehringer A">A. Gehringer</name></author><author><name sortKey="Friedt, W" uniqKey="Friedt W">W. Friedt</name></author><author><name sortKey="Luhs, W" uniqKey="Luhs W">W. Luhs</name></author><author><name sortKey="Snowdon, R J" uniqKey="Snowdon R">R. J. Snowdon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Moser, B R" uniqKey="Moser B">B. R. Moser</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Seguin Swartz, G" uniqKey="Seguin Swartz G">G. Séguin-Swartz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Beilstein, M A" uniqKey="Beilstein M">M. A. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Nat Commun</journal-id><journal-id journal-id-type="iso-abbrev">Nat Commun</journal-id><journal-title-group><journal-title>Nature Communications</journal-title></journal-title-group><issn pub-type="epub">2041-1723</issn><publisher><publisher-name>Nature Pub. Group</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24759634</article-id><article-id pub-id-type="pmc">4015329</article-id><article-id pub-id-type="pii">ncomms4706</article-id><article-id pub-id-type="doi">10.1038/ncomms4706</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>The emerging biofuel crop <italic>Camelina sativa</italic> retains a highly undifferentiated hexaploid genome structure</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Kagale</surname><given-names>Sateesh</given-names></name><xref ref-type="aff" rid="a1">1</xref><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>Koh</surname><given-names>Chushin</given-names></name><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>Nixon</surname><given-names>John</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Bollina</surname><given-names>Venkatesh</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Clarke</surname><given-names>Wayne E.</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Tuteja</surname><given-names>Reetu</given-names></name><xref ref-type="aff" rid="a3">3</xref></contrib><contrib contrib-type="author"><name><surname>Spillane</surname><given-names>Charles</given-names></name><xref ref-type="aff" rid="a3">3</xref></contrib><contrib contrib-type="author"><name><surname>Robinson</surname><given-names>Stephen J.</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Links</surname><given-names>Matthew G.</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Clarke</surname><given-names>Carling</given-names></name><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>Higgins</surname><given-names>Erin E.</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Huebert</surname><given-names>Terry</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Sharpe</surname><given-names>Andrew G.</given-names></name><xref ref-type="corresp" rid="c1">a</xref><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>Parkin</surname><given-names>Isobel A. P.</given-names></name><xref ref-type="corresp" rid="c2">b</xref><xref ref-type="aff" rid="a1">1</xref></contrib><aff id="a1"><label>1</label><institution>Saskatoon Research Centre, Agriculture and Agri-Food Canada</institution>, 107 Science Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0X2</aff><aff id="a2"><label>2</label><institution>National Research Council Canada</institution>, 110 Gymnasium Place, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0W9</aff><aff id="a3"><label>3</label><institution>Plant and AgriBiosciences Centre (PABC), School of Natural Sciences, National University of Ireland Galway</institution>, Galway,<country>Ireland</country></aff></contrib-group><author-notes><corresp id="c1"><label>a</label><email>andrew.sharpe@nrc-cnrc.gc.ca</email></corresp><corresp id="c2"><label>b</label><email>isobel.parkin@agr.gc.ca</email></corresp></author-notes><pub-date pub-type="epub"><day>23</day><month>04</month><year>2014</year></pub-date><volume>5</volume><elocation-id>3706</elocation-id><history><date date-type="received"><day>06</day><month>01</month><year>2014</year></date><date date-type="accepted"><day>21</day><month>03</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by-nc-sa/3.0/"><pmc-comment>author-paid</pmc-comment>
<license-p>This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/</license-p></license></permissions><abstract><p><italic>Camelina sativa</italic> is an oilseed with desirable agronomic and oil-quality attributes for a viable industrial oil platform crop. Here we generate the first chromosome-scale high-quality reference genome sequence for <italic>C. sativa</italic> and annotated 89,418 protein-coding genes, representing a whole-genome triplication event relative to the crucifer model <italic>Arabidopsis thaliana</italic>. <italic>C. sativa</italic> represents the first crop species to be sequenced from lineage I of the Brassicaceae. The well-preserved hexaploid genome structure of <italic>C. sativa</italic> surprisingly mirrors those of economically important amphidiploid <italic>Brassica</italic> crop species from lineage II as well as wheat and cotton. The three genomes of <italic>C. sativa</italic> show no evidence of fractionation bias and limited expression-level bias, both characteristics commonly associated with polyploid evolution. The highly undifferentiated polyploid genome of <italic>C. sativa</italic> presents significant consequences for breeding and genetic manipulation of this industrial oil crop.</p></abstract><abstract abstract-type="web-summary"><p><inline-graphic id="i1" xlink:href="ncomms4706-i1.jpg"></inline-graphic><italic>Camelina sativa</italic> is an oilseed crop with important industrial applications. Here, the authors sequence the <italic>C. sativa</italic> genome to investigate the genome organization and evolution of this species, and to provide a valuable tool for genetic engineering and potential crop improvement.</p></abstract></article-meta></front><floats-group><fig id="f1"><label>Figure 1</label><caption><title>The <italic>Camelina sativa</italic> genome.</title><p>From the outside ring to the centre: (1) the twenty <italic>C. sativa</italic> pseudochromosomes (Chr1–20 represented on Mb scale) are shown in different colours with putative centromeric regions indicated by black bands; (2) gene expression levels (log10(average FPKM), bin=250 Kb)), values range from 0 (yellow) to 3.92 (red); (3) the distribution of protein-coding regions (nucleotides per 500 Kb; orange) compared with repetitive sequences (nucleotides per 500 Kb; yellow); and (4) <italic>Ka</italic>/<italic>Ks</italic> ratios (median, bin=500 kb) of syntenic (blue) and non-syntenic (green) genes. The centre shows a graphical view of the triplicated segments of annotated genes connected with lines of colours matching those for the pseudochromosomes.</p></caption><graphic xlink:href="ncomms4706-f1"></graphic></fig><fig id="f2"><label>Figure 2</label><caption><title>Comparison of gene number in <italic>C. sativa</italic> plotted against genome size with a subset of completely sequenced plant genomes (<italic>N</italic>=35).</title><p>The significance test for a single outlier in regression data was performed as described in detail in <xref ref-type="supplementary-material" rid="S1">Supplementary Note 8</xref> and the confidence intervals for the regression line are shown as dotted lines. Mes, <italic>Manihot esculenta</italic>; Rco, <italic>Ricinus communis</italic>; Lus, <italic>Linum usitatissimum</italic>; Ptr, <italic>Populus trichocarpa</italic>; Mtr, <italic>Medicago truncatula</italic>; Pvu, <italic>Phaseolus vulgaris</italic>; Gma, <italic>Glycine max</italic>; Csa, <italic>Cucumis sativis</italic>; Ppe, <italic>Prunus persica</italic>; Mdo, <italic>Malus domestica</italic>; Fve, <italic>Fragaria vesca</italic>; Ath, <italic>Arabidopsis thaliana</italic>; Aly, <italic>Arabidopsis lyrata</italic>; Csa, <italic>Camelina sativa</italic>; Cru, <italic>Capsella rubella</italic>; Bra, <italic>Brassica rapa</italic>; Tha, <italic>Thellungiella halophila</italic>; Cpa, <italic>Carica papaya</italic>; Gra, <italic>Gossypium raimondii</italic>; Tca, <italic>Theobroma cacao</italic>; Csi, <italic>Citrus sinensis</italic>; Egr, <italic>Eucalyptus grandis</italic>; Vvi, <italic>Vitis vinifera</italic>; Stu, <italic>Solanum tuberosum</italic>; Sly, <italic>Solanum lycopersicum</italic>; Mgu, <italic>Mimulus guttatus</italic>; Aco, <italic>Aquilegia coerulea</italic>; Sbi, <italic>Sorghum bicolour</italic>; Zma, <italic>Zea mays</italic>; Sit, <italic>Setaria italica</italic>; Pvi, <italic>Panicum virgatum</italic>; Osa, <italic>Oryza sativa</italic>; Bdi, <italic>Brachypodium distachyon</italic>; Smo, <italic>Selaginella moellendorfii</italic>; Ppa, <italic>Physcomitrella patens</italic>.</p></caption><graphic xlink:href="ncomms4706-f2"></graphic></fig><fig id="f3"><label>Figure 3</label><caption><title>Comparative analysis and evolution of the <italic>C. sativa</italic> genome.</title><p>(<bold>a</bold>) MUMer plot comparing the <italic>C. sativa</italic> and <italic>A. lyrata</italic> genomes. Syntenic and collinear regions making the three complete sub-genomes in <italic>C. sativa</italic> are circled in red, blue and green. (<bold>b</bold>) Reconstruction of the three sub-genomes of <italic>C. sativa.</italic> Chromosome and ancestral genomic-block-level organization of the sub-genomes in <italic>C. sativa</italic> is shown. Based on synteny and collinearity between <italic>C. sativa</italic> and <italic>Arabidopsis</italic> species, and GB contiguity in the ancestral karyotype, pseudochromosomes were assigned to three sub-genomes in <italic>C. sativa</italic>. Each pseudochromosome was subdivided among ancestral genomic blocks (A–X), which are coloured based on their occurrence in the ACK. (<bold>c</bold>) ACK consisting of the 24 conserved genomic blocks (A–X). (<bold>d</bold>) The ancestral diploid karyotype (derivative of ACK) of <italic>C. sativa</italic>. (<bold>e</bold>) The presumed origin and reconstruction of the fusion chromosome (AK2/4) of the dACK.</p></caption><graphic xlink:href="ncomms4706-f3"></graphic></fig><fig id="f4"><label>Figure 4</label><caption><title>Phylogenetic relationship between the three sub-genomes of <italic>C. sativa</italic> and lower-chromosome <italic>Camelina</italic> species.</title><p>A maximum-likelihood tree produced from a supermatrix constructed using 4,867 orthologous sequences. Clade support values near nodes represent bootstrap proportions in percentages. Branch lengths represent estimated nucleotide substitutions per site.</p></caption><graphic xlink:href="ncomms4706-f4"></graphic></fig><fig id="f5"><label>Figure 5</label><caption><title>Age distribution of duplicated genes in <italic>C. sativa</italic>.</title><p>Gaussian mixture models fitted to frequency distributions of <italic>K</italic>s (synonymous substitution) values obtained by comparing pairs of paralogous (<italic>C. sativa</italic>—neopolyploidy) and orthologous (Sub-genomes 1/2/3 <italic>versus A. thaliana</italic>) genes are shown. The mixture model analysis is described in <xref ref-type="supplementary-material" rid="S1">Supplementary Note 9</xref> and the complete list of Gaussian components is provided in <xref ref-type="supplementary-material" rid="S1">Supplementary Table 23</xref>.</p></caption><graphic xlink:href="ncomms4706-f5"></graphic></fig><fig id="f6"><label>Figure 6</label><caption><title>Gene expression dynamics reveal genome dominance and functional diversification of <italic>C. sativa</italic> homeologous genes.</title><p>(<bold>a</bold>) Relationship between gene retention rate following whole-genome triplication and the gene expression levels. (<bold>b</bold>) Cumulative frequency of homeologous genes belonging to the three sub-genomes within <italic>C. sativa</italic> with highest expression across all tissue types. <italic>P</italic> values (ANOVA test for interaction, <italic>N</italic>=108 per gene triplet) were calculated for interaction between sub-genomes (G) and tissue-type (T) effects on expression. To highlight differences between sub-genomes only the subset of the data with <italic>P</italic>>10<sup>−10</sup> is shown. (<bold>c</bold>) Scatterplot showing the magnitude of interaction effect calculated as the s.d. from a random effects model estimate for G × T interaction variance. Homeologous triplets were classified into groups, no interaction (<italic>P</italic>>0.05; ANOVA test for interaction, <italic>N</italic>=108), negligible interaction (<italic>P</italic><0.05 and STDEV(G × T)<0.25) and interaction (<italic>P</italic><0.05 and STDEV(G × T)>0.25).</p></caption><graphic xlink:href="ncomms4706-f6"></graphic></fig><table-wrap position="float" id="t1"><label>Table 1</label><caption><title>Incidence of expression and functional diversification of fully retained acyl-lipid metabolism related genes in <italic>C. sativa</italic>.</title></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="center"></col><col align="center"></col></colgroup><thead valign="bottom"><tr><th align="left" valign="top" charoff="50"> </th><th align="center" valign="top" charoff="50"><bold>All</bold></th><th align="center" valign="top" charoff="50"><bold>Acyl-lipid metabolism</bold></th></tr></thead><tbody valign="top"><tr><td align="left" valign="top" charoff="50">Fully retained triplets</td><td align="center" valign="top" charoff="50">18,565</td><td align="center" valign="top" charoff="50">586</td></tr><tr><td align="left" valign="top" charoff="50">Significant expression divergence<xref ref-type="fn" rid="t1-fn1">*</xref></td><td align="char" valign="top" char="(" charoff="50">14,391 (77.5%)</td><td align="char" valign="top" char="(" charoff="50">497 (84.8%)</td></tr><tr><td align="left" valign="top" charoff="50">Significant interaction effect<xref ref-type="fn" rid="t1-fn2">†</xref></td><td align="char" valign="top" char="(" charoff="50">4,106 (22.1%)</td><td align="char" valign="top" char="(" charoff="50">181 (30.9%)</td></tr><tr><td align="left" valign="top" charoff="50">Gene silencing</td><td align="char" valign="top" char="(" charoff="50">900 (4.8%)</td><td align="char" valign="top" char="(" charoff="50">23 (3.9%)</td></tr><tr><td align="left" valign="top" charoff="50">Functional divergence</td><td align="char" valign="top" char="(" charoff="50">2,603 (14.0%)</td><td align="char" valign="top" char="(" charoff="50">90 (15.4%)</td></tr></tbody></table><table-wrap-foot><fn id="t1-fn1"><p><sup>*</sup>G × T interaction; <italic>P</italic><0.05 (ANOVA test for interaction); sample size <italic>N</italic>=108 per gene triplet (number of genes × number of tissue types (12) × number of replications (3)).</p></fn><fn id="t1-fn2"><p><sup>†</sup><italic>P</italic><0.05 (ANOVA test for interaction); STDEV (G × T random effects)>0.25); sample size <italic>N</italic>=108 per gene triplet (number of genes × number of tissue types (12) × number of replications (3)).</p></fn></table-wrap-foot></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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