Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane

Detalhes bibliográficos
Autor(a) principal: Zanca, Almir S.
Data de Publicação: 2010
Outros Autores: Vicentini, Renato, Ortiz-Morea, Fausto A., Del Bem, Luiz E. V., da Silva, Marcio J., Vincentz, Michel, Nogueira, Fabio Tebaldi Silveira [UNESP]
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1186/1471-2229-10-260
http://hdl.handle.net/11449/18011
Resumo: Background: MicroRNAs (miRNAs) are small regulatory RNAs, some of which are conserved in diverse plant genomes. Therefore, computational identification and further experimental validation of miRNAs from non-model organisms is both feasible and instrumental for addressing miRNA-based gene regulation and evolution. Sugarcane (Saccharum spp.) is an important biofuel crop with publicly available expressed sequence tag and genomic survey sequence databases, but little is known about miRNAs and their targets in this highly polyploid species.Results: In this study, we have computationally identified 19 distinct sugarcane miRNA precursors, of which several are highly similar with their sorghum homologs at both nucleotide and secondary structure levels. The accumulation pattern of mature miRNAs varies in organs/tissues from the commercial sugarcane hybrid as well as in its corresponding founder species S. officinarum and S. spontaneum. Using sugarcane MIR827 as a query, we found a novel MIR827 precursor in the sorghum genome. Based on our computational tool, a total of 46 potential targets were identified for the 19 sugarcane miRNAs. Several targets for highly conserved miRNAs are transcription factors that play important roles in plant development. Conversely, target genes of lineage-specific miRNAs seem to play roles in diverse physiological processes, such as SsCBP1. SsCBP1 was experimentally confirmed to be a target for the monocot-specific miR528. Our findings support the notion that the regulation of SsCBP1 by miR528 is shared at least within graminaceous monocots, and this miRNA-based post-transcriptional regulation evolved exclusively within the monocots lineage after the divergence from eudicots.Conclusions: Using publicly available nucleotide databases, 19 sugarcane miRNA precursors and one new sorghum miRNA precursor were identified and classified into 14 families. Comparative analyses between sugarcane and sorghum suggest that these two species retain homologous miRNAs and targets in their genomes. Such conservation may help to clarify specific aspects of miRNA regulation and evolution in the polyploid sugarcane. Finally, our dataset provides a framework for future studies on sugarcane RNAi-dependent regulatory mechanisms.
id UNSP_3395428ef97317b0a7c4d4ead39c9205
oai_identifier_str oai:repositorio.unesp.br:11449/18011
network_acronym_str UNSP
network_name_str Repositório Institucional da UNESP
repository_id_str 2946
spelling Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcaneBackground: MicroRNAs (miRNAs) are small regulatory RNAs, some of which are conserved in diverse plant genomes. Therefore, computational identification and further experimental validation of miRNAs from non-model organisms is both feasible and instrumental for addressing miRNA-based gene regulation and evolution. Sugarcane (Saccharum spp.) is an important biofuel crop with publicly available expressed sequence tag and genomic survey sequence databases, but little is known about miRNAs and their targets in this highly polyploid species.Results: In this study, we have computationally identified 19 distinct sugarcane miRNA precursors, of which several are highly similar with their sorghum homologs at both nucleotide and secondary structure levels. The accumulation pattern of mature miRNAs varies in organs/tissues from the commercial sugarcane hybrid as well as in its corresponding founder species S. officinarum and S. spontaneum. Using sugarcane MIR827 as a query, we found a novel MIR827 precursor in the sorghum genome. Based on our computational tool, a total of 46 potential targets were identified for the 19 sugarcane miRNAs. Several targets for highly conserved miRNAs are transcription factors that play important roles in plant development. Conversely, target genes of lineage-specific miRNAs seem to play roles in diverse physiological processes, such as SsCBP1. SsCBP1 was experimentally confirmed to be a target for the monocot-specific miR528. Our findings support the notion that the regulation of SsCBP1 by miR528 is shared at least within graminaceous monocots, and this miRNA-based post-transcriptional regulation evolved exclusively within the monocots lineage after the divergence from eudicots.Conclusions: Using publicly available nucleotide databases, 19 sugarcane miRNA precursors and one new sorghum miRNA precursor were identified and classified into 14 families. Comparative analyses between sugarcane and sorghum suggest that these two species retain homologous miRNAs and targets in their genomes. Such conservation may help to clarify specific aspects of miRNA regulation and evolution in the polyploid sugarcane. Finally, our dataset provides a framework for future studies on sugarcane RNAi-dependent regulatory mechanisms.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)ESALQ USP, Ctr Biotecnol Agr CEBTEC, Escola Super Agr Luiz de Queiroz, Piracicaba, SP, BrazilUniv Estadual Campinas, CBMEG, Campinas, SP, BrazilUniv Estadual Campinas, Dept Biol Vegetal, Inst Biol, Campinas, SP, BrazilUniv Estadual Paulista UNESP, Dept Genet, Inst Biociencias, Botucatu, SP, BrazilUniv Estadual Paulista UNESP, Dept Genet, Inst Biociencias, Botucatu, SP, BrazilFAPESP: 07/58289-5CNPq: 474635/2008-2Biomed Central Ltd.Universidade de São Paulo (USP)Universidade Estadual de Campinas (UNICAMP)Universidade Estadual Paulista (Unesp)Zanca, Almir S.Vicentini, RenatoOrtiz-Morea, Fausto A.Del Bem, Luiz E. V.da Silva, Marcio J.Vincentz, MichelNogueira, Fabio Tebaldi Silveira [UNESP]2014-05-20T13:50:27Z2014-05-20T13:50:27Z2010-11-24info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article13application/pdfhttp://dx.doi.org/10.1186/1471-2229-10-260Bmc Plant Biology. London: Biomed Central Ltd., v. 10, p. 13, 2010.1471-2229http://hdl.handle.net/11449/1801110.1186/1471-2229-10-260WOS:000285520000001WOS000285520000001.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBmc Plant Biology3.9301,887info:eu-repo/semantics/openAccess2023-12-09T06:23:12Zoai:repositorio.unesp.br:11449/18011Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T19:52:13.488297Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane
title Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane
spellingShingle Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane
Zanca, Almir S.
title_short Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane
title_full Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane
title_fullStr Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane
title_full_unstemmed Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane
title_sort Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane
author Zanca, Almir S.
author_facet Zanca, Almir S.
Vicentini, Renato
Ortiz-Morea, Fausto A.
Del Bem, Luiz E. V.
da Silva, Marcio J.
Vincentz, Michel
Nogueira, Fabio Tebaldi Silveira [UNESP]
author_role author
author2 Vicentini, Renato
Ortiz-Morea, Fausto A.
Del Bem, Luiz E. V.
da Silva, Marcio J.
Vincentz, Michel
Nogueira, Fabio Tebaldi Silveira [UNESP]
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade de São Paulo (USP)
Universidade Estadual de Campinas (UNICAMP)
Universidade Estadual Paulista (Unesp)
dc.contributor.author.fl_str_mv Zanca, Almir S.
Vicentini, Renato
Ortiz-Morea, Fausto A.
Del Bem, Luiz E. V.
da Silva, Marcio J.
Vincentz, Michel
Nogueira, Fabio Tebaldi Silveira [UNESP]
description Background: MicroRNAs (miRNAs) are small regulatory RNAs, some of which are conserved in diverse plant genomes. Therefore, computational identification and further experimental validation of miRNAs from non-model organisms is both feasible and instrumental for addressing miRNA-based gene regulation and evolution. Sugarcane (Saccharum spp.) is an important biofuel crop with publicly available expressed sequence tag and genomic survey sequence databases, but little is known about miRNAs and their targets in this highly polyploid species.Results: In this study, we have computationally identified 19 distinct sugarcane miRNA precursors, of which several are highly similar with their sorghum homologs at both nucleotide and secondary structure levels. The accumulation pattern of mature miRNAs varies in organs/tissues from the commercial sugarcane hybrid as well as in its corresponding founder species S. officinarum and S. spontaneum. Using sugarcane MIR827 as a query, we found a novel MIR827 precursor in the sorghum genome. Based on our computational tool, a total of 46 potential targets were identified for the 19 sugarcane miRNAs. Several targets for highly conserved miRNAs are transcription factors that play important roles in plant development. Conversely, target genes of lineage-specific miRNAs seem to play roles in diverse physiological processes, such as SsCBP1. SsCBP1 was experimentally confirmed to be a target for the monocot-specific miR528. Our findings support the notion that the regulation of SsCBP1 by miR528 is shared at least within graminaceous monocots, and this miRNA-based post-transcriptional regulation evolved exclusively within the monocots lineage after the divergence from eudicots.Conclusions: Using publicly available nucleotide databases, 19 sugarcane miRNA precursors and one new sorghum miRNA precursor were identified and classified into 14 families. Comparative analyses between sugarcane and sorghum suggest that these two species retain homologous miRNAs and targets in their genomes. Such conservation may help to clarify specific aspects of miRNA regulation and evolution in the polyploid sugarcane. Finally, our dataset provides a framework for future studies on sugarcane RNAi-dependent regulatory mechanisms.
publishDate 2010
dc.date.none.fl_str_mv 2010-11-24
2014-05-20T13:50:27Z
2014-05-20T13:50:27Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1186/1471-2229-10-260
Bmc Plant Biology. London: Biomed Central Ltd., v. 10, p. 13, 2010.
1471-2229
http://hdl.handle.net/11449/18011
10.1186/1471-2229-10-260
WOS:000285520000001
WOS000285520000001.pdf
url http://dx.doi.org/10.1186/1471-2229-10-260
http://hdl.handle.net/11449/18011
identifier_str_mv Bmc Plant Biology. London: Biomed Central Ltd., v. 10, p. 13, 2010.
1471-2229
10.1186/1471-2229-10-260
WOS:000285520000001
WOS000285520000001.pdf
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Bmc Plant Biology
3.930
1,887
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 13
application/pdf
dc.publisher.none.fl_str_mv Biomed Central Ltd.
publisher.none.fl_str_mv Biomed Central Ltd.
dc.source.none.fl_str_mv Web of Science
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
repository.mail.fl_str_mv
_version_ 1808129132247121920