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Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs

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  • Ricardo A. Chávez Montes

    (Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN))

  • de Fátima Flor Rosas-Cárdenas

    (Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN)
    Present address: Centro de Investigación en Biotecnología Aplicada del Instituto Politécnico Nacional (CIBA-IPN), Exhacienda San Juan Molino, Tepetitla de Lardizábal, Tlaxcala, México)

  • Emanuele De Paoli

    (University of Delaware
    Delaware Biotechnology Institute, University of Delaware
    Present address: Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Udine, via delle Scienze 206, 33100 Udine, Italy)

  • Monica Accerbi

    (University of Delaware
    Delaware Biotechnology Institute, University of Delaware)

  • Linda A. Rymarquis

    (University of Delaware
    Delaware Biotechnology Institute, University of Delaware
    Present address: Monsanto Company, Chesterfield, Missouri 63017, USA)

  • Gayathri Mahalingam

    (University of Delaware
    Delaware Biotechnology Institute, University of Delaware)

  • Nayelli Marsch-Martínez

    (CINVESTAV-IPN)

  • Blake C. Meyers

    (University of Delaware
    Delaware Biotechnology Institute, University of Delaware)

  • Pamela J. Green

    (University of Delaware
    Delaware Biotechnology Institute, University of Delaware)

  • Stefan de Folter

    (Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN))

Abstract

Small RNAs are pivotal regulators of gene expression that guide transcriptional and post-transcriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences. Using miRBase mature sequences as a reference, we identify the miRNA sequences present in these libraries. We apply diverse profiling methods to examine critical sRNA and miRNA features, such as size distribution, tissue-specific regulation and sequence conservation between species, as well as to predict putative new miRNA sequences. We also develop database resources, computational analysis tools and a dedicated website, http://smallrna.udel.edu/ . This study provides new insights on plant sRNAs and miRNAs, and a foundation for future studies.

Suggested Citation

  • Ricardo A. Chávez Montes & de Fátima Flor Rosas-Cárdenas & Emanuele De Paoli & Monica Accerbi & Linda A. Rymarquis & Gayathri Mahalingam & Nayelli Marsch-Martínez & Blake C. Meyers & Pamela J. Green &, 2014. "Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs," Nature Communications, Nature, vol. 5(1), pages 1-15, September.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms4722
    DOI: 10.1038/ncomms4722
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