Comparative genomics of domesticated peppers and its wild progenitor reveal signature of artificial selection by human
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA193076 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR771924_1.fastq.gz | Fastqsanger.gz | |||
| SRR771924_2.fastq.gz | Fastqsanger.gz | |||
| SRR771925_1.fastq.gz | Fastqsanger.gz | |||
| SRR771925_2.fastq.gz | Fastqsanger.gz | |||
| SRR771926_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 71 |
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below.
2014-03-14 | GSE45154 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-03-14 | E-GEOD-45154 | biostudies-arrayexpress
Project description:Comparison of gene expression profiles of widespread peanut cultivars for exploring the expression data in pod and leaf with regard to signatures of artificial selection
2012-06-19 | GSE30128 | GEO
Project description:Genes relevant to manifestion of and variation in locomotor behavior might be differentially expressed in lines selected for divergent levels of locomotion. Experiment Overall Design: Drosophila adults were assessed for locomotor reactivity levels in a behavioral assay that quantified the locomotor response to a mechanical stimulus. A subset of the sampled population was selected as parents for the next generation, with High, Low, and Control selection groups maintained. This artificial selection was continued for 25 generations, with a variety of other behavioral and life history traits assessed for correlation with response to selection for locomotion. At generation 25, male and female flies were collected for RNA extraction and subsequent gene expression analysis.
2006-10-03 | E-GEOD-5956 | biostudies-arrayexpress
Project description:Reactive oxygen species (ROS) play a prominent role in signal transduction and cellular homeostasis in plants. However, imbalances between generation and elimination of ROS can give rise to oxidative stress in growing cells. Because ROS are important to cell growth, ROS modulation could be responsive to natural or human-mediated selection pressure in plants. To study the evolution of oxidative stress related genes in a single plant cell, we conducted comparative expression profiling analyses of the elongated seed trichomes (‘‘fibers’’) of cotton (Gossypium), using a phylogenetic approach. We measured expression changes during diploid progenitor species divergence, allopolyploid formation and parallel domestication of diploid and allopolyploid species, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes in progenitor diploid species revealed significant up-regulation of ROS scavenging and potential signaling processes in domesticated G. arboreum. Similarly, in two independently domesticated allopolyploid species (G. barbadense and G. hirsutum) antioxidant genes were substantially up-regulated in comparison to antecedent wild forms. In contrast, analyses of three wild allopolyploid species indicate that genomic merger and ancient allopolyploid formation had no significant influences on regulation of ROS related genes. Remarkably, many of the ROS-related processes diagnosed as possible targets of selection were shared among diploid and allopolyploid cultigens, but involved different sets of antioxidant genes. Our data suggests that parallel human selection for enhanced fiber growth in several geographically widely dispersed species of domesticated cotton resulted in similar and overlapping metabolic transformations of the manner in which cellular redox levels have become modulated. We measured expression changes during diploid progenitor species divergence, allopolyploid formation and parallel domestication of diploid and allopolyploid species, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes was studied for domesticated G. arboreum and two independently domesticated allopolyploid species (G. barbadense and G. hirsutum). These were compared to three wild allopolyploid species. Three biological replicates were performed.
2009-07-24 | E-GEOD-17084 | biostudies-arrayexpress
Project description:Reactive oxygen species (ROS) play a prominent role in signal transduction and cellular homeostasis in plants. However, imbalances between generation and elimination of ROS can give rise to oxidative stress in growing cells. Because ROS are important to cell growth, ROS modulation could be responsive to natural or human-mediated selection pressure in plants. To study the evolution of oxidative stress related genes in a single plant cell, we conducted comparative expression profiling analyses of the elongated seed trichomes (‘‘fibers’’) of cotton (Gossypium), using a phylogenetic approach. We measured expression changes during diploid progenitor species divergence, allopolyploid formation and parallel domestication of diploid and allopolyploid species, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes in progenitor diploid species revealed significant up-regulation of ROS scavenging and potential signaling processes in domesticated G. arboreum. Similarly, in two independently domesticated allopolyploid species (G. barbadense and G. hirsutum) antioxidant genes were substantially up-regulated in comparison to antecedent wild forms. In contrast, analyses of three wild allopolyploid species indicate that genomic merger and ancient allopolyploid formation had no significant influences on regulation of ROS related genes. Remarkably, many of the ROS-related processes diagnosed as possible targets of selection were shared among diploid and allopolyploid cultigens, but involved different sets of antioxidant genes. Our data suggests that parallel human selection for enhanced fiber growth in several geographically widely dispersed species of domesticated cotton resulted in similar and overlapping metabolic transformations of the manner in which cellular redox levels have become modulated.
2009-07-25 | GSE17084 | GEO
Project description:Comparison of gene expression profiles of widespread peanut cultivars for exploring the expression data in pod and leaf with regard to signatures of artificial selection We investigated the overall expression by hybridizing the microarray (GPL13178) with RNA samples from pods and leaves of five selected representative peanut varieties (Fuhuasheng, Shitouqi, Yueyou116, Shanyou523, and Yueyou7), which were widely cultivated in different periods of the past fifty years in southern China. We used the RNA sample from Yueyou7 pod as a reference for all the pod hybridizations, and used the Yueyou7 leaf sample as a reference for all the leaf hybridizations. Field grown plants under normal irrigation were used for sample collection. Replicates with dye-swap were performed for each genotype.
2012-06-18 | E-GEOD-30128 | biostudies-arrayexpress
Project description:Although domestication has dramatically altered the phenotype, physiology, and life history of ramie (Boehmeria nivea) plants, few studies have investigated the effects of domestication on the structure and expression pattern of genes in this fiber crop. To investigate the selective pattern and genetic relationships among a cultivated variety of ramie (BNZ: B. nivea, ZZ1) and four wild species, BNT (B. nivea var. tenacissima), BNN (B. nivea var. nipononivea), BNW (B. nivea var. nivea), and BAN (B. nivea var. viridula), in the section Tilocnide, we performed an RNA sequencing analysis of these ramie species. The de novo assembly of the "all-ramie" transcriptome yielded 119,114 unigenes with an average length of 633 bp, and a total of 7,084 orthologous gene pairs were identified. The phylogenetic tree showed that the cultivar BNZ clustered with BAN in one group, BNW was closely related to BNT, and BNN formed a separate group. Introgression analysis indicated that gene flow occurred from BNZ to BNN and BAN, and between BAN and BNN. Among these orthologs, 2,425 and 269 genes underwent significant purifying and positive selection, respectively. For these positively selected genes, oxidation-reduction process (GO:0055114) and stress response pathways (GO:0006950) were enriched, indicating that modulation of the cellular redox status was important during both ramie fiber evolution and improvement. Two genes related to the suppression of flowering and one gene annotated as a flowering-promoting factor were subjected to positive selection, probably caused by human manipulation. Additionally, five genes were homologs of those involved in abiotic stress tolerance and disease resistance, with higher expression levels in the cultivar BNZ than in the wild species. Collectively, the results of this study indicated that domestication has resulted in the upregulation of many genes involved in the abiotic and biotic stress responses, fiber yield, and plant growth of ramie.
| S-EPMC6662332 | biostudies-literature
Project description:Gossypium barbadense is widely cultivated because of its extra-long staple cotton with superior luster, silkiness and high yield. These economically important traits were selected during initial domestication of an agronomically inferior wild ancestor, followed by millennia of human- mediated selection. To reveal the effects of this history on the cotton fiber transcriptome, we conducted comparative expression profiling on mechanically isolated fiber cells at three different stages encompassing early, mid, and late fiber elongation in wild (K101) and domesticated (Pima S-7) accessions, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes across developmental stages was different in the two accessions, with a shift toward greater change earlier in cultivated than in wild G. barbadense. Approximately 4200 genes were differentially expressed between wild and domesticated accessions at one or more of the stages studied. Domestication appears to have led to enhanced modulation of cellular redox levels and the avoidance or delay of stress-like processes. Prolonged fiber growth in cultivated relative to wild G. barbadense is associated with upregulation of signal transduction and hormone signaling genes and down-regulation of cell wall maturation genes. Clues are provided into the processes and genes that may unwittingly have been selected by humans during domestication and development of modern elite lines. Several of the transcriptomic differences between wild and domesticated G. barbadense described here appear to have parallels in a second domesticated cotton species, Gossypium hirsutum, suggesting that replicated domestication of two different species has resulted in overlapping, parallel, metabolic transformations.
2008-11-13 | GSE13022 | GEO
Project description:Induction of somatic oncogenic mutations by the domesticated DNA transposase PGBD5 in cerebellar progenitor cells promotes medulloblastoma development.
2024-03-27 | GSE249785 | GEO