GEO DataSets

(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) This study examines genomic copy-number variation among African cichlids spanning multiple tribes and radiations. We map CNVs and hotspots throughout the Oreochromis niloticus reference genome, categorize gene ontology enrichment within CNV regions, and compare results with sequence-based cichlid phylogenies.

Organism:

Cyathopharynx furcifer; Oreochromis alcalicus; Pseudocrenilabrus multicolor victoriae; Cyprichromis leptosoma; Labeotropheus fuelleborni; Oreochromis ndalalani; Astatotilapia flaviijosephi; Xenotilapia spiloptera; Julidochromis ornatus; Rhamphochromis longiceps; Coptodon fusiforme; Coptodon kottae; Sarotherodon lamprechti; Lobochilotes labiata; Sarotherodon galilaeus; Tropheus moorii; Haplochromis burtoni; Ophthalmotilapia ventralis; Boulengerochromis microlepis; Neolamprologus brichardi; Eretmodus cyanostictus; Hemichromis fasciatus; Stomatepia mariae; Copadichromis virginalis; Diplotaxodon greenwoodi; Pallidochromis tokolosh; Konia eisentrauti; Benthodesmus elongatus; Coptodon zillii; Cyphotilapia frontosa; Lepidiolamprologus elongatus; Sarotherodon melanotheron; Oreochromis grahami; Pungu maclareni; Nyassachromis microcephalus; Tropheops sp. 'red cheek'; Haplochromis thereuterion; Coptodon deckerti; Oreochromis niloticus; Astatotilapia calliptera; Callochromis macrops; Variabilichromis moorii; Astatoreochromis alluaudi; Paralabidochromis sp.; Astatotilapia bloyeti; Oreochromis latilabris; Maylandia zebra; Copadichromis borleyi; Haplochromis chilotes; Pundamilia nyererei; Neochromis omnicaeruleus; Coptodon ejagham; Sarotherodon knauerae; Rubricatochromis bimaculatus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL25405

168 Samples

Download data: PAIR, TXT

(Submitter supplied) Whole-genome methylomes and total transcriptomes for muscle and liver tissues of Lake Malawi cichlid species characterised in the context of phenotypic diversification.

Organism:

Aulonocara stuartgranti; Astatotilapia calliptera; Pundamilia nyererei; Petrotilapia genalutea; Maylandia zebra; Rhamphochromis longiceps; Diplotaxodon limnothrissa

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

11 related Platforms

60 Samples

Download data: BW, FA, TXT

(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) Cichlids fishes exhibit extensive phenotypic diversification and speciation. In this study we integrate transcriptomic and proteomic signatures from two cichlids species, identify novel open reading frames (nORFs) and perform evolutionary analysis on these nORF regions. We embark comparative transrcriptomics and proteogenomic analysis of two metabolically active tissues, the testes and liver, of two cichlid species Oreochromis niloticus (Nile tilapia, ON) and Pundamilia nyererei (Makobe Island, PN). more...

Organism:

Oreochromis niloticus; Pundamilia nyererei

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23067 GPL28548

6 Samples

Download data: TXT

(Submitter supplied) East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. more...

Organism:

Oreochromis niloticus; Maylandia zebra; Astatotilapia calliptera; Tropheops sp. 'mauve'; Pundamilia nyererei; Haplochromis burtoni

Type:

Expression profiling by high throughput sequencing

6 related Platforms

40 Samples

Download data: TXT

(Submitter supplied) East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. more...

Organism:

Tropheops sp. 'mauve'; Astatotilapia calliptera; Pundamilia nyererei; Oreochromis niloticus; Haplochromis burtoni; Maylandia zebra

Type:

Non-coding RNA profiling by high throughput sequencing

6 related Platforms

31 Samples

Download data: TXT

(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