De novo assembly of siRNA immunity in wild plants
Ontology highlight
ABSTRACT:
ORGANISM(S): Tilia platyphyllos Quercus robur Fagus sylvatica Ulmus glabra Betula pendula Aesculus hippocastanum Fraxinus excelsior Corylus avellana Acer pseudoplatanus
PROVIDER: GSE22079 | GEO | 2012/06/01
SECONDARY ACCESSION(S): PRJNA128925
REPOSITORIES: GEO
Similar Datasets
Project description:We describe an application of deep sequencing and de novo assembly of short RNA reads to investigate small interfering (si)RNAs mediated immunity in leaf samples from eight tree taxa naturally occurring in Wytham Woods, Oxfordshire, UK. BLAST search for homologues of contigs in the GenBank identified siRNA populations against a number of RNA viruses and a Ty1-copia retrotransposons in these tree species. Small RNA sequencing and de novo assembly
2012-06-01 | E-GEOD-22079 | biostudies-arrayexpress
Project description:Retroelements, the prevalent class of plant transposons, have major impacts on host genome integrity and evolution. They produce multiple proteins from highly compact genomes and, similarly to viruses, must have evolved original strategies to optimize gene expression, although this aspect has been seldom investigated thus far. Here, we have established a high-resolution transcriptome/translatome map for the near-entirety of Arabidopsis thaliana transposons, using two distinct DNA methylation mutants in which transposon expression is broadly de-repressed. The value of this map to study potentially intact and transcriptionally active transposons in Arabidopsis thaliana is illustrated by our comprehensive analysis of the co-transcriptional and translational features of Ty1/Copia elements, a family of young and active retroelements in plant genomes, and how such features impact their biology. Genome-wide transcript profiling revealed a unique and widely conserved alternative splicing event coupled to premature termination that allows for the synthesis of a short subgenomic RNA solely dedicated to production of the Gag structural protein and preferentially associates with polysomes for efficient translation. Mutations engineered in a transgenic version of the Arabidopsis EVD Ty1/Copia element further show how alternative splicing is crucial for the appropriate coordination of full length and subgenomic RNA transcription. We propose that this hitherto undescribed genome expression strategy, conserved amongst plant Ty1/Copia elements, enables an excess of structural versus catalytic components, mandatory for mobilization.
2017-07-18 | GSE93584 | GEO
Project description:In organisms ranging from vertebrates to plants, major components of centromeres are rapidly-evolving repeat sequences, such as tandem repeats (TRs) and transposable elements (TEs). These repeats harbor centromere-specific histone H3 (CENH3), which also evolves rapidly. Complete centromere structures recently determined in human and Arabidopsis suggest frequent integration and purging of retrotransposons within the TR regions of centromeres. Despite the high impact of “centrophilic” retrotransposons on the paradox of rapid centromere evolution, the mechanisms involved in centromere targeting remain poorly understood in any organism. Here we show that both Ty3 and Ty1/Copia LTR elements rapidly turnover within the centromeric TRs of Arabidopsis species. We demonstrate that the Ty1/Copia element Tal1 (Transposon of Arabidopsis lyrata 1) integrates de novo into regions occupied by CENH3 in A. thaliana, and that ectopic expansion of the CENH3 region results in spread of Tal1 integration regions. The integration spectra of chimeric TEs revealed the key structural variations responsible for the contrasting chromatin targeting specificities to centromeres versus gene-rich regions, which have recurrently converted during the evolution of these TEs. Our findings reveal the impact of centromeric chromatin on TE-mediated rapid centromere evolution, with relevance across eukaryotic genomes.
2024-08-08 | GSE263224 | GEO
Project description:In organisms ranging from vertebrates to plants, major components of centromeres are rapidly-evolving repeat sequences, such as tandem repeats (TRs) and transposable elements (TEs). These repeats harbor centromere-specific histone H3 (CENH3), which also evolves rapidly. Complete centromere structures recently determined in human and Arabidopsis suggest frequent integration and purging of retrotransposons within the TR regions of centromeres. Despite the high impact of “centrophilic” retrotransposons on the paradox of rapid centromere evolution, the mechanisms involved in centromere targeting remain poorly understood in any organism. Here we show that both Ty3 and Ty1/Copia LTR elements rapidly turnover within the centromeric TRs of Arabidopsis species. We demonstrate that the Ty1/Copia element Tal1 (Transposon of Arabidopsis lyrata 1) integrates de novo into regions occupied by CENH3 in A. thaliana, and that ectopic expansion of the CENH3 region results in spread of Tal1 integration regions. The integration spectra of chimeric TEs revealed the key structural variations responsible for the contrasting chromatin targeting specificities to centromeres versus gene-rich regions, which have recurrently converted during the evolution of these TEs. Our findings reveal the impact of centromeric chromatin on TE-mediated rapid centromere evolution, with relevance across eukaryotic genomes.
2024-08-08 | GSE263225 | GEO
Project description:Co-evolution between hosts' and parasites' genomes shapes diverse pathways of acquired immunity based on silencing small (s)RNAs. In plants, sRNAs cause heterochromatinization, sequence-degeneration and, ultimately, loss-of-autonomy of most transposable elements (TEs). Recognition of newly-invasive plant TEs, by contrast, involves an innate antiviral-like silencing response. To investigate this response's activation, we studied the single-copy element EVADÉ (EVD), one of few representatives of the large Ty1/Copia family able to proliferate in Arabidopsis when epigenetically-reactivated. In Ty1/Copia-elements, a short subgenomic mRNA (shGAG) provides the necessary excess of structural GAG protein over the catalytic components encoded by the full-length genomic flGAG-POL. We show here that the predominant cytosolic distribution of shGAG strongly favors its translation over mostly-nuclear flGAG-POL. During this process, an unusually intense ribosomal stalling event coincides with mRNA breakage yielding unconventional 5'OH RNA fragments that evade RNA-quality-control. The starting-point of sRNA production by RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6), exclusively on shGAG, occurs precisely at this breakage point. This hitherto-unrecognized "translation-dependent silencing" (TdS) is independent of codon-usage or GC-content and is not observed on TE remnants populating the Arabidopsis genome, consistent with their poor association, if any, with polysomes. We propose that TdS forms a primal defense against EVD de novo invasions that underlies its associated sRNA pattern.
2021-08-08 | GSE167484 | GEO
Project description:Genome-wide DNA sequence resources are expected to enhance our understanding of the molecular basis of plant development and lead to improvements in desirable traits in horticultural crops. In this study, we sequenced 643,366 ESTs from Eustoma grandiflorum flowers using a normalised cDNA library constructed for several different flower development stages, times of day, and pollinated stamens. The sequences were assembled into 63,401 contigs and 242,212 singletons. BlastX searches for all of the contigs in the GenBank database matched 65% of the contigs to registered sequences, while 35% presented no hits. GO mapping assigned 48% of the 63,401 contigs to GO terms. Microarray analysis showed that subsets of genes were up- or downregulated as the flower developed. The downregulated genes were enriched for GO terms related to 1) oligopeptide transport, 2) response to jasmonic acid stimulus, and 3) cell wall modification, whereas the upregulated genes were enriched for GO terms involved in 1) secondary metabolism, such as the flavonoid biosynthetic process and the terpenoid biosynthetic process, and 2) epidermal cell modification.
2012-09-01 | GSE34332 | GEO
Project description:To identify yeast proteins associated with Ty1 integrase (IN) that could regulate Ty1 replication, we co-purified IN partners using the tandem chromatin affinity purification procedure after in vivo cross-link (TChAP), which we developed previously (Nguyen et al. 2014). We first identified RNA Pol I and Pol III complexes and also a small subset of additional evolutionary conserved complexes, including PAF1 (Polymerase-Associated Factor 1),FACT (FAcilitates Chromatin Transcription), the proteasome and the CK2 kinase. We next confirmed that CK2 interacts with Ty1 integrase in vivo and repress Ty1 retromobility. We showed that Ty1 IN is a substrate of CK2 in vitro and identified 12 phosphorylated residues. In vivo approaches showed that only part of the protein was phosphorylated in the cells and did not demonstrate any direct evidence between Ty1 IN phosphorylation and retromobility inhibition.
2022-11-17 | PXD027420 | Pride
Project description:In the recent years, RNA silencing has been studied extensively to be a conserved regulatory process in plants. In the antiviral silencing, the intermediate double-stranded RNA form during the replication of RNA viruses were recognized and processed into abundant of overlapping viral siRNA (viRNAs). Accordingly, the cloned viRNAs could be conversely assembled into some contigs of viruses, which is recently exploited for identifying new viruses and their genome sequences.To obtain rapidly the complete genome sequence of BYSMV, we carried out deep sequencing of small RNAs from healthy and BYSMV infected wheat, respectively. Thirteen contigs were assembled from the overlapping viRNAs only present in the infected wheat but not in the healthy wheat. The results of BLAST showed that ten contigs shared about 96% identity with the reported L gene of BYSMV isolate Zanjan-1.
2015-09-15 | GSE61565 | GEO
Project description:To identify blast pathogen elicited miRNAs, four sRNA libraries were constructed: 8749036, A library, susceptible rice cultivar Zhonger-Ruanzhan; 12157795, B library, mock-treated blast resistant line H4; 9937360, C library, blast-treated susceptible rice cultivar Zhonger-Ruanzhan; and 11138187 clean reads, D library, blast-treated blast resistant line H4. The Short Oligonucleotide Analysis Package (SOAP; Beijing Genomics Institute) matched 85.46% (A, 7476714), 79.35% (B, 9647324), 77.70% (C, 7721715) and 76.10% (D, 8476386) sRNA reads to the genome. After removing other RNA categories matched to NCBI Genbank, Rfam database, known rice miRNA precursor, repeat associated RNA and siRNA, the remaining reads: 1681359(A); 3829741(B); 3182403(C); and 3970132(D), were used for further novel miRNA prediction. Since some miRNAs were tissue-specific, time-specific or stress-induced, only 291, 210, 164 and 220 registered miRNAs were identified in libraries A, B, C and D respectively. Thirty-one (A, 9385 reads), 399(B, 41024 read), 351(C, 36622 reads) and 333(D, 38064 reads) unique sRNAs were projected to be candidate miRNAs. Examination of mock-treated rice cultivar, mock-treated blast resistant rice line H4, blast-treated susceptible rice cultivar, and blast-treated blast resistant rice line H4.
2016-07-03 | E-GEOD-36205 | biostudies-arrayexpress
Project description:Genome-wide DNA sequence resources are expected to enhance our understanding of the molecular basis of plant development and lead to improvements in desirable traits in horticultural crops. In this study, we sequenced 643,366 ESTs from Eustoma grandiflorum flowers using a normalised cDNA library constructed for several different flower development stages, times of day, and pollinated stamens. The sequences were assembled into 63,401 contigs and 242,212 singletons. BlastX searches for all of the contigs in the GenBank database matched 65% of the contigs to registered sequences, while 35% presented no hits. GO mapping assigned 48% of the 63,401 contigs to GO terms. Microarray analysis showed that subsets of genes were up- or downregulated as the flower developed. The downregulated genes were enriched for GO terms related to 1) oligopeptide transport, 2) response to jasmonic acid stimulus, and 3) cell wall modification, whereas the upregulated genes were enriched for GO terms involved in 1) secondary metabolism, such as the flavonoid biosynthetic process and the terpenoid biosynthetic process, and 2) epidermal cell modification. Two-condition experiment, loop-design among 4 developmental stages. Biological replicates: 4.
2012-09-01 | E-GEOD-34332 | biostudies-arrayexpress