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Nat Commun. 2014 Apr 23;5:3722. doi: 10.1038/ncomms4722.

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

Author information

1
1] Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato, CP 36821 Guanajuato, México [2].
2
1] Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato, CP 36821 Guanajuato, México [2] [3].
3
1] Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19717, USA [2] Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA [3] [4].
4
1] Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19717, USA [2] Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA.
5
1] Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19717, USA [2] Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA [3].
6
Departamento de Biotecnología y Bioquímica, CINVESTAV-IPN, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato, CP 36821 Guanajuato, México.
7
Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato, CP 36821 Guanajuato, México.

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.

PMID:
24759728
DOI:
10.1038/ncomms4722
[Indexed for MEDLINE]

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