DOI: 10.5061/dryad.46pk7
title: Data from: Resequencing of common bean identifies regions of inter-gene pool introgression and provides comprehensive resources for molecular breeding

description: Common bean is the most important grain legume for human consumption and a
 main nutrition source in the tropics. Because bean production is reduced
 by both abiotic and biotic constraints, current breeding efforts are
 focused on the development of improved varieties with tolerance to these
 stresses. We characterized materials from different breeding programs
 spanning three continents to understand their sequence diversity and
 advance the development of molecular breeding tools. For this, 37
 varieties belonging to P. vulgaris, P. acutifolius, and P. coccineus were
 sequenced by whole-genome sequencing (WGS), identifying more than 40
 million genomic variants. Evaluation of nuclear DNA content and analysis
 of copy number variation revealed important differences in genomic content
 not only between P. vulgaris and two other domesticated Phaseolus species,
 but also within P. vulgaris, affecting hundreds of protein-coding genomic
 regions. A large number of inter-gene-pool introgressions were identified.
 Furthermore, interspecific introgressions for disease resistance in
 breeding lines were mapped. Evaluation of newly developed SNP markers
 within previously discovered QTL for common bacterial blight and angular
 leaf spot provide improved specificity to tag sources of resistance to
 these diseases. We expect that this dataset will provide a deeper
 molecular understanding of breeding germplasm and deliver molecular tools
 for germplasm development, aiming to increase the efficiency of bean
 breeding programs.
description: Bean variation catalog
 relative to the reference genome v2.1Bean variation catalog
 relative to the reference genome v2.1. See README.txt file for
 instructions on how to perform different filters of this VCF file using
 NGSEPBeanWGS_RefV2_CIAT_UCDAVIS_Q40.vcf.gzGZI index file for the bean variation catalog relative to the reference genome v2.1Index file generated with the bgzip tool for the VCF file having the bean variation catalog (BeanWGS_RefV2_CIAT_UCDAVIS_Q40.vcf.gz)BeanWGS_RefV2_CIAT_UCDAVIS_Q40.vcf.gz.gziTabix index for the bean variation catalog aligned to the reference genome v2.1Tabix index for the bean variation catalog aligned to the reference genome v2.1. This file is useful to make quick queries using the tabix tool of htslib (http://www.htslib.org/doc/tabix.html)BeanWGS_RefV2_CIAT_UCDAVIS_Q40.vcf.gz.tbiRegions masked as repetitive in the reference genome v2.1Catalog of regions marked as repetitive in the softmasked version of the bean reference genome v2.1. See https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Pvulgaris for details.BeanWGS_RefV2_repeatsMasked.txtRegions from the reference genome v2.1 called repetitive based on reads with non-unique alignmentsCatalog of regions marked as repetitive by NGSEP, based on Illumina reads from G19833 with non-unique alignments to the reference genomeBeanWGS_RefV2_CIAT_UCDAVIS_repeatsNGSEP.txtMerging of regions identified as repetitive in the reference genome v2.1Catalog of regions marked as repetitive in the softmasked version of the bean reference genome v2.1, or marked as repetitive by NGSEP, based on Illumina reads from G19833 with non-unique alignments to the reference genome. This is the file provided here containing the largest amount of predicted repetitive regions in the reference genomeBeanWGS_RefV2_CIAT_UCDAVIS_repeatsNGSEPMergedMasked.txtVCF file with Copy Number Variation events over 35 accessions relative to the reference genome v2.1Catalog of copy number variants identified over 35 accessions relative to the reference genome v2.1. The file was assembled clustering events predicted in individual accessions using the implementation of the CNVnator algorithm implemented in NGSEP. The file was compressed with bgzip. GZI and tbi indexes for this file are also provided with this data publicationBeanWGS_CNVs_RefV2_CIAT_UCDAVIS_Q10.vcf.gzGZI index for the file with copy number variation events relative to the bean reference genome v2.1GZI index for the file with copy number variation events relative to the bean reference genome v2.1. This file was generated using the bgzip tool (http://www.htslib.org/doc/tabix.html)BeanWGS_CNVs_RefV2_CIAT_UCDAVIS_Q10.vcf.gz.gziTBI index for the file with copy number variation events relative to the bean reference genome v2.1TBI index for the file with copy number variation events relative to the bean reference genome v2.1. This file was generated using the tabix tool (http://www.htslib.org/doc/tabix.html)BeanWGS_CNVs_RefV2_CIAT_UCDAVIS_Q10.vcf.gz.tbi