Expression array from mature leaves in the genus Arabidopsis
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana Arabidopsis thaliana x Arabidopsis halleri subsp. gemmifera Arabidopsis lyrata subsp. lyrata Arabidopsis thaliana x Arabidopsis lyrata Arabidopsis halleri subsp. gemmifera
PROVIDER: GSE23318 | GEO | 2013/09/29
SECONDARY ACCESSION(S): PRJNA131235
REPOSITORIES: GEO
Similar Datasets
Project description:We compared the expression between inter-specific hybrids (A. thaliana-A. lyrata, A. thaliana-A. halleri) and mid parent values of their parental lines. Mature leaves in A. thaliana (Col), A. lyrata ssp. lyrata, A. halleri ssp. gemmifera and interspecific hybrid between A. thaliana and A. lyrata and between A. thaliana and A. halleri
2013-09-29 | E-GEOD-23318 | biostudies-arrayexpress
Project description:We generated F1 hybrids of each of the sister species A. halleri and A. lyrata with their outgroup relative of A. thaliana and monitored allele-specific levels of expression in standard growth conditions, in response to dehydration or cold exposure. This data allowed us to map the genome-wide distribution of cis-regulatory mutations active in three distinct environments reflecting divergent adaptations of the two species. Because the sister species were both crossed to an outgroup species, it was possible to assign a phylogenetic origin to cis-acting mutations. Cis-acting mutations observed in only one of the two hybrids were likely to be derived, whereas those observed in both hybrids either predate predated the split between the two species or arose along the A. thaliana lineage. By contrasting the distribution of cis-regulatory mutations derived in the A. halleri to those derived on the A. lyrata lineage, we could establish relative rates of cis-acting evolution across polygenic molecular functions and detect lineage-specific polygenic adaptation to environmental challenges.
2016-06-01 | GSE80462 | GEO
Project description:We generated F1 hybrids of each of the sister species A. halleri and A. lyrata with their outgroup relative of A. thaliana and monitored allele-specific levels of expression in standard growth conditions, in response to dehydration or cold exposure. This data allowed us to map the genome-wide distribution of cis-regulatory mutations active in three distinct environments reflecting divergent adaptations of the two species. Because the sister species were both crossed to an outgroup species, it was possible to assign a phylogenetic origin to cis-acting mutations. Cis-acting mutations observed in only one of the two hybrids were likely to be derived, whereas those observed in both hybrids either predate predated the split between the two species or arose along the A. thaliana lineage. By contrasting the distribution of cis-regulatory mutations derived in the A. halleri to those derived on the A. lyrata lineage, we could establish relative rates of cis-acting evolution across polygenic molecular functions and detect lineage-specific polygenic adaptation to environmental challenges. A.thalianaxA.lyrata under cold, dehydration and standard conditions, 3 biological replicates; A.thalianaxA.halleri under cold, dehydration and standard conditions, 3 biological replicates; toal 18 RNA-seq samples
2016-06-01 | E-GEOD-80462 | biostudies-arrayexpress
Project description:We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species of Arabidopsis thaliana and Arabidopsis lyrata with a whole-genome SNP tiling array (AtSNPtile1).
2011-07-27 | GSE29037 | GEO
Project description:We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species of Arabidopsis thaliana and Arabidopsis lyrata with a whole-genome SNP tiling array (AtSNPtile1). 24 sampes, 12 DNA samples from parents and hybrids, 12 RNA sample from leaf and flowers of hybrids
2011-07-26 | E-GEOD-29037 | biostudies-arrayexpress
Project description:Gene copy number variation (CNV) is a form of genetic polymorphism that contributes significantly to genome size and function but remains poorly characterized due to technological limitations. Inter-specific comparisons of CNVs in recently diverged plant species are crucial to uncover selection patterns underlying adaptation of a species to stressful environments. Especially given that gene amplifications have long been implicated in emergence of species-specific traits, we conducted a genome-wide survey to identify species-specific gene copy number expansions and deletions in the model extremophile species - Arabidopsis halleri that has diverged in evolutionarily recent time from Arabidopsis thaliana. Cross-species cDNA array based comparative genomic hybridization was employed to compare and identify gene copy number variation in the two sister-species - the metallophyte Arabidopsis halleri and non-metallophyte Arabidopsis lyrata, both relative to Arabidopsis thaliana. We uncovered an unprecedented level of gene copy number polymorphism in Arabidopsis halleri, with a species-specific enrichment of metal homeostasis function in the genes found to be copy number expanded, thus indicating CNV as a mechanism that underlies the key physiological trait of metal hyperaccumulation and hypetolerance in A. halleri.
2016-09-30 | GSE52003 | GEO
Project description:In plants, imprinted gene expression occurs in endosperm seed tissue and can be associated with differential DNA methylation between maternal and paternal alleles. Imprinting is theorized to have been selected for because of conflict between parental genomes in offspring, but most studies of imprinting have been conducted in Arabidopsis thaliana, an inbred primarily self-fertilizing species that should have limited parental conflict. We examined embryo and endosperm allele-specific expression and DNA methylation genome-wide in the wild outcrossing species Arabidopsis lyrata. Here we show that the majority of A. lyrata imprinted genes exhibit parentally-biased expression in A. thaliana, suggesting that there is evolutionary conservation in gene imprinting. Surprisingly, we discovered substantial interspecies differences in methylation features associated with paternally expressed imprinted genes (PEGs). Unlike A. thaliana, the maternal allele of many A. lyrata PEGs was hypermethylated in the CHG context. Increased maternal allele CHG methylation was associated with increased expression bias in favor of the paternal allele. We propose that CHG methylation maintains or reinforces repression of maternal alleles of PEGs. These data suggest that while the genes subject to imprinting are largely conserved, there is flexibility in the epigenetic mechanisms employed between closely related species to maintain monoallelic expression. This supports the idea that imprinting of specific genes is a functional phenomenon, and not simply a byproduct of seed epigenomic reprogramming. Examination of total gene expression, parent-of-origin specific allelic bias, or DNA methylation in embryo, endosperm, flower bud or seedcoat tissue from Arabidopsis lyrata accessions MN47 (MN), Karhumaki (Kar or KA), and crosses between them. High-throughput Illumina poly-A-selected mRNA-seq was used to identify imprinted genes in A. lyrata, and high-throughput Illumina whole genome bisulfite-sequencing was used to examine DNA methylation. mRNA-seq samples are designated MMxFF_T# where MM is the mother of the cross (either MN for MN47 or KA for Kar), FF is the father, T is the tissue (E for embryo, N for endosperm, S for seedcoat, b for buds), and # is the replicate numbers. Samples obtained from bisulfite sequencing follow the same naming but have suffix _BS and indicate cytosine methylation context (CpG, CHG, or CHH). For KAxMN bisulfite sequencing, additional files MMxFF_T#_BS_P_C.txt follow the same naming scheme but contain context-specific methylation data (C) from reads that mapped preferentially to one parent strain (P).
2016-09-01 | E-GEOD-76076 | biostudies-arrayexpress
Project description:In plants, imprinted gene expression occurs in endosperm seed tissue and can be associated with differential DNA methylation between maternal and paternal alleles. Imprinting is theorized to have been selected for because of conflict between parental genomes in offspring, but most studies of imprinting have been conducted in Arabidopsis thaliana, an inbred primarily self-fertilizing species that should have limited parental conflict. We examined embryo and endosperm allele-specific expression and DNA methylation genome-wide in the wild outcrossing species Arabidopsis lyrata. Here we show that the majority of A. lyrata imprinted genes exhibit parentally-biased expression in A. thaliana, suggesting that there is evolutionary conservation in gene imprinting. Surprisingly, we discovered substantial interspecies differences in methylation features associated with paternally expressed imprinted genes (PEGs). Unlike A. thaliana, the maternal allele of many A. lyrata PEGs was hypermethylated in the CHG context. Increased maternal allele CHG methylation was associated with increased expression bias in favor of the paternal allele. We propose that CHG methylation maintains or reinforces repression of maternal alleles of PEGs. These data suggest that while the genes subject to imprinting are largely conserved, there is flexibility in the epigenetic mechanisms employed between closely related species to maintain monoallelic expression. This supports the idea that imprinting of specific genes is a functional phenomenon, and not simply a byproduct of seed epigenomic reprogramming.
2016-09-01 | GSE76076 | GEO
Project description:Despite of the paramount importance of heterosis in agriculture, the molecular mechanisms underlying heterosis remain elusive. Recent studies in Arabidopsis suggested possible involvement of DNA methylation in heterosis. We tested this hypothesis genetically by crossing homozygous mutants in DNA methylation-related genes in the Columbia (Col) ecotype with homozygous mutants in the same DNA methylation-related genes in the C24 ecotype. When genes in the RNA-directed DNA methylation (RdDM) pathway were mutated, the resultant F1 hybrids did not show appreciable loss of best parent heterosis (BPH) performances in early seedling growth. In contrast, mutations in the putative chromatin remodeling protein DECREASE OF DNA METHYLATION 1 (DDM1) caused ddm1-Col like growth pattern of ddm1-F1 hybrids, a mid-parent heterosis (MPH) performance. To understand the underlying molecular mechanisms, we compared the transcriptomes of the parental plants and reciprocal F1 hybrids in the wild type and ddm1 mutant backgrounds, and identified 183 non-additively expressed (NAE) genes, which were functionally enriched in defense response, a group of genes negatively associated with plant size. Interestingly, for the expression levels of the NAE genes, WT-F1 hybrids were enriched in the Golden Ration between mid-parent values (MPVs) and Col parents in WT, but ddm1-F1 hybrids were comparable to ddm1-Col parent in ddm1 mutant, which explained the MPH performance of ddm1-F1 hybrids. DNA methylation analyses revealed only one third of the NAE genes with highly methylated promoters whose expression is negatively associated with DNA methylation of promoters, strongly suggesting that DDM1 regulates heterosis by multiple epigenetic modifications.
2016-11-07 | GSE74551 | GEO
Project description:Loop-design (triangle design with the comparison of each triplet: hybrid + parent 1 and parent 2) and pairwise design (hybrid + parent 1, hybrid + parent 2) were used in the experiment.<br> Four inbred lines and their four inter-pool hybrids were hybridized respectively in two-colour chips experiments. <br> The objective of our study was to:(i) identify differentially expressed genes in relation to heterosis for plant height, (ii) relate gene expression patterns to the dominance and overdominance hypothesis, (iii) determine the consistency of expression patterns between inbred parent - hybrid triplets also in view of differing degrees of relatedness of triplets, and to (iv) validate consistently differentially expressed genes between hybrids and their parental inbreds by real-time (qRT) PCR.
2006-08-17 | E-MEXP-764 | biostudies-arrayexpress