Ontology highlight
ABSTRACT:
PROVIDER: PRJNA411797 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6074026_1.fastq.gz | Fastqsanger.gz | |||
| SRR6074026_2.fastq.gz | Fastqsanger.gz | |||
| SRR6074027_1.fastq.gz | Fastqsanger.gz | |||
| SRR6074027_2.fastq.gz | Fastqsanger.gz | |||
| SRR6074028_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
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Project description:From the 15th to the 19th century, the Trans-Atlantic Slave-Trade influenced the genetic and cultural diversity of numerous populations. We explore genomic and linguistic data from the nine islands of Cabo Verde, the earliest European colony of the era in Africa, a major Slave-Trade platform between the 16th and 19th centuries, and a previously uninhabited location ideal for investigating early admix-ture events between Europeans and Africans. We find that genetic admixture in Cabo Verde occurred primarily between Iberian and Senegambian populations, although forced and voluntary migrations to the archipelago involved numerous other populations. Inter-individual genetic and linguistic variation recapitulate geographic distribution of individuals’ birth-places across Cabo Verdean islands, suggest-ing that Kriolu language variants have developed together with genetic divergences. Furthermore, we find that admixture occurred both early in each island, long before the 18th-century massive TAST deportations triggered by the expansion of plantation economy in Africa and the Americas, and after this era mostly during the abolition of the TAST and of slavery in European colonial empires. Our results illustrate how shifting socio-cultural relationships between enslaved and non-enslaved commu-nities shaped enslaved-African descendants’ genomic diversity and structure on both sides of the At-lantic.
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Project description:Datasets used in the article "The admixture histories of Cabo Verde", by Romain Laurent et al. 2022 - doi pending
As per Materials and Methods herein, the genotype data corresponds to 2,118,722 autosomal SNPs genotyped from the IlluminaOmni 2.5 Million BeadChip for 233 Cabo Verdean volunteer participants, family unrelated at the 2nd degree based on population genetics analyses (see Material and Methods).
SNP rsID, Chromosome position and genetic position in (bp) are in Build GRCh38.
Cabo Verdean individuals are designated with an alphanumeric unique code
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Project description:Microbial food web diversity in reservoirs and rivers
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Project description:Datasets used in the article "The admixture histories of Cabo Verde", by Romain Laurent et al. 2022 - doi pending
File name "eGAdeposit_233CaboVerde_GEOcoordFULL_FINAL_01062022.txt"
Column 1 corresponds to individual alphanumeric codes as in the "eGAdeposit_233CaboVerde_GenotypeFile_FINAL_01062022.vcf" genotype file
Column 2-3 corresponds to X-Y GPS coordinates of individual's interview location in Cabo Verde
Column 4-5 corresponds to X-Y GPS coordinates of individual's self-reported residence location at the time of the interview
Column 6-7 corresponds to X-Y GPS coordinates of individual's self-reported birth-place location
Column 8-9 corresponds to X-Y GPS coordinates of individual's self-reported paternal birth-place location
Column 10-11 corresponds to X-Y GPS coordinates of individual's self-reported maternal birth-place location
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Project description:To effectively monitor microbial populations in acidic environments and bioleaching systems, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the known genes associated with the acidophiles. This array contained 1,072 probes in which there were 571 related to 16S rRNA and 501 related to functional genes. Acid mine drainage (AMD) presents numerous problems to the aquatic life and surrounding ecosystems. However, little is known about the geographic distribution, diversity, composition, structure and function of AMD microbial communities. In this study, we analyzed the geographic distribution of AMD microbial communities from twenty sites using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA genes, and the results showed that AMD microbial communities were geographically distributed and had high variations among different sites. Then an AMD-specific microarray was used to further analyze nine AMD microbial communities, and showed that those nine AMD microbial communities had high variations measured by the number of detected genes, overlapping genes between samples, unique genes, and diversity indices. Statistical analyses indicated that the concentrations of Fe, S, Ca, Mg, Zn, Cu and pH had strong impacts on both phylogenetic and functional diversity, composition, and structure of AMD microbial communities. This study provides insights into our understanding of the geographic distribution, diversity, composition, structure and functional potential of AMD microbial communities and key environmental factors shaping them. This study investigated the geographic distribution of Acid Mine Drainages microbial communities using a 16S rRNA gene-based RFLP method and the diversity, composition and structure of AMD microbial communities phylogenetically and functionally using an AMD-specific microarray which contained 1,072 probes ( 571 related to 16S rRNA and 501 related to functional genes). The functional genes in the microarray were involved in carbon metabolism (158), nitrogen metabolism (72), sulfur metabolism (39), iron metabolism (68), DNA replication and repair (97), metal-resistance (27), membrane-relate gene (16), transposon (13) and IST sequence (11).
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