Comparative analysis of the root and leaf transcriptomes in Chelidonium majus L
Chelidonium majus is a traditional medicinal plant, which commonly known as a rich resource for the major benzylisoquinoline alkaloids (BIAs), including morphine, sanguinarine, and berberine. To understand the biosynthesis of C. majus BIAs, we performed de novo transcriptome sequencing of its leaf a...
Gespeichert in:
| Veröffentlicht in: | PloS one 2019-04, Vol.14 (4), p.e0215165-e0215165 |
|---|---|
| Hauptverfasser: | , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e0215165 |
|---|---|
| container_issue | 4 |
| container_start_page | e0215165 |
| container_title | PloS one |
| container_volume | 14 |
| creator | Pourmazaheri, Helen Soorni, Aboozar Kohnerouz, Bahram Baghban Dehaghi, Nafiseh Khosravi Kalantar, Enayatollah Omidi, Mansoor Naghavi, Mohammad Reza |
| description | Chelidonium majus is a traditional medicinal plant, which commonly known as a rich resource for the major benzylisoquinoline alkaloids (BIAs), including morphine, sanguinarine, and berberine. To understand the biosynthesis of C. majus BIAs, we performed de novo transcriptome sequencing of its leaf and root tissues using Illumina technology. Following comprehensive evaluation of de novo transcriptome assemblies produced with five programs including Trinity, Bridger, BinPacker, IDBA-tran, and Velvet/Oases using a series of k-mer sizes (from 25 to 91), BinPacker was found to produce the best assembly using a k-mer of 25. This study reports the results of differential gene expression (DGE), functional annotation, gene ontology (GO) analysis, classification of transcription factor (TF)s, and SSR and miRNA discovery. Our DGE analysis identified 6,028 transcripts that were up-regulated in the leaf, and 4,722 transcripts that were up-regulated in the root. Further investigations showed that most of the genes involved in the BIA biosynthetic pathway are significantly expressed in the root compared to the leaf. GO analysis showed that the predominant GO domain is "cellular component", while TF analysis found bHLH to be the most highly represented TF family. Our study further identified 10 SSRs, out of a total of 39,841, that showed linkage to five unigenes encoding enzymes in the BIA pathway, and 10 conserved miRNAs that were previously not detected in this plant. The comprehensive transcriptome information presented herein provides a foundation for further explorations on study of the molecular mechanisms of BIA synthesis in C. majus. |
| doi_str_mv | 10.1371/journal.pone.0215165 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_2211278099</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A582459946</galeid><doaj_id>oai_doaj_org_article_801cbb516076471d9e5159e074b0a601</doaj_id><sourcerecordid>A582459946</sourcerecordid><originalsourceid>FETCH-LOGICAL-c585t-313de6a4bb4d1177619a7aae7d507955dacf0694c3645d213e20e5ce4cd3b8a03</originalsourceid><addsrcrecordid>eNptkltrGzEQhZfS0qRp_0FpFwqlL3Z11-olEEwvAUNe2mcxK2ltGe3KlXYD-feV402wS58kRkffzBxOVb3HaImpxF93cUoDhOU-Dm6JCOZY8BfVJVaULARB9OXJ_aJ6k_MOIU4bIV5XFxSpRhCuLqu7Vez3kGD0966GwnvIPtexq8etq1OMYynaOjgolQRDNsnvx9i7XPuhXm1d8DYOfurrHnZTrtdvq1cdhOzezedV9fv7t1-rn4v13Y_b1c16YXjDxwXF1DoBrG2ZxVhKgRVIACctR1JxbsF0SChmqGDcEkwdQY4bx4ylbQOIXlUfj9x9iFnPXmRNCMZENkiporg9KmyEnd4n30N60BG8fizEtNGQRm-C0w3Cpm2LgUgKJrFVjmOuHJKsRSAQLqzrudvU9s4aNxQzwhn0_GXwW72J91owwbBkBfBlBqT4Z3J51L3PxoUAg4vT49yIUiKFKNJP_0j_v92s2kBZwA9dLH3NAapveEMYV4odWJ9PVFsHYdzmGKbRxyGfC9lRaFLMObnueTeM9CFuT0PoQ9z0HLfy7cOpL8-fnvJF_wJ7R9Cp</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2211278099</pqid></control><display><type>article</type><title>Comparative analysis of the root and leaf transcriptomes in Chelidonium majus L</title><source>Public Library of Science (PLoS) Journals Open Access</source><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Pourmazaheri, Helen ; Soorni, Aboozar ; Kohnerouz, Bahram Baghban ; Dehaghi, Nafiseh Khosravi ; Kalantar, Enayatollah ; Omidi, Mansoor ; Naghavi, Mohammad Reza</creator><creatorcontrib>Pourmazaheri, Helen ; Soorni, Aboozar ; Kohnerouz, Bahram Baghban ; Dehaghi, Nafiseh Khosravi ; Kalantar, Enayatollah ; Omidi, Mansoor ; Naghavi, Mohammad Reza</creatorcontrib><description>Chelidonium majus is a traditional medicinal plant, which commonly known as a rich resource for the major benzylisoquinoline alkaloids (BIAs), including morphine, sanguinarine, and berberine. To understand the biosynthesis of C. majus BIAs, we performed de novo transcriptome sequencing of its leaf and root tissues using Illumina technology. Following comprehensive evaluation of de novo transcriptome assemblies produced with five programs including Trinity, Bridger, BinPacker, IDBA-tran, and Velvet/Oases using a series of k-mer sizes (from 25 to 91), BinPacker was found to produce the best assembly using a k-mer of 25. This study reports the results of differential gene expression (DGE), functional annotation, gene ontology (GO) analysis, classification of transcription factor (TF)s, and SSR and miRNA discovery. Our DGE analysis identified 6,028 transcripts that were up-regulated in the leaf, and 4,722 transcripts that were up-regulated in the root. Further investigations showed that most of the genes involved in the BIA biosynthetic pathway are significantly expressed in the root compared to the leaf. GO analysis showed that the predominant GO domain is "cellular component", while TF analysis found bHLH to be the most highly represented TF family. Our study further identified 10 SSRs, out of a total of 39,841, that showed linkage to five unigenes encoding enzymes in the BIA pathway, and 10 conserved miRNAs that were previously not detected in this plant. The comprehensive transcriptome information presented herein provides a foundation for further explorations on study of the molecular mechanisms of BIA synthesis in C. majus.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0215165</identifier><identifier>PMID: 30986259</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agriculture ; Alkaloids ; Annotations ; Berberine ; Bias ; Biochemistry ; Biology and Life Sciences ; Biosynthesis ; Biotechnology ; Chelidonium - genetics ; Chelidonium - metabolism ; Chelidonium majus ; Chemical synthesis ; Comparative analysis ; Enzymes ; Gene expression ; Gene Expression Regulation, Plant - physiology ; Genes ; Genetic aspects ; Genomics ; Greater celandine ; Herbal medicine ; Identification ; Leaves ; Medicinal plants ; Metabolites ; MicroRNA ; MicroRNAs ; MicroRNAs - biosynthesis ; MicroRNAs - genetics ; miRNA ; Molecular modelling ; Morphine ; Natural resources ; Oases ; Pharmacy ; Physiological aspects ; Plant Leaves - genetics ; Plant Leaves - metabolism ; Plant Proteins - biosynthesis ; Plant Proteins - genetics ; Plant Roots - genetics ; Plant Roots - metabolism ; Research and Analysis Methods ; Ribonucleic acid ; RNA ; RNA, Plant - biosynthesis ; RNA, Plant - genetics ; Roots (Botany) ; Sanguinarine ; Sequences ; Technology ; Technology assessment ; Transcription (Genetics) ; Transcriptome - physiology</subject><ispartof>PloS one, 2019-04, Vol.14 (4), p.e0215165-e0215165</ispartof><rights>COPYRIGHT 2019 Public Library of Science</rights><rights>2019 Pourmazaheri et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2019 Pourmazaheri et al 2019 Pourmazaheri et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c585t-313de6a4bb4d1177619a7aae7d507955dacf0694c3645d213e20e5ce4cd3b8a03</citedby><cites>FETCH-LOGICAL-c585t-313de6a4bb4d1177619a7aae7d507955dacf0694c3645d213e20e5ce4cd3b8a03</cites><orcidid>0000-0002-2427-3332</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6464174/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6464174/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79569,79570</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30986259$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Pourmazaheri, Helen</creatorcontrib><creatorcontrib>Soorni, Aboozar</creatorcontrib><creatorcontrib>Kohnerouz, Bahram Baghban</creatorcontrib><creatorcontrib>Dehaghi, Nafiseh Khosravi</creatorcontrib><creatorcontrib>Kalantar, Enayatollah</creatorcontrib><creatorcontrib>Omidi, Mansoor</creatorcontrib><creatorcontrib>Naghavi, Mohammad Reza</creatorcontrib><title>Comparative analysis of the root and leaf transcriptomes in Chelidonium majus L</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Chelidonium majus is a traditional medicinal plant, which commonly known as a rich resource for the major benzylisoquinoline alkaloids (BIAs), including morphine, sanguinarine, and berberine. To understand the biosynthesis of C. majus BIAs, we performed de novo transcriptome sequencing of its leaf and root tissues using Illumina technology. Following comprehensive evaluation of de novo transcriptome assemblies produced with five programs including Trinity, Bridger, BinPacker, IDBA-tran, and Velvet/Oases using a series of k-mer sizes (from 25 to 91), BinPacker was found to produce the best assembly using a k-mer of 25. This study reports the results of differential gene expression (DGE), functional annotation, gene ontology (GO) analysis, classification of transcription factor (TF)s, and SSR and miRNA discovery. Our DGE analysis identified 6,028 transcripts that were up-regulated in the leaf, and 4,722 transcripts that were up-regulated in the root. Further investigations showed that most of the genes involved in the BIA biosynthetic pathway are significantly expressed in the root compared to the leaf. GO analysis showed that the predominant GO domain is "cellular component", while TF analysis found bHLH to be the most highly represented TF family. Our study further identified 10 SSRs, out of a total of 39,841, that showed linkage to five unigenes encoding enzymes in the BIA pathway, and 10 conserved miRNAs that were previously not detected in this plant. The comprehensive transcriptome information presented herein provides a foundation for further explorations on study of the molecular mechanisms of BIA synthesis in C. majus.</description><subject>Agriculture</subject><subject>Alkaloids</subject><subject>Annotations</subject><subject>Berberine</subject><subject>Bias</subject><subject>Biochemistry</subject><subject>Biology and Life Sciences</subject><subject>Biosynthesis</subject><subject>Biotechnology</subject><subject>Chelidonium - genetics</subject><subject>Chelidonium - metabolism</subject><subject>Chelidonium majus</subject><subject>Chemical synthesis</subject><subject>Comparative analysis</subject><subject>Enzymes</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Plant - physiology</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomics</subject><subject>Greater celandine</subject><subject>Herbal medicine</subject><subject>Identification</subject><subject>Leaves</subject><subject>Medicinal plants</subject><subject>Metabolites</subject><subject>MicroRNA</subject><subject>MicroRNAs</subject><subject>MicroRNAs - biosynthesis</subject><subject>MicroRNAs - genetics</subject><subject>miRNA</subject><subject>Molecular modelling</subject><subject>Morphine</subject><subject>Natural resources</subject><subject>Oases</subject><subject>Pharmacy</subject><subject>Physiological aspects</subject><subject>Plant Leaves - genetics</subject><subject>Plant Leaves - metabolism</subject><subject>Plant Proteins - biosynthesis</subject><subject>Plant Proteins - genetics</subject><subject>Plant Roots - genetics</subject><subject>Plant Roots - metabolism</subject><subject>Research and Analysis Methods</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA, Plant - biosynthesis</subject><subject>RNA, Plant - genetics</subject><subject>Roots (Botany)</subject><subject>Sanguinarine</subject><subject>Sequences</subject><subject>Technology</subject><subject>Technology assessment</subject><subject>Transcription (Genetics)</subject><subject>Transcriptome - physiology</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNptkltrGzEQhZfS0qRp_0FpFwqlL3Z11-olEEwvAUNe2mcxK2ltGe3KlXYD-feV402wS58kRkffzBxOVb3HaImpxF93cUoDhOU-Dm6JCOZY8BfVJVaULARB9OXJ_aJ6k_MOIU4bIV5XFxSpRhCuLqu7Vez3kGD0966GwnvIPtexq8etq1OMYynaOjgolQRDNsnvx9i7XPuhXm1d8DYOfurrHnZTrtdvq1cdhOzezedV9fv7t1-rn4v13Y_b1c16YXjDxwXF1DoBrG2ZxVhKgRVIACctR1JxbsF0SChmqGDcEkwdQY4bx4ylbQOIXlUfj9x9iFnPXmRNCMZENkiporg9KmyEnd4n30N60BG8fizEtNGQRm-C0w3Cpm2LgUgKJrFVjmOuHJKsRSAQLqzrudvU9s4aNxQzwhn0_GXwW72J91owwbBkBfBlBqT4Z3J51L3PxoUAg4vT49yIUiKFKNJP_0j_v92s2kBZwA9dLH3NAapveEMYV4odWJ9PVFsHYdzmGKbRxyGfC9lRaFLMObnueTeM9CFuT0PoQ9z0HLfy7cOpL8-fnvJF_wJ7R9Cp</recordid><startdate>20190415</startdate><enddate>20190415</enddate><creator>Pourmazaheri, Helen</creator><creator>Soorni, Aboozar</creator><creator>Kohnerouz, Bahram Baghban</creator><creator>Dehaghi, Nafiseh Khosravi</creator><creator>Kalantar, Enayatollah</creator><creator>Omidi, Mansoor</creator><creator>Naghavi, Mohammad Reza</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PHGZM</scope><scope>PHGZT</scope><scope>PIMPY</scope><scope>PJZUB</scope><scope>PKEHL</scope><scope>PPXIY</scope><scope>PQEST</scope><scope>PQGLB</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-2427-3332</orcidid></search><sort><creationdate>20190415</creationdate><title>Comparative analysis of the root and leaf transcriptomes in Chelidonium majus L</title><author>Pourmazaheri, Helen ; Soorni, Aboozar ; Kohnerouz, Bahram Baghban ; Dehaghi, Nafiseh Khosravi ; Kalantar, Enayatollah ; Omidi, Mansoor ; Naghavi, Mohammad Reza</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c585t-313de6a4bb4d1177619a7aae7d507955dacf0694c3645d213e20e5ce4cd3b8a03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Agriculture</topic><topic>Alkaloids</topic><topic>Annotations</topic><topic>Berberine</topic><topic>Bias</topic><topic>Biochemistry</topic><topic>Biology and Life Sciences</topic><topic>Biosynthesis</topic><topic>Biotechnology</topic><topic>Chelidonium - genetics</topic><topic>Chelidonium - metabolism</topic><topic>Chelidonium majus</topic><topic>Chemical synthesis</topic><topic>Comparative analysis</topic><topic>Enzymes</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Plant - physiology</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genomics</topic><topic>Greater celandine</topic><topic>Herbal medicine</topic><topic>Identification</topic><topic>Leaves</topic><topic>Medicinal plants</topic><topic>Metabolites</topic><topic>MicroRNA</topic><topic>MicroRNAs</topic><topic>MicroRNAs - biosynthesis</topic><topic>MicroRNAs - genetics</topic><topic>miRNA</topic><topic>Molecular modelling</topic><topic>Morphine</topic><topic>Natural resources</topic><topic>Oases</topic><topic>Pharmacy</topic><topic>Physiological aspects</topic><topic>Plant Leaves - genetics</topic><topic>Plant Leaves - metabolism</topic><topic>Plant Proteins - biosynthesis</topic><topic>Plant Proteins - genetics</topic><topic>Plant Roots - genetics</topic><topic>Plant Roots - metabolism</topic><topic>Research and Analysis Methods</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA, Plant - biosynthesis</topic><topic>RNA, Plant - genetics</topic><topic>Roots (Botany)</topic><topic>Sanguinarine</topic><topic>Sequences</topic><topic>Technology</topic><topic>Technology assessment</topic><topic>Transcription (Genetics)</topic><topic>Transcriptome - physiology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Pourmazaheri, Helen</creatorcontrib><creatorcontrib>Soorni, Aboozar</creatorcontrib><creatorcontrib>Kohnerouz, Bahram Baghban</creatorcontrib><creatorcontrib>Dehaghi, Nafiseh Khosravi</creatorcontrib><creatorcontrib>Kalantar, Enayatollah</creatorcontrib><creatorcontrib>Omidi, Mansoor</creatorcontrib><creatorcontrib>Naghavi, Mohammad Reza</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>ProQuest Central (New)</collection><collection>ProQuest One Academic (New)</collection><collection>Publicly Available Content Database</collection><collection>ProQuest Health & Medical Research Collection</collection><collection>ProQuest One Academic Middle East (New)</collection><collection>ProQuest One Health & Nursing</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Applied & Life Sciences</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Pourmazaheri, Helen</au><au>Soorni, Aboozar</au><au>Kohnerouz, Bahram Baghban</au><au>Dehaghi, Nafiseh Khosravi</au><au>Kalantar, Enayatollah</au><au>Omidi, Mansoor</au><au>Naghavi, Mohammad Reza</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparative analysis of the root and leaf transcriptomes in Chelidonium majus L</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2019-04-15</date><risdate>2019</risdate><volume>14</volume><issue>4</issue><spage>e0215165</spage><epage>e0215165</epage><pages>e0215165-e0215165</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Chelidonium majus is a traditional medicinal plant, which commonly known as a rich resource for the major benzylisoquinoline alkaloids (BIAs), including morphine, sanguinarine, and berberine. To understand the biosynthesis of C. majus BIAs, we performed de novo transcriptome sequencing of its leaf and root tissues using Illumina technology. Following comprehensive evaluation of de novo transcriptome assemblies produced with five programs including Trinity, Bridger, BinPacker, IDBA-tran, and Velvet/Oases using a series of k-mer sizes (from 25 to 91), BinPacker was found to produce the best assembly using a k-mer of 25. This study reports the results of differential gene expression (DGE), functional annotation, gene ontology (GO) analysis, classification of transcription factor (TF)s, and SSR and miRNA discovery. Our DGE analysis identified 6,028 transcripts that were up-regulated in the leaf, and 4,722 transcripts that were up-regulated in the root. Further investigations showed that most of the genes involved in the BIA biosynthetic pathway are significantly expressed in the root compared to the leaf. GO analysis showed that the predominant GO domain is "cellular component", while TF analysis found bHLH to be the most highly represented TF family. Our study further identified 10 SSRs, out of a total of 39,841, that showed linkage to five unigenes encoding enzymes in the BIA pathway, and 10 conserved miRNAs that were previously not detected in this plant. The comprehensive transcriptome information presented herein provides a foundation for further explorations on study of the molecular mechanisms of BIA synthesis in C. majus.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>30986259</pmid><doi>10.1371/journal.pone.0215165</doi><orcidid>https://orcid.org/0000-0002-2427-3332</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2019-04, Vol.14 (4), p.e0215165-e0215165 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2211278099 |
| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Agriculture Alkaloids Annotations Berberine Bias Biochemistry Biology and Life Sciences Biosynthesis Biotechnology Chelidonium - genetics Chelidonium - metabolism Chelidonium majus Chemical synthesis Comparative analysis Enzymes Gene expression Gene Expression Regulation, Plant - physiology Genes Genetic aspects Genomics Greater celandine Herbal medicine Identification Leaves Medicinal plants Metabolites MicroRNA MicroRNAs MicroRNAs - biosynthesis MicroRNAs - genetics miRNA Molecular modelling Morphine Natural resources Oases Pharmacy Physiological aspects Plant Leaves - genetics Plant Leaves - metabolism Plant Proteins - biosynthesis Plant Proteins - genetics Plant Roots - genetics Plant Roots - metabolism Research and Analysis Methods Ribonucleic acid RNA RNA, Plant - biosynthesis RNA, Plant - genetics Roots (Botany) Sanguinarine Sequences Technology Technology assessment Transcription (Genetics) Transcriptome - physiology |
| title | Comparative analysis of the root and leaf transcriptomes in Chelidonium majus L |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-21T17%3A42%3A56IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Comparative%20analysis%20of%20the%20root%20and%20leaf%20transcriptomes%20in%20Chelidonium%20majus%20L&rft.jtitle=PloS%20one&rft.au=Pourmazaheri,%20Helen&rft.date=2019-04-15&rft.volume=14&rft.issue=4&rft.spage=e0215165&rft.epage=e0215165&rft.pages=e0215165-e0215165&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0215165&rft_dat=%3Cgale_plos_%3EA582459946%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2211278099&rft_id=info:pmid/30986259&rft_galeid=A582459946&rft_doaj_id=oai_doaj_org_article_801cbb516076471d9e5159e074b0a601&rfr_iscdi=true |