CANTATAdb 2.0: Expanding the Collection of Plant Long Noncoding RNAs

  • Michał Wojciech SzcześniakEmail author
  • Oleksii Bryzghalov
  • Joanna Ciomborowska-Basheer
  • Izabela Makałowska
Part of the Methods in Molecular Biology book series (MIMB, volume 1933)


Long non-coding RNAs (lncRNAs) are a class of potent regulators of gene expression that are found in a wide array of eukaryotes; however, our knowledge about these molecules in plants is very limited. In particular, a number of plant species with important roles in biotechnology, agriculture and basic research still lack comprehensively identified and annotated sets of lncRNAs. To address these shortcomings, we previously created a database of lncRNAs in 10 model species, called CANTATAdb, and now we are expanding this online resource to encompass 39 species, including three algae. The lncRNAs were identified computationally using publicly available RNA sequencing (RNA-Seq) data. Expression values, coding potential calculations and other types of information were used to provide annotations for the identified lncRNAs. The data are freely available for searching, browsing and downloading from an online database called CANTATAdb 2.0 (,

Key words

Database Long noncoding RNAs Plant RNAs lncRNA identification 



This work was supported by the National Science Centre (grant No. 2014/15/D/NZ2/00525 to M.W.S); the KNOW Poznan RNA Centre (grant No. 01/KNOW2/2014); the Polish Ministry of Science and Higher Education (decision No. 1268/MOB/IV/2015/0 to M.W.S - Mobility Plus project).


  1. 1.
    Zhao Y, Li H, Fang S, Kang Y, Wu W, Hao Y et al (2016) NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Res 44:D203–D208CrossRefGoogle Scholar
  2. 2.
    Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J et al (2018) Ensembl 2018. Nucleic Acids Res 46:D754–D761CrossRefGoogle Scholar
  3. 3.
    Paytuvi Gallart A, Hermoso Pulido A, Anzar Martinez de Lagran I, Sanseverino W, Aiese Cigliano R (2016) GREENC: a Wiki-based database of plant lncRNAs. Nucleic Acids Res 44:D1161–D1166CrossRefGoogle Scholar
  4. 4.
    Szczesniak MW, Rosikiewicz W, Makalowska I (2016) CANTATAdb: a collection of plant long non-coding RNAs. Plant Cell Physiol 57:e8CrossRefGoogle Scholar
  5. 5.
    Kim DH, Xi Y, Sung S (2017) Modular function of long noncoding RNA, COLDAIR, in the vernalization response. PLoS Genet 13:e1006939CrossRefGoogle Scholar
  6. 6.
    Zhang YC, Liao JY, Li ZY, Yu Y, Zhang JP, Li QF et al (2014) Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol 15:512CrossRefGoogle Scholar
  7. 7.
    Wang Y, Li J, Deng XW, Zhu D (2017) Arabidopsis noncoding RNA modulates seedling greening during deetiolation. Sci China Life Sci 61:199. Scholar
  8. 8.
    Yuan J, Zhang Y, Dong J, Sun Y, Lim BL, Liu D et al (2016) Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana. BMC Genomics 17:655CrossRefGoogle Scholar
  9. 9.
    Zhang J, Wang C, Ke N, Bliesath J, Chionis J, He QS et al (2007) A more efficient RNAi inducible system for tight regulation of gene expression in mammalian cells and xenograft animals. RNA 13:1375–1383CrossRefGoogle Scholar
  10. 10.
    Ben Amor B, Wirth S, Merchan F, Laporte P, d'Aubenton-Carafa Y, Hirsch J et al (2009) Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res 19:57–69CrossRefGoogle Scholar
  11. 11.
    Deng F, Zhang X, Wang W, Yuan R, Shen F (2018) Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress. BMC Plant Biol 18:23CrossRefGoogle Scholar
  12. 12.
    Bardou F, Ariel F, Simpson CG, Romero-Barrios N, Laporte P, Balzergue S et al (2014) Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev Cell 30:166–176CrossRefGoogle Scholar
  13. 13.
    Bazin J, Baerenfaller K, Gosai SJ, Gregory BD, Crespi M, Bailey-Serres J (2017) Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation. Proc Natl Acad Sci U S A 114:E10018–E10027CrossRefGoogle Scholar
  14. 14.
    Bolser DM, Staines DM, Perry E, Kersey PJ (2017) Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomic data. Methods Mol Biol 1533:1–31CrossRefGoogle Scholar
  15. 15.
    Kodama Y, Shumway M, Leinonen R (2012) The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res 40:D54–D56CrossRefGoogle Scholar
  16. 16.
    Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21CrossRefGoogle Scholar
  17. 17.
    Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33:290–295CrossRefGoogle Scholar
  18. 18.
    Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ et al (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515CrossRefGoogle Scholar
  19. 19.
    Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512CrossRefGoogle Scholar
  20. 20.
    Kong L, Zhang Y, Ye Z, Liu X, Zhao S, Wei L et al (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 35:W345–W349CrossRefGoogle Scholar
  21. 21.
    Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A et al (2018) Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res 46:D335–D342CrossRefGoogle Scholar
  22. 22.
    Sun L, Luo H, Bu D, Zhao G, Yu K, Zhang C et al (2013) Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res 41:e166CrossRefGoogle Scholar
  23. 23.
    The UniProt Consortium (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res 45:D158–D169CrossRefGoogle Scholar
  24. 24.
    Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C (2017) Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14:417–419CrossRefGoogle Scholar
  25. 25.
    Yi X, Zhang Z, Ling Y, Xu W, Su Z (2015) PNRD: a plant non-coding RNA database. Nucleic Acids Res 43:D982–D989CrossRefGoogle Scholar
  26. 26.
    Xuan H, Zhang L, Liu X, Han G, Li J, Li X et al (2015) PLNlncRbase: a resource for experimentally identified lncRNAs in plants. Gene 573:328–332CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Michał Wojciech Szcześniak
    • 1
    Email author
  • Oleksii Bryzghalov
    • 1
  • Joanna Ciomborowska-Basheer
    • 1
  • Izabela Makałowska
    • 1
  1. 1.Laboratory of Integrative Genomics, Institute of AnthropologyAdam Mickiewicz UniversityPoznanPoland

Personalised recommendations