TY - JOUR
T1 - Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs
AU - Chávez Montes, Ricardo A.
AU - De Fátima Rosas-Cárdenas, Flor
AU - De Paoli, Emanuele
AU - Accerbi, Monica
AU - Rymarquis, Linda A.
AU - Mahalingam, Gayathri
AU - Marsch-Martínez, Nayelli
AU - Meyers, Blake C.
AU - Green, Pamela J.
AU - De Folter, Stefan
N1 - Funding Information:
P.J.G. and B.C.M. gratefully acknowledge the many labs and researchers listed in Supplementary Data 1 who have generously provided plant and algal samples used for construction of the sRNA libraries sequenced in this study. R.A.C.M. was a recipient of a postdoctoral fellowship from the Mexican National Council of Science and Technology (CONACyT). F.d.F.R.-C. was a recipient of a PhD fellowship (199450) from CONACyT. The work in the de Folter laboratory was financed by the CONACyT Grant 177739. The generation of the data, the website, and work in the Green and Meyers lab was supported by US National Science Foundation award #0638525 from the Plant Genome Research Program.
PY - 2014/4/23
Y1 - 2014/4/23
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84899487011&partnerID=8YFLogxK
U2 - 10.1038/ncomms4722
DO - 10.1038/ncomms4722
M3 - Artículo
C2 - 24759728
SN - 2041-1723
VL - 5
JO - Nature Communications
JF - Nature Communications
M1 - 3722
ER -