East African Arabidopsis Genomes
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB79562 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene. However, its origin and evolutionary history is somewhat contentious due to discordances being found between morphological, nuclear, and mitochondrial data. Due to the limited molecular data from east Asian Crocuta, and the difficulty of extracting ancient DNA from this area, here we present proteomic analysis of cave hyenas from three locations in northern China. This marks the first proteomic data generated from cave hyenas, adding new molecular data to the east Asian populations. Phylogenetic analysis based on these protein sequences reveals two different groups of cave hyenas in east Asia, one of which could not be distinguished from modern spotted hyenas from northern Africa, tentatively the result of previously suggested gene flow between these lineages. With developments of instrumentation and analytical methods, proteomics holds promising potential for the phylogenetic reconstruction of ancient fauna previously thought to be unreachable using ancient DNA.
2020-10-19 | PXD020530 | Pride
Project description:Root branching in response to changes in nitrogen status in the soil, is a dramatic example of the plant’s remarkable developmental plasticity. In recent work we investigated the genetic architecture of developmental plasticity, combining phenoclustering and genome-wide association studies in 96 Arabidopsis thaliana ecotypes with expression profiling in 7 ecotypes, to characterise natural variation in root architectural plasticity at the phenotypic, genetic, and transcriptional levels. This series contains the microarray expression data for 7 ecotypes that represent a range of root branching strategies. We used microarrays to detail the global programme of gene expression involved in the plants response to nitrogen in the root and identified distinct classes of up- and down-regulated genes in the seven different Arabidopsis ecotypes during this process.
2013-09-01 | GSE34130 | GEO
Project description:The aim of this study was to compare the transcriptomes of Plasmodium falciparum parasites sourced from high vs. low malaria transmission settings in east Africa in order to test the hypothesis that malaria parasites are locally adapted to their environment. In three separate experiments, parasites from ‘High’ vs. ‘Low’ transmission populations were taken from non-immune children and measured for gene expression levels by microarray against a reference genome. Two of these population comparisons were geographic in nature while the third was temporal, i.e., before and after a marked decline in malaria. This study is described in Rono MK, Nyonda MA, Simam JJ, Ngoi, JM et al. Nat Ecol Evol. PMID: .
2017-12-18 | GSE108034 | GEO
Project description:The two Arabidopsis ecotypes that are adapted to Italy and Sweden, respectively, showed different degree of freezing tolerance. By comparing the low temperature transcriptomes of the IT and SW ecotypes, we showed CBF pathway plays a significant role in natural variation of freezing tolerance.
2015-12-30 | GSE67332 | GEO
Project description:The aim of this study was to describe gene copy number variation in Plasmodium falciparum parasites sourced from high vs. low malaria transmission settings in east Africa in order to test the hypothesis that malaria parasites are locally adapted to their environment. In three separate experiments, parasites from ‘High’ vs. ‘Low’ transmission populations were taken from non-immune children and evaluated for copy number variants by microarray against a reference genome. Two of these population comparisons were geographic in nature while the third was temporal, i.e., before and after a marked decline in malaria. This study is described in Simam et al. 2018 BMC Genomics.
2018-05-30 | GSE113087 | GEO
Project description:ra06-05_potyvirus-ecotypes - arabidopsis ecotypes - Common and specific genes deregulated in response to various potyviruses in different Arabidopsis genetic backgrounds. - Four different Arabidopsis ecotypes were inoculated with one Potyviruse. About 4 weeks after sowing, the 6 expanded leaves plants were inoculated with the different viruses or were mock-inoculated. Seven days after inoculation, inoculated leaves were collected, RNA was extracted and virus infection controlled. RNA fron infected plants was then used for microarrays hybridization. Three biological repeat have been done and two dye-swap. Keywords: normal vs disease comparison
2008-10-20 | GSE10711 | GEO
Project description:We examined sRNA populations in the Arabidopsis ecotypes C24, Landsberg erecta (Ler), and their reciprocal hybrids which display strong intra-species heterosis. The parental ecotypes had significant differences in their sRNA epigenomes and associated methylation profiles. The hybrids differed greatly from the parents in their sRNA epigenomes including a marked reduction in 24nt sRNA associated with loci that differed in the frequency of 24nt sRNAs between the parents. Examination of sRNA populations from two-week old seedlings from Arabidopsis ecotypes C24, Ler, and their two reciprocal hybrids.
2011-01-12 | E-GEOD-25022 | biostudies-arrayexpress
Project description:East African cichlid fishes have radiated in an explosive fashion. The (epi)genetic basis for the abundant phenotypic diversity of these fishes remains largely unknown. As transposable elements (TEs) contribute extensively to genome evolution, we reasoned that TEs may have fuelled cichlid radiations. While TE-derived genetic and epigenetic variability has been associated with phenotypic traits, TE expression and epigenetic silencing remain unexplored in cichlids. Here, we profiled TE expression in African cichlids, and describe dynamic expression patterns during embryogenesis and according to sex. Most TE silencing factors are conserved and expressed in cichlids. We describe an expansion of two truncated Piwil1 genes in Lake Malawi/Nyasa cichlids, encoding a Piwi domain with catalytic potential. To further dissect epigenetic silencing of TEs, we focused on small RNA-driven epigenetic silencing. We detect a small RNA population in gonads consistent with an active Piwi-interacting RNA (piRNA) pathway targeting TEs. We uncover fluid genomic origins of piRNAs in closely related cichlid species. This, along with signatures of positive selection in piRNA pathway factors, points towards fast co-evolution of TEs and the piRNA pathway. Our study is the first step to understand the contribution of ongoing TE-host arms races to the cichlid radiations in Africa.
2024-04-02 | PXD047439 | Pride
Project description:Fe deficiency stimulates a coordinated response involving reduction, transport and redistribution of Fe in the roots. The expression of genes regulated by Fe deficiency in the two contrasting Arabidopsis thaliana ecotypes, Tsu-1 and Kas-1, shows that different ecotypes can respond in diverse ways, with different Fe regulated overrepresented categories. We use microarrays to analyze the Fe deficiency responses of contrasting Arabidopsis thaliana ecotypes (Tsu-1 and Kas-1).
2011-10-06 | GSE29086 | GEO
Project description:We examined sRNA populations in the Arabidopsis ecotypes C24, Landsberg erecta (Ler), and their reciprocal hybrids which display strong intra-species heterosis. The parental ecotypes had significant differences in their sRNA epigenomes and associated methylation profiles. The hybrids differed greatly from the parents in their sRNA epigenomes including a marked reduction in 24nt sRNA associated with loci that differed in the frequency of 24nt sRNAs between the parents.
2011-01-12 | GSE25022 | GEO