Ontology highlight
ABSTRACT:
PROVIDER: PRJNA726938 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14415000_1.fastq.gz | Fastqsanger.gz | |||
| SRR14415000_2.fastq.gz | Fastqsanger.gz | |||
| SRR14415001_1.fastq.gz | Fastqsanger.gz | |||
| SRR14415001_2.fastq.gz | Fastqsanger.gz | |||
| SRR14415002_1.fastq.gz | Fastqsanger.gz |
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Project description:Evolution and adaptation of living organisms are results of permanent fights against diverse threats, which imply specific responses from the genome itself. Allopolyploidy, combining interspecific hybridization with whole genome duplication, is recognised as an important evolutionary force in plants. Its evolutionary success can be related to the rapid and profound genome reorganizations generated in response to the “Genome Shock” that allow the neo-allopolyploid to adapt efficiently to new environments. While work has focused on the structural and functional consequences of allopolyploidy, studies dedicated to the response of the neo-allopolyploid genome at the level of the functional regulation of genome expression have been rarely conducted. Recently, the hypothesis of a major role for small non coding RNAs (sRNAs) in mediating the immediate functional response of neo-allopolyploid genomes has progressively emerged. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independent resynthesized B. napus allotetraploids surveyed at two different generations in comparison with their diploid progenitors, by high-throughput sequencing of sRNAs. Our evidence suggests an immediate but transient response of specific sRNA populations, targeting non-coding components of the genome. We identify the early accumulation of both 21- and 24-nt sRNAs involved in the regulation of the same targets, supporting a PTGS-to-TGS shift at the first stages of the neo-allopolyploid formation. We propose that sRNAs are early mobilized in response to allopolyploidy to control the unexpected transcriptional reactivation of various non-coding elements thus, playing the role of guardians of genome integrity during the first steps of neo-allopolyploid formation.
2017-09-15 | GSE94076 | GEO
Project description:Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae) Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaption of newly formed allopolyploid species. In spite of significant progress made the last years, a few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions. We used Agilent Rice oligo-microarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classical example of recent allopolyploid speciation, S. anglica formed during the 19th century following genome duplication of the hybrid S. x townsendii. Our data indicate important, thought different effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered. Maternal dominance is attenuated following genome duplication in S. anglica while this species exhibits an increased number of transgressively over expressed genes. These results reflect the decoupled effects of the “genomic shock” following hybridization and genome redundancy, on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploids.
2010-11-10 | GSE18961 | GEO
Project description:Allopolyploidy is long recognized as an essential driving force in plant evolution. Recent studies have demonstrated that small RNAs, including microRNAs (miRNAs), play important roles in the process of allopolyploidy. However, the question that how the distinct parent-of-origin miRNAs are maintained in allopolyploids and how these small RNAs affect gene expression and phenotypes remain to be answered. Therefore, we investigated the miRNA expression profiles of a synthesized allotetraploid, Cucumis ×hytivus and its parents. The different developmental stages of leaves of C. ×hytivus showing contrasting leaf colour were compared as well. Following high-throughput sequencing, 546 conserved and 287 novel miRNAs were identified. The expression levels of nine miRNAs obtained by quantitative real-time PCR were consistent with the sequencing results. We detected that 15 miRNAs were divergently expressed between the parent species, and 23 miRNAs were differentially expressed in C. ×hytivus compared to either of its parents or both, which suggests the significant effect of allopolyploidization on miRNAs accumulation. Additionally, 26 conserved and 13 novel miRNAs differed in expression between the young and mature leaves of C. ×hytivus, indicating an essential role of miRNA-mediated regulation of leaf development following allopolyploidization. This study enriches the context of allopolyploidy effect on miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in phenotypic variation in allopolyploids.
2019-08-25 | GSE79757 | GEO
Project description:Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae) Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaption of newly formed allopolyploid species. In spite of significant progress made the last years, a few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions. We used Agilent Rice oligo-microarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classical example of recent allopolyploid speciation, S. anglica formed during the 19th century following genome duplication of the hybrid S. x townsendii. Our data indicate important, thought different effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered. Maternal dominance is attenuated following genome duplication in S. anglica while this species exhibits an increased number of transgressively over expressed genes. These results reflect the decoupled effects of the “genomic shock” following hybridization and genome redundancy, on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploids. We used Agilent Rice oligo-microarrays to explore gene expression changes among Spartina species, following interspesific hybridization and genome duplication (allopolyploidy). The analysed species included the parents S. maritima & S.alterniflora, the hybrid F1 S x. towensendii and the allopolyploid S.anglica. A total of 20 slides (five replicates per species) were hybridized on a 44 K Rice Agilent array using a one color desgin.
2010-11-10 | E-GEOD-18961 | biostudies-arrayexpress
Project description:Investigation of genetic changes following allopolyploidy speciation in coffee
| PRJEB5543 | ENA
Project description:Primary outcome(s): EuroQol 5 Dimension-5L (EQ5D-5L)
| 2637537 | ecrin-mdr-crc
Project description:Alteration in gene expression accompanying initial stages of allopolyploidy is a prominent feature in plants, but its spectrum and model are highly idiosyncratic. We used multi-colour GISH to identify individuals from two nascent allohexaploid wheat lines between Triticum turgidum and Aegilops tauschii, which had a transgenerationally stable chromosomal constitution mimicking that of common wheat. We performed genomewide analysis of gene expression for these plants along with their parental species using the Affymetrix GeneChip Wheat Genome-Array. Comparison with parental species coupled with inclusion of empirical mid-parent values (MPVs) revealed two patterns of alteration in gene expression in the allohexaploid lines: parental dominance expression and nonadditive expression. Genes involved in each altered pattern could be classified into three distinct groups, stochastic, heritable and persistent, based on their transgenerational heritability and inter-line conservation. Whereas both altered patterns of gene expression showed a propensity of inheritance, identity of the involved genes is stochastic, consistent with the involvement of diverse Gene Ontology (GO) terms. Nonetheless, those genes showing nonadditive expression exhibited a significant enrichment for vesicle-function. Our results suggest global alteration in gene expression conditioned by nascent allopolyploidy likely play functional roles in stabilization and establishment of the newly formed plants, and consequential to evolution.
2012-05-01 | GSE29882 | GEO
Project description:We report the use of high-throughput single-cell RNA sequencing (scRNA-seq) to analyze gene expression in Mesophyll cells from Maize. We using the 10x genomics platform to generate several millions of RNA-seq reads and enable transcriptional profiling of all genes of maize in a single-cell resolution. Tsne methods was used to perform dimension reduction analysis to visualize cells in a two-dimension axis.
2021-10-07 | GSE138526 | GEO