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Computational identification and analysis of novel sugarcane microRNAs

Flávia Thiebaut1, Clícia Grativol1, Mariana Carnavale-Bottino1, Cristian Antonio Rojas2, Milos Tanurdzic4, Laurent Farinelli5, Robert A Martienssen3, Adriana Silva Hemerly1 and Paulo Cavalcanti Gomes Ferreira1*

Author Affiliations

1 Laboratorio de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rua Rodolpho Paulo Rocco s/n°, CCS, Bl.B-33A, Cidade Universitária 21941-590, Rio de Janeiro, RJ, Brazil

2 Universidade Federal da Integração Latino-Americana, Av. Tancredo Neves, 6731, Bl.4, 85867-970, Foz do Iguaçu, PR, Brazil

3 Cold Spring Harbor Laboratory, 1 Bungtown RD, Cold Spring Harbor, NY, 11724, USA

4 School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia

5 Fasteris SA, 1228-Plan-les-Ouates, Switzerland

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BMC Genomics 2012, 13:290  doi:10.1186/1471-2164-13-290

Published: 2 July 2012

Additional files

Additional file 1:

Table S1. Summary of results obtained after computational data mining for each small RNA library. Overall information of all and filtered reads, numbers of miRNAs detected, known and novel miRNAs candidates. Table S2. miRCat analyses results of new miRNAs precursors. Overall information of precursors that matched to the criteria for miRNA prediction. Table S3. Correspondence among names of high confidence new microRNAs. List of names used in this paper, and the new names of microRNAs after deposit in the miRBase. Figure S4. Predicted precursor structure of high confidence novel miRNAs (class I) identified. The sugarcane mature miRNA (red), miRNA* (pink) were illustrated in pre-miRNA with chromosome and locus information based in sorghum genome. All novel miRNAs sequences were denominated sof-miR-Seq following the number. Figure S5. Confirmation of new miRNA expression. Validation by stem-loop RT-PCR of eight new miRNAs chosen from our libraries. Primers used were listed in the table. Z. Table S6. Electronic Northern of all new miRNAs candidates in each library. The mature new miRNA reads were normalized to transcripts per million. Table S7. Putative targets of all new miRNAs candidates in sugarcane. EST sugarcane data from Gene Index version 3.0 was used to search for potential new miRNA targets by UEA sRNA toolkit-Plant target prediction pipeline. Table S8. Putative targets of all new miRNAs candidates in sorghum. EST sorghum data from Gene Index version 9.0 and Sorghum gene models (JGI v.1.0) were used to search for potential new miRNA targets by UEA sRNA toolkit-Plant target prediction pipeline. Figure S9. Relative expression profile of MADS Box. Relative expression of putative targets of sof-miR-seq09 and sof-miR-seq19 estimated within control and 1 h after saline treatment.

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