Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy.
Identifieur interne : 000240 ( Main/Corpus ); précédent : 000239; suivant : 000241Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy.
Auteurs : Qiushi Li ; Sukanya Ramasamy ; Pooja Singh ; Jillian M. Hagel ; Sonja M. Dunemann ; Xue Chen ; Rongji Chen ; Lisa Yu ; Joseph E. Tucker ; Peter J. Facchini ; Sam YeamanSource :
- Nature communications [ 2041-1723 ] ; 2020.
English descriptors
- KwdEn :
- Benzylisoquinolines (metabolism), DNA Copy Number Variations (MeSH), Evolution, Molecular (MeSH), Gene Expression Regulation, Plant (MeSH), Genome, Plant (genetics), Genomics (MeSH), Metabolic Networks and Pathways (genetics), Multigene Family (MeSH), Papaver (genetics), Papaver (metabolism), Secondary Metabolism (genetics).
- MESH :
- chemical , metabolism : Benzylisoquinolines.
- genetics : Genome, Plant, Metabolic Networks and Pathways, Papaver, Secondary Metabolism.
- metabolism : Papaver.
- DNA Copy Number Variations, Evolution, Molecular, Gene Expression Regulation, Plant, Genomics, Multigene Family.
Abstract
Genes in plant secondary metabolic pathways enable biosynthesis of a range of medically and industrially important compounds, and are often clustered on chromosomes. Here, we study genomic clustering in the benzylisoquinoline alkaloid (BIA) pathway in opium poppy (Papaver somniferum), exploring relationships between gene expression, copy number variation, and metabolite production. We use Hi-C to improve the existing draft genome assembly, yielding chromosome-scale scaffolds that include 35 previously unanchored BIA genes. We find that co-expression of BIA genes increases within clusters and identify candidates with unknown function based on clustering and covariation in expression and alkaloid production. Copy number variation in critical BIA genes correlates with stark differences in alkaloid production, linking noscapine production with an 11-gene deletion, and increased thebaine/decreased morphine production with deletion of a T6ODM cluster. Our results show that the opium poppy genome is still dynamically evolving in ways that contribute to medically and industrially important phenotypes.
DOI: 10.1038/s41467-020-15040-2
PubMed: 32132540
PubMed Central: PMC7055283
Links to Exploration step
pubmed:32132540Le document en format XML
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Hagel</name><affiliation><nlm:affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Dunemann, Sonja M" sort="Dunemann, Sonja M" uniqKey="Dunemann S" first="Sonja M" last="Dunemann">Sonja M. Dunemann</name><affiliation><nlm:affiliation>Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Xue" sort="Chen, Xue" uniqKey="Chen X" first="Xue" last="Chen">Xue Chen</name><affiliation><nlm:affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Rongji" sort="Chen, Rongji" uniqKey="Chen R" first="Rongji" last="Chen">Rongji Chen</name><affiliation><nlm:affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Yu, Lisa" sort="Yu, Lisa" uniqKey="Yu L" first="Lisa" last="Yu">Lisa Yu</name><affiliation><nlm:affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Tucker, Joseph E" sort="Tucker, Joseph E" uniqKey="Tucker J" first="Joseph E" last="Tucker">Joseph E. 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Hagel</name><affiliation><nlm:affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Dunemann, Sonja M" sort="Dunemann, Sonja M" uniqKey="Dunemann S" first="Sonja M" last="Dunemann">Sonja M. Dunemann</name><affiliation><nlm:affiliation>Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Xue" sort="Chen, Xue" uniqKey="Chen X" first="Xue" last="Chen">Xue Chen</name><affiliation><nlm:affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Rongji" sort="Chen, Rongji" uniqKey="Chen R" first="Rongji" last="Chen">Rongji Chen</name><affiliation><nlm:affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Yu, Lisa" sort="Yu, Lisa" uniqKey="Yu L" first="Lisa" last="Yu">Lisa Yu</name><affiliation><nlm:affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Tucker, Joseph E" sort="Tucker, Joseph E" uniqKey="Tucker J" first="Joseph E" last="Tucker">Joseph E. Tucker</name><affiliation><nlm:affiliation>Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Facchini, Peter J" sort="Facchini, Peter J" uniqKey="Facchini P" first="Peter J" last="Facchini">Peter J. Facchini</name><affiliation><nlm:affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Yeaman, Sam" sort="Yeaman, Sam" uniqKey="Yeaman S" first="Sam" last="Yeaman">Sam Yeaman</name><affiliation><nlm:affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada. samuel.yeaman@ucalgary.ca.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Nature communications</title><idno type="eISSN">2041-1723</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Benzylisoquinolines (metabolism)</term><term>DNA Copy Number Variations (MeSH)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genome, Plant (genetics)</term><term>Genomics (MeSH)</term><term>Metabolic Networks and Pathways (genetics)</term><term>Multigene Family (MeSH)</term><term>Papaver (genetics)</term><term>Papaver (metabolism)</term><term>Secondary Metabolism (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Benzylisoquinolines</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome, Plant</term><term>Metabolic Networks and Pathways</term><term>Papaver</term><term>Secondary Metabolism</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Papaver</term></keywords><keywords scheme="MESH" xml:lang="en"><term>DNA Copy Number Variations</term><term>Evolution, Molecular</term><term>Gene Expression Regulation, Plant</term><term>Genomics</term><term>Multigene Family</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Genes in plant secondary metabolic pathways enable biosynthesis of a range of medically and industrially important compounds, and are often clustered on chromosomes. Here, we study genomic clustering in the benzylisoquinoline alkaloid (BIA) pathway in opium poppy (Papaver somniferum), exploring relationships between gene expression, copy number variation, and metabolite production. We use Hi-C to improve the existing draft genome assembly, yielding chromosome-scale scaffolds that include 35 previously unanchored BIA genes. We find that co-expression of BIA genes increases within clusters and identify candidates with unknown function based on clustering and covariation in expression and alkaloid production. Copy number variation in critical BIA genes correlates with stark differences in alkaloid production, linking noscapine production with an 11-gene deletion, and increased thebaine/decreased morphine production with deletion of a T6ODM cluster. Our results show that the opium poppy genome is still dynamically evolving in ways that contribute to medically and industrially important phenotypes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">32132540</PMID><DateCompleted><Year>2020</Year><Month>06</Month><Day>26</Day></DateCompleted><DateRevised><Year>2020</Year><Month>06</Month><Day>28</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2041-1723</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><Issue>1</Issue><PubDate><Year>2020</Year><Month>03</Month><Day>04</Day></PubDate></JournalIssue><Title>Nature communications</Title><ISOAbbreviation>Nat Commun</ISOAbbreviation></Journal><ArticleTitle>Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy.</ArticleTitle><Pagination><MedlinePgn>1190</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41467-020-15040-2</ELocationID><Abstract><AbstractText>Genes in plant secondary metabolic pathways enable biosynthesis of a range of medically and industrially important compounds, and are often clustered on chromosomes. Here, we study genomic clustering in the benzylisoquinoline alkaloid (BIA) pathway in opium poppy (Papaver somniferum), exploring relationships between gene expression, copy number variation, and metabolite production. We use Hi-C to improve the existing draft genome assembly, yielding chromosome-scale scaffolds that include 35 previously unanchored BIA genes. We find that co-expression of BIA genes increases within clusters and identify candidates with unknown function based on clustering and covariation in expression and alkaloid production. Copy number variation in critical BIA genes correlates with stark differences in alkaloid production, linking noscapine production with an 11-gene deletion, and increased thebaine/decreased morphine production with deletion of a T6ODM cluster. Our results show that the opium poppy genome is still dynamically evolving in ways that contribute to medically and industrially important phenotypes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Qiushi</ForeName><Initials>Q</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-7317-5168</Identifier><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ramasamy</LastName><ForeName>Sukanya</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Singh</LastName><ForeName>Pooja</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hagel</LastName><ForeName>Jillian M</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dunemann</LastName><ForeName>Sonja M</ForeName><Initials>SM</Initials><AffiliationInfo><Affiliation>Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Xue</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Rongji</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yu</LastName><ForeName>Lisa</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tucker</LastName><ForeName>Joseph E</ForeName><Initials>JE</Initials><AffiliationInfo><Affiliation>Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Facchini</LastName><ForeName>Peter J</ForeName><Initials>PJ</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-7693-290X</Identifier><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yeaman</LastName><ForeName>Sam</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada. samuel.yeaman@ucalgary.ca.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>Dryad</DataBankName><AccessionNumberList><AccessionNumber>10.5061/dryad.m0cfxpnz9</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>03</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Nat Commun</MedlineTA><NlmUniqueID>101528555</NlmUniqueID><ISSNLinking>2041-1723</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance 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