Sequencing, de novo assembly and annotation of digitalis ferruginea subsp. schischkinii transcriptome

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dc.authorid0000-0001-6262-2866en_US
dc.authorid0000-0002-7631-823Xen_US
dc.authorid0000-0003-0097-1125
dc.authorid0000-0002-7376-3709
dc.contributor.authorÜnlü, Ercan Selçuk
dc.contributor.authorKaya, Özge
dc.contributor.authorEker, İsmail
dc.contributor.authorGürel, Ekrem
dc.date.accessioned2021-06-23T19:55:07Z
dc.date.available2021-06-23T19:55:07Z
dc.date.issued2021
dc.departmentBAİBÜ, Fen Edebiyat Fakültesi, Kimya Bölümüen_US
dc.descriptionThis study was financially supported by Bolu Abant Izzet Baysal University [Grant Number 2016.03.01.1074].
dc.description.abstractThere is an increasing demand for elucidating the biosynthetic pathway of medicinal plants, which are capable of producing several metabolites with great potentials for industrial drug production. Digitalis species are important medicinal plants for the production of cardenolide compounds. Advancement on culture techniques is strictly related to our understanding of the genomic background of species. There are a limited number of genomic studies on Digitalis species. The goal of this study is to contribute to the genomic data of Digitalis ferruginea subsp. schischkinii by presenting transcriptome annotation. Digitalis ferruginea subsp. schischkinii has a limited distribution in Turkey and Transcaucasia, and has a high level of lanatoside C, an important cardenolide. In the study, we sequenced the cDNA library prepared from RNA pools of D. ferruginea subsp. schischkinii tissues treated with various stress conditions. Comprehensive bioinformatics approaches were used for de novo assembly and functional annotation of D. ferruginea subsp. schischkinii transcriptome sequence data along with TF families predictions and phylogenetic analysis. In the study, 58,369 unigenes were predicted and unigenes were annotated by analyzing the sequence data in the non-redundant (NR) protein database, the non-redundant nucleotide (NT) database, Gene Orthology (GO), EuKaryotic Orthologous Groups (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG), SwissProt, and InterPro databases. This study is the first transcriptome data for D. ferruginea subsp. schischkinii.en_US
dc.description.sponsorshipBolu Abant Izzet Baysal University [2016.03.01.1074]
dc.identifier.doi10.1007/s11033-020-05982-7
dc.identifier.endpage137en_US
dc.identifier.issn0301-4851
dc.identifier.issn1573-4978
dc.identifier.issue1en_US
dc.identifier.pmid33403559en_US
dc.identifier.scopus2-s2.0-85099015151en_US
dc.identifier.scopusqualityQ2en_US
dc.identifier.startpage127en_US
dc.identifier.urihttps://doi.org/10.1007/s11033-020-05982-7
dc.identifier.urihttps://hdl.handle.net/20.500.12491/10732
dc.identifier.volume48en_US
dc.identifier.wosWOS:000607269900006en_US
dc.identifier.wosqualityQ4en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.institutionauthorÜnlü, Ercan Selçuk
dc.institutionauthorGürel, Ekrem
dc.institutionauthorEker, İsmail
dc.institutionauthorKaya, Özge
dc.language.isoenen_US
dc.publisherSpringeren_US
dc.relation.ispartofMolecular Biology Reportsen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectDigitalis ferruginea subspen_US
dc.subjectSchischkiniien_US
dc.subjectRNA-seqen_US
dc.subjectDe Novo Assemblyen_US
dc.subjectBioinformaticsen_US
dc.subjectNon-model Organismen_US
dc.subjectMedicinal Planten_US
dc.titleSequencing, de novo assembly and annotation of digitalis ferruginea subsp. schischkinii transcriptomeen_US
dc.typeArticleen_US

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