title: Identifying microRNAs and transcript targets in Jatropha seeds.
abstract: MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received significant attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library of mature seeds and three mRNA libraries from three different seed development stages were generated by deep sequencing to identify and characterize the miRNAs and pre-miRNAs of J. curcas. Computational analysis was used for the identification of 180 conserved miRNAs and 41 precursors (pre-miRNAs) as well as 16 novel pre-miRNAs. The predicted miRNA target genes are involved in a broad range of physiological functions, including cellular structure, nuclear function, translation, transport, hormone synthesis, defense, and lipid metabolism. Some pre-miRNA and miRNA targets vary in abundance between the three stages of seed development. A search for sequences that produce siRNA was performed, and the results indicated that J. curcas siRNAs play a role in nuclear functions, transport, catalytic processes and disease resistance. This study presents the first large scale identification of J. curcas miRNAs and their targets in mature seeds based on deep sequencing, and it contributes to a functional understanding of these miRNAs.
authors.affiliation: Center of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Populations, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil ; Brazilian Agricultural Research - EMBRAPA, Pelotas, RS, Brazil.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Galli
authors.affiliation: PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
authors.forename: Frank
authors.initials: F
authors.lastname: Guzman
authors.affiliation: Center of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Populations, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
authors.forename: Luiz F V
authors.initials: LF
authors.lastname: de Oliveira
authors.affiliation: Center of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Populations, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
authors.forename: Guilherme
authors.initials: G
authors.lastname: Loss-Morais
authors.affiliation: PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
authors.forename: Ana P
authors.initials: AP
authors.lastname: Körbes
authors.affiliation: Brazilian Agricultural Research - EMBRAPA, Pelotas, RS, Brazil.
authors.forename: Sérgio D A
authors.initials: SD
authors.lastname: Silva
authors.affiliation: PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
authors.forename: Márcia M A N
authors.initials: MM
authors.lastname: Margis-Pinheiro
authors.affiliation: Center of Biotechnology and PPGBCM, Laboratory of Genomes and Plant Populations, Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil ; PPGGBM at Federal University of Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
authors.forename: Rogério
authors.initials: R
authors.lastname: Margis
mesh_terms: D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D031286:Jatropha / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics*; D012639:Seeds / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant