Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships.

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  • Additional Information
    • Author-Supplied Keywords:
      CREMA
      evolution
      lncRNA
      phylogenetic
      RNASeq
      signal
    • NAICS/Industry Codes:
      413150 Fresh fruit and vegetable merchant wholesalers
      115114 Postharvest Crop Activities (except Cotton Ginning)
      111211 Potato Farming
    • Abstract:
      Long non-coding RNAs (lncRNAs) represent a diverse class of regulatory loci with roles in development and stress responses throughout all kingdoms of life. LncRNAs, however, remain understudied in plants compared to animal systems. To address this deficiency, we applied a machine learning prediction tool, Classifying RNA by Ensemble Machine learning Algorithm (CREMA), to analyze RNAseq data from 11 plant species chosen to represent a wide range of evolutionary histories. Transcript sequences of all expressed and/or annotated loci from plants grown in unstressed (control) conditions were assembled and input into CREMA for comparative analyses. On average, 6.4% of the plant transcripts were identified by CREMA as encoding lncRNAs. Gene annotation associated with the transcripts showed that up to 99% of all predicted lncRNAs for Solanum tuberosum and Amborella trichopoda were missing from their reference annotations whereas the reference annotation for the genetic model plant Arabidopsis thaliana contains 96% of all predicted lncRNAs for this species. Thus a reliance on reference annotations for use in lncRNA research in less well-studied plants can be impeded by the near absence of annotations associated with these regulatory transcripts. Moreover, our work using phylogenetic signal analyses suggests that molecular traits of plant lncRNAs display different evolutionary patterns than all other transcripts in plants and have molecular traits that do not follow a classic evolutionary pattern. Specifically, GC content was the only tested trait of lncRNAs with consistently significant and high phylogenetic signal, contrary to high signal in all tested molecular traits for the other transcripts in our tested plant species. [ABSTRACT FROM AUTHOR]
    • Abstract:
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    • Author Affiliations:
      1Department of Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4K1
    • ISSN:
      2160-1836
    • Accession Number:
      10.1534/g3.119.400201
    • Accession Number:
      138289698
  • Citations
    • ABNT:
      SIMOPOULOS, C. M. A.; WERETILNYK, E. A.; GOLDING, G. B. Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships. G3: Genes | Genomes | Genetics, [s. l.], v. 9, n. 8, p. 2511–2520, 2019. DOI 10.1534/g3.119.400201. Disponível em: http://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=asn&AN=138289698&custid=s8280428. Acesso em: 10 dez. 2019.
    • AMA:
      Simopoulos CMA, Weretilnyk EA, Golding GB. Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships. G3: Genes | Genomes | Genetics. 2019;9(8):2511-2520. doi:10.1534/g3.119.400201.
    • APA:
      Simopoulos, C. M. A., Weretilnyk, E. A., & Golding, G. B. (2019). Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships. G3: Genes | Genomes | Genetics, 9(8), 2511–2520. https://doi.org/10.1534/g3.119.400201
    • Chicago/Turabian: Author-Date:
      Simopoulos, Caitlin M. A., Elizabeth A. Weretilnyk, and G. Brian Golding. 2019. “Molecular Traits of Long Non-Protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships.” G3: Genes | Genomes | Genetics 9 (8): 2511–20. doi:10.1534/g3.119.400201.
    • Harvard:
      Simopoulos, C. M. A., Weretilnyk, E. A. and Golding, G. B. (2019) ‘Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships’, G3: Genes | Genomes | Genetics, 9(8), pp. 2511–2520. doi: 10.1534/g3.119.400201.
    • Harvard: Australian:
      Simopoulos, CMA, Weretilnyk, EA & Golding, GB 2019, ‘Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships’, G3: Genes | Genomes | Genetics, vol. 9, no. 8, pp. 2511–2520, viewed 10 December 2019, .
    • MLA:
      Simopoulos, Caitlin M. A., et al. “Molecular Traits of Long Non-Protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships.” G3: Genes | Genomes | Genetics, vol. 9, no. 8, Aug. 2019, pp. 2511–2520. EBSCOhost, doi:10.1534/g3.119.400201.
    • Chicago/Turabian: Humanities:
      Simopoulos, Caitlin M. A., Elizabeth A. Weretilnyk, and G. Brian Golding. “Molecular Traits of Long Non-Protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships.” G3: Genes | Genomes | Genetics 9, no. 8 (August 2019): 2511–20. doi:10.1534/g3.119.400201.
    • Vancouver/ICMJE:
      Simopoulos CMA, Weretilnyk EA, Golding GB. Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships. G3: Genes | Genomes | Genetics [Internet]. 2019 Aug [cited 2019 Dec 10];9(8):2511–20. Available from: http://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=asn&AN=138289698&custid=s8280428