Skip to main content

Advertisement

SpringerLink
Log in

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

  • Original Article
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  1. Pichersky E, Gang DR (2000) Genetics and biochemistry of secondary metabolites in plants: an evolutionary perspective. Trends Plant Sci 5:439–445. https://doi.org/10.1016/S1360-1385(00)01741-6

    Article  CAS  PubMed  Google Scholar 

  2. Kroymann J (2011) Natural diversity and adaptation in plant secondary metabolism. Curr Opin Plant Biol 14:246–251. https://doi.org/10.1016/j.pbi.2011.03.021

    Article  CAS  PubMed  Google Scholar 

  3. Wink M (2010) Introduction: biochemistry, physiology and ecological functions of secondary metabolites. Biochem Plant Second Metab Second Ed 40:1–19

    CAS  Google Scholar 

  4. Sudha G, Ravishankar GA (2002) Involvement and interaction of various signaling compounds on the plant metabolic events during defense response, resistance to stress factors, formation of secondary metabolites and their molecular aspects. Plant cell. Tissue Organ Cult 71:181–212

    Article  CAS  Google Scholar 

  5. Hussain MS, Fareed S, Ansari S et al (2012) Current approaches toward production of secondary plant metabolites. J Pharm Bioallied Sci 4:10–20

    Article  PubMed  PubMed Central  Google Scholar 

  6. Verpoorte R, Memelink J (2002) Engineering secondary metabolite production in plants. Curr Opin Biotechnol 13:181–187. https://doi.org/10.1016/S0958-1669(02)00308-7

    Article  CAS  PubMed  Google Scholar 

  7. Oksman-Caldentey KM, Inzé D (2004) Plant cell factories in the post-genomic era: new ways to produce designer secondary metabolites. Trends Plant Sci 9:433–440

    Article  CAS  PubMed  Google Scholar 

  8. Xiao M, Zhang Y, Chen X et al (2013) Transcriptome analysis based on next-generation sequencing of non-model plants producing specialized metabolites of biotechnological interest. J Biotechnol 166:122–134. https://doi.org/10.1016/j.jbiotec.2013.04.004

    Article  CAS  PubMed  Google Scholar 

  9. Sharma S, Shrivastava N (2016) Renaissance in phytomedicines: promising implications of NGS technologies. Planta 244:19–38

    Article  CAS  PubMed  Google Scholar 

  10. Shirai K, Hanada K (2019) Contribution of functional divergence through copy number variations to the ınter-species and ıntra-species diversity in specialized metabolites. Front Plant Sci. https://doi.org/10.3389/fpls.2019.01567

    Article  PubMed  PubMed Central  Google Scholar 

  11. Strickler SR, Bombarely A, Mueller LA (2012) Designing a transcriptome next-generation sequencing project for a nonmodel plant species. Am J Bot 99:257–266. https://doi.org/10.3732/ajb.1100292

    Article  CAS  PubMed  Google Scholar 

  12. Prassas I, Diamandis EP (2008) Novel therapeutic applications of cardiac glycosides. Nat Rev Drug Discov 7:926–935

    Article  CAS  PubMed  Google Scholar 

  13. Verma SK, Das AK, Cingoz GS, Gurel E (2016) In vitro culture of Digitalis L. (Foxglove) and the production of cardenolides: an up-to-date review. Ind Crops Prod 94:20–51

    Article  CAS  Google Scholar 

  14. Gurel E, Karvar S, Yucesan B et al (2017) An overview of cardenolides in Digitalis—more than a cardiotonic compound. Curr Pharm Des. https://doi.org/10.2174/1381612823666170825125426

    Article  PubMed  Google Scholar 

  15. Amarelle L, Katzen J, Shigemura M et al (2019) Cardiac glycosides decrease influenza virus replication by inhibiting cell protein translational machinery. Am J Physiol Lung Cell Mol Physiol 316:L1094–L1106. https://doi.org/10.1152/ajplung.00173.2018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Kapoor A, Cai H, Forman M et al (2012) Human cytomegalovirus inhibition by cardiac glycosides: evidence for involvement of the hERG gene. Antimicrob Agents Chemother 56:4891–4899. https://doi.org/10.1128/AAC.00898-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Kreis W (2017) The foxgloves (Digitalis) revisited. Planta Med 83:962–976

    Article  CAS  PubMed  Google Scholar 

  18. Bräuchler C, Meimberg H, Heubl G (2004) Molecular phylogeny of the genera Digitalis L. and Isoplexis (Lindley) Loudon (Veronicaceae) based on ITS- and trnL-F sequences. Plant Syst Evol 248:111–128. https://doi.org/10.1007/s00606-004-0145-z

    Article  Google Scholar 

  19. Bertol JW, Rigotto C, de Pádua RM et al (2011) Antiherpes activity of glucoevatromonoside, a cardenolide isolated from a Brazilian cultivar of Digitalis lanata. Antiviral Res 92:73–80. https://doi.org/10.1016/j.antiviral.2011.06.015

    Article  CAS  PubMed  Google Scholar 

  20. Davıs PH (1978) Digitalis. In: Flora of Turkey and East Aegean Islands, 6th ed. Edinburgh University Press, Edinburgh, pp 680–687

  21. Eker İ, Yücesan B, Sameeullah M et al (2016) Phylogeny of Anatolian (Turkey) species in the Digitalis sect. Globiflorae (Plantaginaceae). Phytotaxa 244:263

    Article  Google Scholar 

  22. Yücesan B, Mohammed A, Eker İ et al (2016) In vitro propagation and cardenolide profiling of Digitalis ferruginea subsp. schischkinii, a medicinally important foxglove species with limited distribution in Northern Turkey. Vitr Cell Dev Biol Plant 52:322–329. https://doi.org/10.1007/s11627-016-9759-4

  23. Thiers B (2016) Index herbariorum: a global directory of public herbaria and associated staff

  24. Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15:473–497. https://doi.org/10.1111/j.1399-3054.1962.tb08052.x

    Article  CAS  Google Scholar 

  25. Babu S, Gassmann M (2016) Assessing integrity of plant RNA with the Agilent 2100 Bioanalyzer. https://www.agilent.com/cs/library/applications/5990-8850EN.pdf. Accessed 17 Dec 2020

  26. Haas BJ, Papanicolaou A, Yassour M et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512. https://doi.org/10.1038/nprot.2013.084

    Article  CAS  PubMed  Google Scholar 

  27. Pertea G, Huang X, Liang F et al (2003) TIGR gene ındices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652

    Article  CAS  PubMed  Google Scholar 

  28. Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2

    Article  CAS  PubMed  Google Scholar 

  29. Rice P, Longden L, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16:276–277

    Article  CAS  PubMed  Google Scholar 

  30. PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

  31. Mistry J, Finn RD, Eddy SR et al (2013) Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res. https://doi.org/10.1093/nar/gkt263

    Article  PubMed  PubMed Central  Google Scholar 

  32. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. https://doi.org/10.1093/nar/22.22.4673

    Article  PubMed  PubMed Central  Google Scholar 

  33. Price MN, Dehal PS, Arkin AP (2009) Fasttree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. https://doi.org/10.1093/molbev/msp077

    Article  PubMed  PubMed Central  Google Scholar 

  34. Schroeder A, Mueller O, Stocker S et al (2006) No title. BMC Mol Biol 7:3. https://doi.org/10.1186/1471-2199-7-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Johnson MTJ, Carpenter EJ, Tian Z et al (2012) Evaluating methods for ısolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS ONE 7:e50226. https://doi.org/10.1371/journal.pone.0050226

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Zhao Q-Y, Wang Y, Kong Y-M et al (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinform 12:S2. https://doi.org/10.1186/1471-2105-12-S14-S2

    Article  CAS  Google Scholar 

  37. Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652. https://doi.org/10.1038/nbt.1883

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Wu B, Li Y, Yan H et al (2012) Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea. BMC Genom 13:15. https://doi.org/10.1186/1471-2164-13-15

    Article  CAS  Google Scholar 

  39. Wu B, Suo F, Lei W, Gu L (2014) Comprehensive analysis of alternative splicing in Digitalis purpurea by strand-specific RNA-Seq. PLoS ONE. https://doi.org/10.1371/journal.pone.0106001

    Article  PubMed  PubMed Central  Google Scholar 

  40. Carels N, Bernardi G (2000) Two classes of genes in plants. Genetics 154:1819–1825

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Kanehisa M (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30. https://doi.org/10.1093/nar/28.1.27

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Moriya Y, MISOAYMK (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185

    Article  PubMed  PubMed Central  Google Scholar 

  43. Ganapaty S, Mallika BN, Balaji S et al (2003) A review of phytochemical studies of Digitalis species. J Nat Rem 3:104–128

    CAS  Google Scholar 

  44. Calis I, Tasdemir D, Sticher O, Nıshıbe S (1999) Phenylethanoid glycosides from Digitalis ferruginea subsp. ferruginea (= D. aurea Lindley) (Scrophulariaceae). Chem Pharm Bull 47:1305–1307. https://doi.org/10.1248/cpb.47.1305

    Article  CAS  Google Scholar 

  45. Katanić J, Ceylan R, Matić S et al (2017) Novel perspectives on two Digitalis species: phenolic profile, bioactivity, enzyme inhibition, and toxicological evaluation. S Afr J Bot 109:50–57. https://doi.org/10.1016/J.SAJB.2016.12.004

    Article  Google Scholar 

  46. Degot’ AV, Fursa NS (1980) Phenolic compounds of Digitalis ferruginea. Khimiya Prir Soedin 3:417–418

    Google Scholar 

  47. Skhirtladze AV, Kopaliani TA, Nebieridze VG et al (2017) New steroidal glycosides from pericarp of Digitalis ferruginea. Chem Nat Compd 53:1083–1087. https://doi.org/10.1007/s10600-017-2206-x

    Article  CAS  Google Scholar 

  48. Deluca ME, Seldes AM, Gros EG (1989) Biosynthesis of digitoxin in Digitalis purpurea. Phytochemistry. https://doi.org/10.1016/0031-9422(89)85019-8

    Article  Google Scholar 

  49. Schöniger R, Lindemann P, Grimm R et al (1998) Cardenolide 16′-O-glucohydrolase from Digitalis lanata. Purification and characterization. Planta. https://doi.org/10.1007/s004250050346

    Article  PubMed  Google Scholar 

  50. Schebitz P, Nothdurft L, Hensel A et al (2010) Norcholanic acids as substrates for recombinant 3β-hydroxysteroid dehydrogenase and progesterone 5β-reductase, enzymes of the 5β-cardenolide biosynthesis. Tetrahedron Lett. https://doi.org/10.1016/j.tetlet.2009.11.029

    Article  Google Scholar 

  51. Pandey A, Swarnkar V, Pandey T et al (2016) Transcriptome and Metabolite analysis reveal candidate genes of the cardiac glycoside biosynthetic pathway from Calotropis procera. Sci Rep. https://doi.org/10.1038/srep34464

    Article  PubMed  PubMed Central  Google Scholar 

  52. Gaudinier A, Tang M, Kliebenstein DJ (2015) Transcriptional networks governing plant metabolism. Curr Plant Biol. https://doi.org/10.1016/j.cpb.2015.07.002

    Article  Google Scholar 

  53. Lee TI, Young RA (2000) Transcription of eukaryotic protein-coding genes. Annu Rev Genet 34:77–137. https://doi.org/10.1146/annurev.genet.34.1.77

    Article  CAS  PubMed  Google Scholar 

  54. Roeder RG (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci 21:327–335

    Article  CAS  PubMed  Google Scholar 

  55. Vom Endt D, Kijne JW, Memelink J (2002) Transcription factors controlling plant secondary metabolism: what regulates the regulators? Phytochemistry 61:107–114. https://doi.org/10.1016/S0031-9422(02)00185-1

    Article  Google Scholar 

  56. Bhattacharyya D, Sinha R, Hazra S et al (2013) De novo transcriptome analysis using 454 pyrosequencing of the Himalayan Mayapple, Podophyllum hexandrum. BMC Genom 14:748. https://doi.org/10.1186/1471-2164-14-748

    Article  CAS  Google Scholar 

  57. Herl V, Albach DC, Müller-Uri F et al (2008) Using progesterone 5β-reductase, a gene encoding a key enzyme in the cardenolide biosynthesis, to infer the phylogeny of the genus Digitalis. Plant Syst Evol. https://doi.org/10.1007/s00606-007-0616-0

    Article  Google Scholar 

Download references

Funding

This study was financially supported by Bolu Abant Izzet Baysal University [Grant Number 2016.03.01.1074].

Author information

Authors and Affiliations

  1. Department of Chemistry, Faculty of Arts and Science, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey

    Ercan Selçuk Ünlü

  2. Department of Biology, Faculty of Arts and Science, Bolu Abant Izzet Baysal University, 14030, Bolu, Turkey

    Özge Kaya, İsmail Eker & Ekrem Gürel

Authors
  1. Ercan Selçuk Ünlü
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Özge Kaya
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. İsmail Eker
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ekrem Gürel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ercan Selçuk Ünlü.

Ethics declarations

Conflict of interest

Ercan Selçuk Ünlü declares that he has no conflict of interest. Özge Kaya declares that she has no conflict of interest. İsmail Eker declares that he has no conflict of interest. Ekrem Gürel declares that he has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 56 kb)

11033_2020_5982_MOESM2_ESM.xlsx

Supplementary material 2 (XLSX 7135 kb) Supplementary Data 2. Annotation details of D. ferruginea subsp. schischkinii transcriptome data

Supplementary material 3 (RAR 4295 kb) Supplementary Data 3. Details of KEGG analysis results and pathway maps

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ünlü, E.S., Kaya, Ö., Eker, İ. et al. Sequencing, de novo assembly and annotation of Digitalis ferruginea subsp. schischkinii transcriptome. Mol Biol Rep 48, 127–137 (2021). https://doi.org/10.1007/s11033-020-05982-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-020-05982-7

Keywords

Search

Navigation