VCF files from the study of low recombining genomic regions in pearl millet

Version 1.0
VCF files from the study of low recombining genomic regions in pearl millet
Salson, Marine; Duranton, Maud; Huynh, Stella; Mariac, Cédric; Tranchant-Dubreuil, Christine; Orjuela, Julie; Cubry,Philippe; Thuillet, Anne-Celine; Burgarella, Concetta; De Navascués, Miguel; Zekraouï, Leïla; Couderc, Marie; Arribat, Sandrine; Rodde, Nathalie; Barnaud, Adeline; Adama Faye; Kane, Ndjido; Vigouroux, Yves; Berthouly-Salazar, Cécile, 2025, "VCF files from the study of low recombining genomic regions in pearl millet", https://doi.org/10.23708/SN2T4A, DataSuds, V1
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Description
We conducted a comprehensive investigation of large low-recombining regions in cultivated populations of pearl millet, an outcrossing diploid African cereal. We adopted a population genomic approach based on the analysis of single nucleotide polymorphisms.

The repository contains the VCF files generated for three datasets: a Senegalese (126 accessions, exome sequencing, 76,018 SNPs), an African (125 wild and cultivated accessions from Western, Central and Eastern Africa, whole genome sequencing, 25,969,513 SNPs) and a temporal dataset (377 accessions from 1976 and 2016, exome sequencing, 39,672 SNPs).

We studied seven large regions ranging from 5 to 88 Mb. These regions exhibit an excess of heterozygotes, a distinctive hallmark of overdominance. They displayed a tendency towards a higher diversity and ratio of non-synonymous and deleterious variants. A total of 17% of the cultivated pearl millet genome exhibits a local population structure suggestive of overdominance or possibly pseudo-overdominance. Our empirical results contribute to the accumulation of knowledge that will enhance our understanding of the potential role of overdominance or pseudo-overdominance in maintaining genetic diversity, particularly in low recombining regions. (2025-06-02)
Subject Agricultural Sciences
Keyword low-recombining regions, pearl millet, inversions, overdominance, introgression
Related Publication Interplay between large low-recombining regions and overdominance in a plant genome? [under revision]
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ReadMe_SN2T4A.txt
documentation_files/Plain Text - 2.0 KB
Published Jun 23, 2025
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MD5: 8f93a5fcb1e298749d0b547f19f85602
Contains citation, description and conditions of use of dataset data
Documentation
Preview "documentation_files/ReadMe_SN2T4A.txt"
Autof-Pod103sr8_scaffolds_assembly.fasta.gz
Fasta_data_file/Gzip Archive - 541.6 MB
Published Jun 23, 2025
1 Download
MD5: c4ae489835bf07b1f4868ccdac0d6cb0
Scaffolds of Autof-Pod103sr8
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Senegalese_dataset_126_samples_SIFT_prediction.vcf.gz
Senegalese_Dataset_VCF_Files/Gzip Archive - 49.9 MB
Published Jun 23, 2025
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MD5: 3541b006ee85d27bfb4a75356c1d7be1
Prediction of the effect of the mutations on protein functions obtained with SIFT.
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African_dataset_chr1.vcf.gz
VCF_Data_Files/Gzip Archive - 2.3 GB
Published Jun 23, 2025
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MD5: b8ff3c935c4f42b483fe1dbd29b1a75b
Chromosome 1 of the VCF file obtained for the African dataset 125 accessions 25,969,513 SNPs for the whole genome
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African_dataset_chr2.vcf.gz
VCF_Data_Files/Gzip Archive - 2.1 GB
Published Jun 23, 2025
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MD5: a416fb338de90a4279d266e5190ff60e
Chromosome 2 of the VCF file obtained for the African dataset 125 accessions 25,969,513 SNPs for the whole genome
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African_dataset_chr3.vcf.gz
VCF_Data_Files/Gzip Archive - 2.5 GB
Published Jun 23, 2025
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MD5: 2483c04c141028350a3072d8d243c255
Chromosome 3 of the VCF file obtained for the African dataset 125 accessions 25,969,513 SNPs for the whole genome
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African_dataset_chr4.vcf.gz
VCF_Data_Files/Gzip Archive - 1.6 GB
Published Jun 23, 2025
0 Downloads
MD5: d7cbf49e86ae9b743a49ac6adb296fa3
Chromosome 4 of the VCF file obtained for the African dataset 125 accessions 25,969,513 SNPs for the whole genome
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African_dataset_chr5.vcf.gz
VCF_Data_Files/Gzip Archive - 1.2 GB
Published Jun 23, 2025
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MD5: 71f9d7a9751c4a62181765f11c2b5c87
Chromosome 5 of the VCF file obtained for the African dataset 125 accessions 25,969,513 SNPs for the whole genome
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African_dataset_chr6.vcf.gz
VCF_Data_Files/Gzip Archive - 2.2 GB
Published Jun 23, 2025
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MD5: 10c0cf6c4b6ba072528cd44c0a72474e
Chromosome 6 of the VCF file obtained for the African dataset 125 accessions 25,969,513 SNPs for the whole genome
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African_dataset_chr7.vcf.gz
VCF_Data_Files/Gzip Archive - 1.9 GB
Published Jun 23, 2025
0 Downloads
MD5: 500b7c8eef5cee8a8586a9fbf5d83122
Chromosome 7 of the VCF file obtained for the African dataset 125 accessions 25,969,513 SNPs for the whole genome
Données
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