Identification of novel microRNAs and their targets in Chlorophytum borivilianum by small RNA and degradome sequencing.
Identifieur interne : 000899 ( Main/Exploration ); précédent : 000898; suivant : 000900Identification of novel microRNAs and their targets in Chlorophytum borivilianum by small RNA and degradome sequencing.
Auteurs : Monika Kajal [Inde] ; Nishant Kaushal [Inde] ; Ravneet Kaur [Inde] ; Kashmir Singh [Inde]Source :
- Non-coding RNA research [ 2468-0540 ] ; 2019.
Abstract
Plant specific miRNAs (Novel miRNAs) are well known to perform distinctive functions in biological processes. Identification of new miRNAs is necessary to understand their gene regulation. Degradome provides an opportunity to explore the miRNA functions by comparing the miRNA population and their degraded products. In the present study, Small RNA sequencing data was used to identify novel miRNAs. Further, degradome sequencing was carried out to identify miRNAs targets in the plant, Chlorophytum borivilianum. The present study supplemented 40 more novel miRNAs correlating degradome data with smallRNAome. Novel miRNAs, complementary to mRNA partial sequences obtained from degradome sequencing were actually targeting the later. A big pool of miRNA was established by using Oryza sativa, Arabidopsis thaliana, Populus trichocarpa, Ricinus communis, and Vitis vinifera genomic data. Targets were identified for novel miRNAs and total 109 targets were predicted. BLAST2GO analysis elaborate about localization of novel miRNAs' targets and their corresponding KEGG (Kyoto Encyclopedia for Genes and Genomes) pathways. Identified targets were annotated and were found to be involved in significant biological processes like Nitrogen metabolism, Pyruvate metabolism, Citrate cycle (TCA cycle), photosynthesis, and Glycolysis/Gluconeogenesis. The present study provides an overall view of the miRNA regulation in multiple metabolic pathways that are involved in plant growth, pathogen resistance and secondary metabolism of C. borivilianum.
DOI: 10.1016/j.ncrna.2019.11.004
PubMed: 32072082
PubMed Central: PMC7012778
Affiliations:
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targets in Chlorophytum borivilianum by small RNA and degradome sequencing.</title><author><name sortKey="Kajal, Monika" sort="Kajal, Monika" uniqKey="Kajal M" first="Monika" last="Kajal">Monika Kajal</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014</wicri:regionArea><wicri:noRegion>160014</wicri:noRegion></affiliation></author><author><name sortKey="Kaushal, Nishant" sort="Kaushal, Nishant" uniqKey="Kaushal N" first="Nishant" last="Kaushal">Nishant Kaushal</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014</wicri:regionArea><wicri:noRegion>160014</wicri:noRegion></affiliation></author><author><name sortKey="Kaur, Ravneet" sort="Kaur, Ravneet" uniqKey="Kaur R" first="Ravneet" last="Kaur">Ravneet Kaur</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014</wicri:regionArea><wicri:noRegion>160014</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Kashmir" sort="Singh, Kashmir" uniqKey="Singh K" first="Kashmir" last="Singh">Kashmir Singh</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014</wicri:regionArea><wicri:noRegion>160014</wicri:noRegion></affiliation></author></analytic><series><title level="j">Non-coding RNA research</title><idno type="eISSN">2468-0540</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Plant specific miRNAs (Novel miRNAs) are well known to perform distinctive functions in biological processes. Identification of new miRNAs is necessary to understand their gene regulation. Degradome provides an opportunity to explore the miRNA functions by comparing the miRNA population and their degraded products. In the present study, Small RNA sequencing data was used to identify novel miRNAs. Further, degradome sequencing was carried out to identify miRNAs targets in the plant, <i>Chlorophytum borivilianum</i>. The present study supplemented 40 more novel miRNAs correlating degradome data with smallRNAome. Novel miRNAs, complementary to mRNA partial sequences obtained from degradome sequencing were actually targeting the later. A big pool of miRNA was established by using <i>Oryza sativa, Arabidopsis thaliana, Populus trichocarpa, Ricinus communis,</i> and <i>Vitis vinifera</i> genomic data. Targets were identified for novel miRNAs and total 109 targets were predicted. BLAST2GO analysis elaborate about localization of novel miRNAs' targets and their corresponding KEGG (Kyoto Encyclopedia for Genes and Genomes) pathways. Identified targets were annotated and were found to be involved in significant biological processes like Nitrogen metabolism, Pyruvate metabolism, Citrate cycle (TCA cycle), photosynthesis, and Glycolysis/Gluconeogenesis. The present study provides an overall view of the miRNA regulation in multiple metabolic pathways that are involved in plant growth, pathogen resistance and secondary metabolism of <i>C. borivilianum</i>.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32072082</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">2468-0540</ISSN><JournalIssue CitedMedium="Internet"><Volume>4</Volume><Issue>4</Issue><PubDate><Year>2019</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Non-coding RNA research</Title><ISOAbbreviation>Noncoding RNA Res</ISOAbbreviation></Journal><ArticleTitle>Identification of novel microRNAs and their targets in Chlorophytum borivilianum by small RNA and degradome sequencing.</ArticleTitle><Pagination><MedlinePgn>141-154</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.ncrna.2019.11.004</ELocationID><Abstract><AbstractText>Plant specific miRNAs (Novel miRNAs) are well known to perform distinctive functions in biological processes. Identification of new miRNAs is necessary to understand their gene regulation. Degradome provides an opportunity to explore the miRNA functions by comparing the miRNA population and their degraded products. In the present study, Small RNA sequencing data was used to identify novel miRNAs. Further, degradome sequencing was carried out to identify miRNAs targets in the plant, <i>Chlorophytum borivilianum</i>. The present study supplemented 40 more novel miRNAs correlating degradome data with smallRNAome. Novel miRNAs, complementary to mRNA partial sequences obtained from degradome sequencing were actually targeting the later. A big pool of miRNA was established by using <i>Oryza sativa, Arabidopsis thaliana, Populus trichocarpa, Ricinus communis,</i> and <i>Vitis vinifera</i> genomic data. Targets were identified for novel miRNAs and total 109 targets were predicted. BLAST2GO analysis elaborate about localization of novel miRNAs' targets and their corresponding KEGG (Kyoto Encyclopedia for Genes and Genomes) pathways. Identified targets were annotated and were found to be involved in significant biological processes like Nitrogen metabolism, Pyruvate metabolism, Citrate cycle (TCA cycle), photosynthesis, and Glycolysis/Gluconeogenesis. The present study provides an overall view of the miRNA regulation in multiple metabolic pathways that are involved in plant growth, pathogen resistance and secondary metabolism of <i>C. borivilianum</i>.</AbstractText><CopyrightInformation>© 2020 Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kajal</LastName><ForeName>Monika</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kaushal</LastName><ForeName>Nishant</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kaur</LastName><ForeName>Ravneet</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Singh</LastName><ForeName>Kashmir</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Biotechnology, Panjab University, BMS Block-I, Sector 25, Chandigarh, 160014, India.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>11</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Noncoding RNA Res</MedlineTA><NlmUniqueID>101688191</NlmUniqueID><ISSNLinking>2468-0540</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">AGO, Argonaute</Keyword><Keyword MajorTopicYN="N">BLAST, Basic local Alignment Search Tool</Keyword><Keyword MajorTopicYN="N">BP, Biological Process</Keyword><Keyword MajorTopicYN="N">CC, Cellular Component</Keyword><Keyword MajorTopicYN="N">Chlorophytum borivilianum</Keyword><Keyword MajorTopicYN="N">Degradome</Keyword><Keyword MajorTopicYN="N">FAO, Food and Agriculture Organization of the United Nations</Keyword><Keyword MajorTopicYN="N">GO, Gene Ontology</Keyword><Keyword MajorTopicYN="N">IL, Interleukin</Keyword><Keyword MajorTopicYN="N">Illumina sequencing</Keyword><Keyword MajorTopicYN="N">KEGG, Kyoto Encyclopedia of Genes and Genomes</Keyword><Keyword MajorTopicYN="N">MCF-7, PC3, HCT-116, Types of cell lines</Keyword><Keyword MajorTopicYN="N">MEP, 2-C-methyl-Derythritol-4-phosphate pathway</Keyword><Keyword MajorTopicYN="N">MF, Molecular Function</Keyword><Keyword MajorTopicYN="N">MFEs, Minimum Fold Energies</Keyword><Keyword MajorTopicYN="N">MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide</Keyword><Keyword MajorTopicYN="N">MVA, Mevalonic Acid Pathway</Keyword><Keyword MajorTopicYN="N">RdDM, RNA-directed DNA methylation</Keyword><Keyword MajorTopicYN="N">SRA</Keyword><Keyword MajorTopicYN="N">SRA, Sequencing Read Archieve</Keyword><Keyword MajorTopicYN="N">TNF, Tumor Necrosis Factor</Keyword><Keyword MajorTopicYN="N">iNOS, Inducible Nitric Oxide Synthase</Keyword><Keyword MajorTopicYN="N">mgmL−1, milligram per millilitre</Keyword><Keyword MajorTopicYN="N">microRNAs</Keyword><Keyword MajorTopicYN="N">nt, nucleotide</Keyword></KeywordList><CoiStatement>The Authors declare that there are no competing interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>10</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>11</Month><Day>20</Day></PubMedPubDate><PubMedPubDate 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