GEO DataSets

(Submitter supplied) 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. more...

Organism:

Arabidopsis lyrata; Arabidopsis halleri; Arabidopsis thaliana

Type:

Genome variation profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) 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. more...

Organism:

Arabidopsis thaliana x Arabidopsis halleri; Arabidopsis thaliana x Arabidopsis lyrata

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21749 GPL21748

18 Samples

Download data: TXT

(Submitter supplied) Following previous work, we extend the use of a reliable detection method to a wide progeny in white spruce in order to genetically map a maximum of inherited gene CNVs and linked those to phenotypic traits related to adaptation. We selected probes targeting 3911 genes likely in CNV in this progeny and performed genetic mapping for those harboring a 1:1 segregation. In addition, the link between gene CNVs and phenotypic variation was tested using budburst, budset and growth data for the same samples. more...

Organism:

Picea glauca

Type:

Genome variation profiling by array

Platform:

GPL23818

115 Samples

Download data: TXT

(Submitter supplied) 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).

Organism:

Arabidopsis thaliana x Arabidopsis lyrata; Arabidopsis thaliana; Arabidopsis lyrata

Type:

Expression profiling by SNP array; Genome variation profiling by SNP array

Platform:

GPL13483

24 Samples

Download data: CEL

(Submitter supplied) We applied previously designed array in order to widely cover all types of genes of 74 A. thaliana accessions.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL14937

148 Samples

Download data: TXT

(Submitter supplied) Metriaclima estherae, Protomelas similis, Rhamphochromis "chilingali", and Astatotilapia tweddlei genomic DNA hybridized with Astatotilapia burtoni genomic DNA

Organism:

Haplochromis burtoni; Rhamphochromis sp. 'chilingali'; Protomelas similis; Haplochromis tweddlei; Maylandia estherae

Type:

Genome variation profiling by array

Platform:

GPL6416

8 Samples

Download data: GPR

(Submitter supplied) We compared the expression between inter-specific hybrids (A. thaliana-A. lyrata, A. thaliana-A. halleri) and mid parent values of their parental lines.

Organism:

Arabidopsis thaliana x Arabidopsis lyrata; Arabidopsis thaliana x Arabidopsis halleri subsp. gemmifera; Arabidopsis lyrata subsp. lyrata; Arabidopsis halleri subsp. gemmifera; Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

10 Samples

Download data: CEL, CHP

(Submitter supplied) Background: Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. more...

Organism:

Littorina fabalis; Littorina compressa; Littorina arcana; Littorina saxatilis

Type:

Genome variation profiling by array

Platform:

GPL19000

36 Samples

Download data: PAIR

(Submitter supplied) Arabidopsis is a suitable system for testing the hypothesis that duplicate genes accelerate evolution of expression diversity among species diverged from shared whole genome duplications (WGDs) and recurrent events of WGD. In Arabidopsis, at least 9 species split after WGD of the common ancestor and new allotetraploids were formed in nature and can be resynthesized between closely related species. Using genomic and gene expression microarrays, we detected WGD duplicate and single-copy genes preserved in A.thaliana and A.arenosa in addition to change of gene expression levels among those species. more...

Organism:

Arabidopsis suecica; Arabidopsis thaliana; Arabidopsis arenosa

Type:

Expression profiling by array

Platform:

GPL7498

1 Sample

Download data: GPR

(Submitter supplied) Polyploidy or whole genome duplication (WGD) provides raw genetic materials for sequence and expression evolution of duplicate genes. However, the mode and tempo of expression divergence between WGD duplicate genes in closely relates species and recurrent allopolyploids are poorly understood. Arabidopsis is a suitable system for testing the hypothesis that duplicate genes increase expression diversity and regulatory networks. more...

Organism:

Arabidopsis thaliana; Arabidopsis arenosa; Arabidopsis suecica

Type:

Expression profiling by array; Genome variation profiling by array

5 related Platforms

5 Samples

Download data: GPR, TAR

(Submitter supplied) Different individuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence-absence variation (PAV) can lead to variation in the genome content of individuals within a species. In order to investigate the potential contribution of CNV and PAV to genomic diversity in maize we used array comparative genomic hybridization (CGH) to compare gene content and copy number variation among 25 diverse maize inbreds 14 genotypes of the wild ancestor of maize, teosinte. more...

Organism:

Zea mays subsp. parviglumis; Zea mays

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10846

58 Samples

Download data: PAIR

(Submitter supplied) This study centered on using a custom made Nimblegen aCGH chip that targeted all segmental duplications in the canine genome to identify associated CNVs. A total of 19 hybridizations were performed in a panel of diverse dogs and a single wolf.

Organism:

Canis lupus; Canis lupus familiaris

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7501

19 Samples

Download data: PAIR, TXT