A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa.
Identifieur interne : 000069 ( Main/Corpus ); précédent : 000068; suivant : 000070A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa.
Auteurs : Brigitte T. Hofmeister ; Johanna Denkena ; Maria Colomé-Tatché ; Yadollah Shahryary ; Rashmi Hazarika ; Jane Grimwood ; Sujan Mamidi ; Jerry Jenkins ; Paul P. Grabowski ; Avinash Sreedasyam ; Shengqiang Shu ; Kerrie Barry ; Kathleen Lail ; Catherine Adam ; Anna Lipzen ; Rotem Sorek ; Dave Kudrna ; Jayson Talag ; Rod Wing ; David W. Hall ; Daniel Jacobsen ; Gerald A. Tuskan ; Jeremy Schmutz ; Frank Johannes ; Robert J. SchmitzSource :
- Genome biology [ 1474-760X ] ; 2020.
Abstract
BACKGROUND
Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local adaption in an ecoevolutionary context, particularly in long-lived perennials.
RESULTS
Here, we generate a new high-quality reference genome from the oldest branch of a wild Populus trichocarpa tree with two dominant stems which have been evolving independently for 330 years. By sampling multiple, age-estimated branches of this tree, we use a multi-omics approach to quantify age-related somatic changes at the genetic, epigenetic, and transcriptional level. We show that the per-year somatic mutation and epimutation rates are lower than in annuals and that transcriptional variation is mainly independent of age divergence and cytosine methylation. Furthermore, a detailed analysis of the somatic epimutation spectrum indicates that transgenerationally heritable epimutations originate mainly from DNA methylation maintenance errors during mitotic rather than during meiotic cell divisions.
CONCLUSION
Taken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.
DOI: 10.1186/s13059-020-02162-5
PubMed: 33023654
PubMed Central: PMC7539514
Links to Exploration step
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa.</title><author><name sortKey="Hofmeister, Brigitte T" sort="Hofmeister, Brigitte T" uniqKey="Hofmeister B" first="Brigitte T" last="Hofmeister">Brigitte T. Hofmeister</name><affiliation><nlm:affiliation>Institute of Bioinformatics, University of Georgia, Athens, GA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Denkena, Johanna" sort="Denkena, Johanna" uniqKey="Denkena J" first="Johanna" last="Denkena">Johanna Denkena</name><affiliation><nlm:affiliation>Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Colome Tatche, Maria" sort="Colome Tatche, Maria" uniqKey="Colome Tatche M" first="Maria" last="Colomé-Tatché">Maria Colomé-Tatché</name><affiliation><nlm:affiliation>Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Shahryary, Yadollah" sort="Shahryary, Yadollah" uniqKey="Shahryary Y" first="Yadollah" last="Shahryary">Yadollah Shahryary</name><affiliation><nlm:affiliation>Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Hazarika, Rashmi" sort="Hazarika, Rashmi" uniqKey="Hazarika R" first="Rashmi" last="Hazarika">Rashmi Hazarika</name><affiliation><nlm:affiliation>Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Grimwood, Jane" sort="Grimwood, Jane" uniqKey="Grimwood J" first="Jane" last="Grimwood">Jane Grimwood</name><affiliation><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Mamidi, Sujan" sort="Mamidi, Sujan" uniqKey="Mamidi S" first="Sujan" last="Mamidi">Sujan Mamidi</name><affiliation><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Jenkins, Jerry" sort="Jenkins, Jerry" uniqKey="Jenkins J" first="Jerry" last="Jenkins">Jerry Jenkins</name><affiliation><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Grabowski, Paul P" sort="Grabowski, Paul P" uniqKey="Grabowski P" first="Paul P" last="Grabowski">Paul P. Grabowski</name><affiliation><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sreedasyam, Avinash" sort="Sreedasyam, Avinash" uniqKey="Sreedasyam A" first="Avinash" last="Sreedasyam">Avinash Sreedasyam</name><affiliation><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Shu, Shengqiang" sort="Shu, Shengqiang" uniqKey="Shu S" first="Shengqiang" last="Shu">Shengqiang Shu</name><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Barry, Kerrie" sort="Barry, Kerrie" uniqKey="Barry K" first="Kerrie" last="Barry">Kerrie Barry</name><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Lail, Kathleen" sort="Lail, Kathleen" uniqKey="Lail K" first="Kathleen" last="Lail">Kathleen Lail</name><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Adam, Catherine" sort="Adam, Catherine" uniqKey="Adam C" first="Catherine" last="Adam">Catherine Adam</name><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Lipzen, Anna" sort="Lipzen, Anna" uniqKey="Lipzen A" first="Anna" last="Lipzen">Anna Lipzen</name><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sorek, Rotem" sort="Sorek, Rotem" uniqKey="Sorek R" first="Rotem" last="Sorek">Rotem Sorek</name><affiliation><nlm:affiliation>Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.</nlm:affiliation></affiliation></author><author><name sortKey="Kudrna, Dave" sort="Kudrna, Dave" uniqKey="Kudrna D" first="Dave" last="Kudrna">Dave Kudrna</name><affiliation><nlm:affiliation>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Talag, Jayson" sort="Talag, Jayson" uniqKey="Talag J" first="Jayson" last="Talag">Jayson Talag</name><affiliation><nlm:affiliation>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Wing, Rod" sort="Wing, Rod" uniqKey="Wing R" first="Rod" last="Wing">Rod Wing</name><affiliation><nlm:affiliation>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Hall, David W" sort="Hall, David W" uniqKey="Hall D" first="David W" last="Hall">David W. Hall</name><affiliation><nlm:affiliation>Department of Genetics, University of Georgia, Athens, GA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Jacobsen, Daniel" sort="Jacobsen, Daniel" uniqKey="Jacobsen D" first="Daniel" last="Jacobsen">Daniel Jacobsen</name><affiliation><nlm:affiliation>The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><affiliation><nlm:affiliation>The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><affiliation><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Johannes, Frank" sort="Johannes, Frank" uniqKey="Johannes F" first="Frank" last="Johannes">Frank Johannes</name><affiliation><nlm:affiliation>Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany. frank@johanneslab.org.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany. frank@johanneslab.org.</nlm:affiliation></affiliation></author><author><name sortKey="Schmitz, Robert J" sort="Schmitz, Robert J" uniqKey="Schmitz R" first="Robert J" last="Schmitz">Robert J. Schmitz</name><affiliation><nlm:affiliation>Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany. schmitz@uga.edu.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Genetics, University of Georgia, Athens, GA, USA. schmitz@uga.edu.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:33023654</idno><idno type="pmid">33023654</idno><idno type="doi">10.1186/s13059-020-02162-5</idno><idno type="pmc">PMC7539514</idno><idno type="wicri:Area/Main/Corpus">000069</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000069</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa.</title><author><name sortKey="Hofmeister, Brigitte T" sort="Hofmeister, Brigitte T" uniqKey="Hofmeister B" first="Brigitte T" last="Hofmeister">Brigitte T. Hofmeister</name><affiliation><nlm:affiliation>Institute of Bioinformatics, University of Georgia, Athens, GA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Denkena, Johanna" sort="Denkena, Johanna" uniqKey="Denkena J" first="Johanna" last="Denkena">Johanna Denkena</name><affiliation><nlm:affiliation>Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Colome Tatche, Maria" sort="Colome Tatche, Maria" uniqKey="Colome Tatche M" first="Maria" last="Colomé-Tatché">Maria Colomé-Tatché</name><affiliation><nlm:affiliation>Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Shahryary, Yadollah" sort="Shahryary, Yadollah" uniqKey="Shahryary Y" first="Yadollah" last="Shahryary">Yadollah Shahryary</name><affiliation><nlm:affiliation>Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Hazarika, Rashmi" sort="Hazarika, Rashmi" uniqKey="Hazarika R" first="Rashmi" last="Hazarika">Rashmi Hazarika</name><affiliation><nlm:affiliation>Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Grimwood, Jane" sort="Grimwood, Jane" uniqKey="Grimwood J" first="Jane" last="Grimwood">Jane Grimwood</name><affiliation><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Mamidi, Sujan" sort="Mamidi, Sujan" uniqKey="Mamidi S" first="Sujan" last="Mamidi">Sujan Mamidi</name><affiliation><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Jenkins, Jerry" sort="Jenkins, Jerry" uniqKey="Jenkins J" first="Jerry" last="Jenkins">Jerry Jenkins</name><affiliation><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Grabowski, Paul P" sort="Grabowski, Paul P" uniqKey="Grabowski P" first="Paul P" last="Grabowski">Paul P. Grabowski</name><affiliation><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sreedasyam, Avinash" sort="Sreedasyam, Avinash" uniqKey="Sreedasyam A" first="Avinash" last="Sreedasyam">Avinash Sreedasyam</name><affiliation><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Shu, Shengqiang" sort="Shu, Shengqiang" uniqKey="Shu S" first="Shengqiang" last="Shu">Shengqiang Shu</name><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Barry, Kerrie" sort="Barry, Kerrie" uniqKey="Barry K" first="Kerrie" last="Barry">Kerrie Barry</name><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Lail, Kathleen" sort="Lail, Kathleen" uniqKey="Lail K" first="Kathleen" last="Lail">Kathleen Lail</name><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Adam, Catherine" sort="Adam, Catherine" uniqKey="Adam C" first="Catherine" last="Adam">Catherine Adam</name><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Lipzen, Anna" sort="Lipzen, Anna" uniqKey="Lipzen A" first="Anna" last="Lipzen">Anna Lipzen</name><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sorek, Rotem" sort="Sorek, Rotem" uniqKey="Sorek R" first="Rotem" last="Sorek">Rotem Sorek</name><affiliation><nlm:affiliation>Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.</nlm:affiliation></affiliation></author><author><name sortKey="Kudrna, Dave" sort="Kudrna, Dave" uniqKey="Kudrna D" first="Dave" last="Kudrna">Dave Kudrna</name><affiliation><nlm:affiliation>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Talag, Jayson" sort="Talag, Jayson" uniqKey="Talag J" first="Jayson" last="Talag">Jayson Talag</name><affiliation><nlm:affiliation>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Wing, Rod" sort="Wing, Rod" uniqKey="Wing R" first="Rod" last="Wing">Rod Wing</name><affiliation><nlm:affiliation>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Hall, David W" sort="Hall, David W" uniqKey="Hall D" first="David W" last="Hall">David W. Hall</name><affiliation><nlm:affiliation>Department of Genetics, University of Georgia, Athens, GA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Jacobsen, Daniel" sort="Jacobsen, Daniel" uniqKey="Jacobsen D" first="Daniel" last="Jacobsen">Daniel Jacobsen</name><affiliation><nlm:affiliation>The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><affiliation><nlm:affiliation>The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><affiliation><nlm:affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Johannes, Frank" sort="Johannes, Frank" uniqKey="Johannes F" first="Frank" last="Johannes">Frank Johannes</name><affiliation><nlm:affiliation>Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany. frank@johanneslab.org.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany. frank@johanneslab.org.</nlm:affiliation></affiliation></author><author><name sortKey="Schmitz, Robert J" sort="Schmitz, Robert J" uniqKey="Schmitz R" first="Robert J" last="Schmitz">Robert J. Schmitz</name><affiliation><nlm:affiliation>Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany. schmitz@uga.edu.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Genetics, University of Georgia, Athens, GA, USA. schmitz@uga.edu.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Genome biology</title><idno type="eISSN">1474-760X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local adaption in an ecoevolutionary context, particularly in long-lived perennials.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Here, we generate a new high-quality reference genome from the oldest branch of a wild Populus trichocarpa tree with two dominant stems which have been evolving independently for 330 years. By sampling multiple, age-estimated branches of this tree, we use a multi-omics approach to quantify age-related somatic changes at the genetic, epigenetic, and transcriptional level. We show that the per-year somatic mutation and epimutation rates are lower than in annuals and that transcriptional variation is mainly independent of age divergence and cytosine methylation. Furthermore, a detailed analysis of the somatic epimutation spectrum indicates that transgenerationally heritable epimutations originate mainly from DNA methylation maintenance errors during mitotic rather than during meiotic cell divisions.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>Taken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.</p></div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">33023654</PMID><DateRevised><Year>2020</Year><Month>11</Month><Day>03</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1474-760X</ISSN><JournalIssue CitedMedium="Internet"><Volume>21</Volume><Issue>1</Issue><PubDate><Year>2020</Year><Month>10</Month><Day>06</Day></PubDate></JournalIssue><Title>Genome biology</Title><ISOAbbreviation>Genome Biol</ISOAbbreviation></Journal><ArticleTitle>A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa.</ArticleTitle><Pagination><MedlinePgn>259</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s13059-020-02162-5</ELocationID><Abstract><AbstractText Label="BACKGROUND">Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local adaption in an ecoevolutionary context, particularly in long-lived perennials.</AbstractText><AbstractText Label="RESULTS">Here, we generate a new high-quality reference genome from the oldest branch of a wild Populus trichocarpa tree with two dominant stems which have been evolving independently for 330 years. By sampling multiple, age-estimated branches of this tree, we use a multi-omics approach to quantify age-related somatic changes at the genetic, epigenetic, and transcriptional level. We show that the per-year somatic mutation and epimutation rates are lower than in annuals and that transcriptional variation is mainly independent of age divergence and cytosine methylation. Furthermore, a detailed analysis of the somatic epimutation spectrum indicates that transgenerationally heritable epimutations originate mainly from DNA methylation maintenance errors during mitotic rather than during meiotic cell divisions.</AbstractText><AbstractText Label="CONCLUSION">Taken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hofmeister</LastName><ForeName>Brigitte T</ForeName><Initials>BT</Initials><AffiliationInfo><Affiliation>Institute of Bioinformatics, University of Georgia, Athens, GA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Denkena</LastName><ForeName>Johanna</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Colomé-Tatché</LastName><ForeName>Maria</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shahryary</LastName><ForeName>Yadollah</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hazarika</LastName><ForeName>Rashmi</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grimwood</LastName><ForeName>Jane</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mamidi</LastName><ForeName>Sujan</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jenkins</LastName><ForeName>Jerry</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grabowski</LastName><ForeName>Paul P</ForeName><Initials>PP</Initials><AffiliationInfo><Affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sreedasyam</LastName><ForeName>Avinash</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shu</LastName><ForeName>Shengqiang</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Barry</LastName><ForeName>Kerrie</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lail</LastName><ForeName>Kathleen</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Adam</LastName><ForeName>Catherine</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lipzen</LastName><ForeName>Anna</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sorek</LastName><ForeName>Rotem</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kudrna</LastName><ForeName>Dave</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Talag</LastName><ForeName>Jayson</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wing</LastName><ForeName>Rod</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hall</LastName><ForeName>David W</ForeName><Initials>DW</Initials><AffiliationInfo><Affiliation>Department of Genetics, University of Georgia, Athens, GA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jacobsen</LastName><ForeName>Daniel</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tuskan</LastName><ForeName>Gerald A</ForeName><Initials>GA</Initials><AffiliationInfo><Affiliation>The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schmutz</LastName><ForeName>Jeremy</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Johannes</LastName><ForeName>Frank</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany. frank@johanneslab.org.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany. frank@johanneslab.org.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schmitz</LastName><ForeName>Robert J</ForeName><Initials>RJ</Initials><Identifier Source="ORCID">0000-0001-7538-6663</Identifier><AffiliationInfo><Affiliation>Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany. schmitz@uga.edu.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Genetics, University of Georgia, Athens, GA, USA. schmitz@uga.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>T32 GM007103</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01-GM134682</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>T32GM007103</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, 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