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

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 libra...

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Detalles Bibliográficos
Autores principales: Szittya, Gyorgy, Moxon, Simon, Santos, Dulce M, Jing, Runchun, Fevereiro, Manuel PS, Moulton, Vincent, Dalmay, Tamas
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2621214/
https://www.ncbi.nlm.nih.gov/pubmed/19068109
http://dx.doi.org/10.1186/1471-2164-9-593
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author Szittya, Gyorgy
Moxon, Simon
Santos, Dulce M
Jing, Runchun
Fevereiro, Manuel PS
Moulton, Vincent
Dalmay, Tamas
author_facet Szittya, Gyorgy
Moxon, Simon
Santos, Dulce M
Jing, Runchun
Fevereiro, Manuel PS
Moulton, Vincent
Dalmay, Tamas
author_sort Szittya, Gyorgy
collection PubMed
description 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.
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spelling pubmed-26212142009-01-13 High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families Szittya, Gyorgy Moxon, Simon Santos, Dulce M Jing, Runchun Fevereiro, Manuel PS Moulton, Vincent Dalmay, Tamas BMC Genomics Research Article 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. BioMed Central 2008-12-09 /pmc/articles/PMC2621214/ /pubmed/19068109 http://dx.doi.org/10.1186/1471-2164-9-593 Text en Copyright © 2008 Szittya et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Szittya, Gyorgy
Moxon, Simon
Santos, Dulce M
Jing, Runchun
Fevereiro, Manuel PS
Moulton, Vincent
Dalmay, Tamas
High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families
title High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families
title_full High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families
title_fullStr High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families
title_full_unstemmed High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families
title_short High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families
title_sort high-throughput sequencing of medicago truncatula short rnas identifies eight new mirna families
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2621214/
https://www.ncbi.nlm.nih.gov/pubmed/19068109
http://dx.doi.org/10.1186/1471-2164-9-593
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