Open Access Highly Accessed Research article

Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing

Pablo Peláez, Minerva S Trejo, Luis P Iñiguez, Georgina Estrada-Navarrete, Alejandra A Covarrubias, José L Reyes and Federico Sanchez*

Author Affiliations

Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico

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BMC Genomics 2012, 13:83  doi:10.1186/1471-2164-13-83

Published: 6 March 2012

Additional files

Additional file 1:

Conserved miRNAs detected only in one library and/or with fewer than 15 reads. MiRNAs in common bean identified in leaves (LL), roots (RL), seedlings (SL) and flowers (FL) detected in just one library and/or with fewer than 15 total reads.

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Open Data

Additional file 2:

Stem-loop miRNA precursors in common bean. EST fragments (new conserved pre-miRNAs) and fragments of stem-loop sequences reported in miRBase (v. 16) for P. vulgaris where aligned against miRNA sequences (blue sequences). Count data number represents the total number of reads in all four libraries. Count data number represents the total number of reads in all four libraries.

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Open Data

Additional file 3:

Novel miRNAs detected in Phaseolus vulgaris. Novel miRNAs in common bean identified in leaves (LL), roots (RL), seedlings (SL) and flowers (FL) using miRDeep.

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Open Data

Additional file 4:

Predicted conserved targets in Phaseolus. Predicted conserved miRNA targets based on ESTs of the genus Phaseolus. GenBank accession numbers are used for EST identification. Calculated MFEs (kcal/mol) using RNAhybrid are shown. MiRNA families 156 and 157 share the same predicted conserved targets. MicroRNA sequences in 3'-5' sense were used to represent miRNA:target pairing. Crosses (x) and asterisks (*) denote one-nucleotide wobbles and mismatches, respectively. G:U base pairing is not considered a mismatch (|)

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Open Data

Additional file 5:

Predicted Putative targets in Phaseolus. Predicted putative miRNA targets based on ESTs of the genus Phaseolus. GenBank accession numbers are used for EST identification. Calculated MFEs (kcal/mol) using RNAhybrid are shown. MicroRNA sequences in 3'-5' sense were used to represent miRNA:target pairing. Crosses (x) and asterisks (*) denote one-nucleotide wobbles and mismatches, respectively. G:U base pairing is not considered a mismatch (|)

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Open Data

Additional file 6:

Putative targets for novel miRNAs identified in Phaseolus. Predicted putative targets for novel miRNAs in common bean based on EST of the genus Phaseolus. MicroRNA sequences in 3'-5' sense were used to represent miRNA:target pairing. Crosses (x) and asterisks (*) denote one-nucleotide wobbles and mismatches, respectively. G:U base pairing is not considered a mismatch (|)

Format: XLSX Size: 18KB Download file

Open Data