Open Access Highly Accessed Research article

High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families

Gyorgy Szittya1, Simon Moxon2, Dulce M Santos3, Runchun Jing1, Manuel PS Fevereiro3, Vincent Moulton2 and Tamas Dalmay1*

Author Affiliations

1 School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK

2 School of Computing Science, University of East Anglia, Norwich, NR4 7TJ, UK

3 Laboratory of Plant Cell Biotechnology, ITQB/IBET – Apt 127, 2781-901 Oeiras, Portugal

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BMC Genomics 2008, 9:593  doi:10.1186/1471-2164-9-593

Published: 9 December 2008

Abstract

Background

High-throughput sequencing technology is capable to identify novel short RNAs in plant species. We used Solexa sequencing to find new microRNAs in one of the model legume species, barrel medic (Medicago truncatula).

Results

3,948,871 reads were obtained from two separate short RNA libraries generated from total RNA extracted from M. truncatula leaves, representing 1,563,959 distinct sequences. 2,168,937 reads were mapped to the available M. truncatula genome corresponding to 619,175 distinct sequences. 174,504 reads representing 25 conserved miRNA families showed perfect matches to known miRNAs. We also identified 26 novel miRNA candidates that were potentially generated from 32 loci. Nine of these loci produced eight distinct sequences, for which the miRNA* sequences were also sequenced. These sequences were not described in other plant species and accumulation of these eight novel miRNAs was confirmed by Northern blot analysis. Potential target genes were predicted for most conserved and novel miRNAs.

Conclusion

Deep sequencing of short RNAs from M. truncatula leaves identified eight new miRNAs indicating that specific miRNAs exist in legume species.