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

Authors
  • Ünlü, Ercan Selçuk1
  • Kaya, Özge2
  • Eker, İsmail2
  • Gürel, Ekrem2
  • 1 Department of Chemistry, Faculty of Arts and Science, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey. [email protected] , (Turkey)
  • 2 Department of Biology, Faculty of Arts and Science, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey. , (Turkey)
Type
Published Article
Journal
Molecular Biology Reports
Publisher
Springer-Verlag
Publication Date
Jan 05, 2021
Identifiers
DOI: 10.1007/s11033-020-05982-7
PMID: 33403559
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

There 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.

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