MicroRNAs (miRNAs) are small noncoding endogenous RNAs playing a regulatory role by negatively affecting gene expression at the post-transcriptional level. miRNAs vary in length between 16 and 35 nucleotides with a mode of 22-nt, and are produced from longer hairpin-like precursor transcripts. Functional studies have demonstrated that miRNAs are involved in various developmental and physiological processes, and recent reports indicate their association with biotic and abiotic stress responses in plants. High-throughput sequencing technology has allowed the identification and profiling of several conserved and non-conserved miRNAs. Additionally, deep sequencing provides quantitative expression information, since frequency of an individual miRNA generally reflects its relative abundance in the sample. This strategy has been successfully applied to both model and non-model plants. In the present study, small RNA (sRNA) libraries were generated separately from roots and leaves of globe artichoke, obtained from plants subjected or not to saline treatment. Libraries were sequenced using Illumina technology, and results were analysed by bioinformatics tools. The majority of sRNAs were 18-28 nt long with 21 nt and 24 nt sRNA as major peaks in the length distribution graph. To identify conserved miRNAs in globe artichoke, all sRNA sequences were Blastn searched against the currently known miRNAs contained in miRbase (http://www.mirbase.org/). Only perfectly matched sequences were considered as putative conserved miRNAs: this analysis highlighted the presence of at least 29 different miRNA families in artichoke. Comparison to artichoke EST database was performed to find potential miRNA targets and precursors, and to predict hairpin structure. Subsequently, miRNAs were validated using a PCR approach. Differential expression of miRNA between tissues (leaves and roots) and untreated and salttreated samples was analysed after sample normalization (count per million). In conclusion we have characterized the sRNA transcriptome in artichoke, in different tissues, in the presence or absence of salt stress, using deep sequencing strategy by Illumina platform.
DISCOVERY AND DIFFERENTIAL EXPRESSION OF ARTICHOKE microRNAs IN RESPONSE TO SALT STRESS
DE PAOLA D;CATALANO D;PIGNONE D;SONNANTE G
2010
Abstract
MicroRNAs (miRNAs) are small noncoding endogenous RNAs playing a regulatory role by negatively affecting gene expression at the post-transcriptional level. miRNAs vary in length between 16 and 35 nucleotides with a mode of 22-nt, and are produced from longer hairpin-like precursor transcripts. Functional studies have demonstrated that miRNAs are involved in various developmental and physiological processes, and recent reports indicate their association with biotic and abiotic stress responses in plants. High-throughput sequencing technology has allowed the identification and profiling of several conserved and non-conserved miRNAs. Additionally, deep sequencing provides quantitative expression information, since frequency of an individual miRNA generally reflects its relative abundance in the sample. This strategy has been successfully applied to both model and non-model plants. In the present study, small RNA (sRNA) libraries were generated separately from roots and leaves of globe artichoke, obtained from plants subjected or not to saline treatment. Libraries were sequenced using Illumina technology, and results were analysed by bioinformatics tools. The majority of sRNAs were 18-28 nt long with 21 nt and 24 nt sRNA as major peaks in the length distribution graph. To identify conserved miRNAs in globe artichoke, all sRNA sequences were Blastn searched against the currently known miRNAs contained in miRbase (http://www.mirbase.org/). Only perfectly matched sequences were considered as putative conserved miRNAs: this analysis highlighted the presence of at least 29 different miRNA families in artichoke. Comparison to artichoke EST database was performed to find potential miRNA targets and precursors, and to predict hairpin structure. Subsequently, miRNAs were validated using a PCR approach. Differential expression of miRNA between tissues (leaves and roots) and untreated and salttreated samples was analysed after sample normalization (count per million). In conclusion we have characterized the sRNA transcriptome in artichoke, in different tissues, in the presence or absence of salt stress, using deep sequencing strategy by Illumina platform.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
