Dataset for the article: Single nucleotide polymorphism (SNP) in the doublesex (dsx) gene splice sites and relevance for its alternative splicing in the malaria vector Anopheles gambiae

Djihinto, Oswald, Saizonou, Helga and Djogbenou, Luc (2022) Dataset for the article: Single nucleotide polymorphism (SNP) in the doublesex (dsx) gene splice sites and relevance for its alternative splicing in the malaria vector Anopheles gambiae. [Data Collection]

Summary

Sequence data and mosquito samples

Genomic sequences used in this study came from the Anopheles 1000 genomes (Ag1000G) project phase 2 released in 2017. The SNP annotation was downloaded (ag1000g.phase2.ar1.variants.pass.2R.vcf.gz, November 11, 2019) from the Malaria Genomic Epidemiology Network (MalariaGEN) website. This file contain all SNPs identified in mosquito whole genomes and that pass the variant filtering process. Only Anopheles gambiae samples were considered in our study. These mosquito samples were collected from natural populations from 2002 to 2012 in eight African countries.

Sequence analysis and SNP identification

From the Agdsx reference sequence, the list of genomic positions of donor and acceptor sites was extracted. VCFtools[SL1] [OD2] version 0.1.15 (https://vcftools.github.io/index.html) was used to extract the SNPs within the genomic region corresponding to the Agdsx sequence from the SNPs annotation file.
Sequence data and mosquito samples

Genomic sequences used in this study came from the Anopheles 1000 genomes (Ag1000G) project phase 2 released in 2017. The SNP annotation was downloaded (ag1000g.phase2.ar1.variants.pass.2R.vcf.gz, November 11, 2019) from the Malaria Genomic Epidemiology Network (MalariaGEN) website. This file contain all SNPs identified in mosquito whole genomes and that pass the variant filtering process. Only Anopheles gambiae samples were considered in our study. These mosquito samples were collected from natural populations from 2002 to 2012 in eight African countries.

Sequence analysis and SNP identification

From the Agdsx reference sequence, the list of genomic positions of donor and acceptor sites was extracted. VCFtools[SL1] [OD2] version 0.1.15 (https://vcftools.github.io/index.html) [28] was used to extract the SNPs within the genomic region corresponding to the Agdsx sequence from the SNPs annotation file.