Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into its domestication process

ABSTRACT: Sequencing of 200 cacao accessions to perform evolutionary and assoociation analyses

INSTRUMENT(S): -

ORGANISM(S): Theobroma Cacao

SUBMITTER: MARS, Stanford University, Indiana University and Washington State University

PROVIDER: PRJEB28591 | EVA | 2018-10-24

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERZ696780_merged.accessioned.vcf.gz	Vcf
	ERZ696780_merged.accessioned.vcf.gz.csi	Vcf
	ERZ696780_merged.accessioned.vcf.gz.tbi	Vcf
	ERZ696780_merged.vcf.gz	Vcf
	ERZ696780_merged.vcf.gz.tbi	Vcf

Items per page:

1 - 5 of 27

Similar Datasets

DNA-seq of various fungi isolated from faecal materials and environmental samples for comparative genomic analyses, SYBARIS project

Project description:Aim of this project is to perform a comparative genomic study (including all S. cerevisiae sequenced and available) of the variability and evolutionary traits of yeast.

2016-04-30 | E-SYBR-12 | biostudies-arrayexpress

Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (RNA-Seq)

Project description:Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation. Here, we report population-wide DNA sequencing of genomes, transcriptomes, and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are unlinked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified 2,372 methylQTL, which revealed the first population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically reactivated during male gametogenesis, which facilitates their silencing across generations. RNA-seq from naturally-occurring Arabidopsis accessions

2013-03-05 | E-GEOD-43858 | biostudies-arrayexpress

Comparative and population genomic analyses of chromosome rearrangements in Brenthis butterflies

Project description:Comparative and population genomic analyses of chromosome rearrangements in Brenthis butterflies

| PRJEB62818 | ENA

Primate iPS cells as tools for evolutionary analyses

Project description:Primate iPS cells as tools for evolutionary analyses

| PRJNA218873 | ENA

Genomic Investigation of Unusual Responders

Project description:Studies have shown that tumors from the same patient may respond very differently to the same therapeutic agents. This study aims to investigate the genetic basis of tumors that respond abnormally well or poorly to therapeutic agents in an effort to understand the fundamental genetic basis of this response. The present protocol seeks to retrospectively perform Exome, next-generation (DNA) sequencing and/or other molecular techniques on tumor samples to identify the genetic basis of a patient’s exceptional response to chemotherapy.

| 2289468 | ecrin-mdr-crc

Genomic DNA hybridizations of Col-0, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana

Project description:These data provide a basis for the detection of sequence based polymorphisms between the Col-1, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of two physiologically extreme accessions (Tsu-1 from a wet environment in Tsushima, Japan and Kas-1 from a dry environment in Kashmir, India). The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit. Genomic hybridization experiments identified 42,503 single feature polymorphisms (SFP) between accessions, providing an initial screen for putative SNPs, indels, or changes in gene content.

2010-02-17 | GSE20340 | GEO

Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (Methyl-Seq)

2013-03-05 | E-GEOD-43857 | biostudies-arrayexpress

Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (RNA-Seq)

2013-03-05 | GSE43858 | GEO

Genomic analyses of yeasts isolated from kimchi

Project description:Genomic analyses of yeasts isolated from kimchi

| PRJNA434537 | ENA

Genomic and transcriptomic analyses of sebacinoid fungi

Project description:Genomic and transcriptomic analyses of sebacinoid fungi

| PRJNA260297 | ENA