Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Homology-guided Assembly of the Genomes of the Four Diverse Accessions Ler, C24, Bur-0 and Kro-0

ABSTRACT: Here we present the first whole-genome assemblies of Arabidopsis thaliana strains since the release of the 125 Mb reference genome sequence a decade ago. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. A. thaliana Col-0, Bur-0 & C24 small RNA-seq data, 2 biological replicates each

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Felix Ott

PROVIDER: E-GEOD-24569 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata.

Hollister Jesse D JD Smith Lisa M LM Guo Ya-Long YL Ott Felix F Weigel Detlef D Gaut Brandon S BS

Proceedings of the National Academy of Sciences of the United States of America 20110120 6

Transposable elements (TEs) are often the primary determinant of genome size differences among eukaryotes. In plants, the proliferation of TEs is countered through epigenetic silencing mechanisms that prevent mobility. Recent studies using the model plant Arabidopsis thaliana have revealed that methylated TE insertions are often associated with reduced expression of nearby genes, and these insertions may be subject to purifying selection due to this effect. Less is known about the genome-wide pa ...[more]

PMID: 21252301

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Project description:Small RNAs (sRNAs) are emerging as important regulators of biological processes in plants. To characterize the small RNA species and expression changes in ‘Anliu’ sweet orange (wild type, WT) and its red-flesh mutant (MT) with lycopene accumulation, we used high-throughput pyrosequencing to identify and quantitatively profile sRNAs. We identified 112 known miRNAs belonging to 64 families from the sweet orange. Comparative analysis revealed that 63 of the 112 known miRNAs exhibited significant expression differences between WT and MT. We also identified 12 novel miRNAs and 9 miRNA candidates from sweet orange; the 12 novel miRNAs are in line with the biogenesis characteristics including the stem-loop structure of the pre-miRNAs and existence of the miRNA*s in the sRNA libraries. Comparative profiling revealed that 10 novel miRNAs and 8 miRNA candidates are differentially expressed between WT and MT. Potential targets of these differentially expressed miRNAs included several important genes that are involved in carotenoid biosynthesis, such as geranylgeranyl pyrophosphate synthase (GGPS) and lycopene β-cyclase (LYCb). Moreover, GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. We proposed that miRNA-target genes are the hot-spots for generating sRNAs. This study provides the first large scale cloning and characterization of citrus miRNAs, which also lays a foundation for unraveling the mechanism of lycopene accumulation in the sweet orange mutant on post-transcription level. Size fractionated small RNAs (16-30 bp) from total RNA extracts was ligated to 5' and 3' adapters, and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing. The resultant 35nt sequence data were filtered according to base quality value. The remained sequences were used to trim 5' and 3' adaptors. The clean tags were used for further analysis.

Dataset Information

Homology-guided Assembly of the Genomes of the Four Diverse Accessions Ler, C24, Bur-0 and Kro-0

Publications

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata.

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