DOI: 10.5061/dryad.9cnp5hqhc
title: Raw genotyped total called structural variant (SV)

description: Genomic structural mutations especially deletion are an important source
 of variation in many species and can play key roles in phenotypic
 diversification and evolution. Previous work in many plant species,
 including some crops, has identified multiple instances of structural
 variations (SVs) occurring in or near genes related to stress response and
 disease resistance, suggesting a possible role for SVs in local
 adaptation. Sorghum (Sorghum bicolor (L.) Moench) is one of the
 most widely grown cereal crops in the world, and over the course of its
 history it has been adapted to an array of different climates as well as
 bred for multiple purposes, resulting in a striking phenotypic diversity
 within the existing germplasm. In this study, we identified genome-wide
 deletions in the Biomass Association Panel (BAP), a collection of 347
 diverse sorghum genotypes collected from multiple countries and
 continents. Using Illumina-based, short-read whole genome resequencing
 data from every genotype, we found a total of 22,359 deletions after
 filtering. The size of deletions ranged from 51 to 89,716 bp with
 a median size of 956 bp. The global site frequency spectrum of the
 deletions fit a model of neutral evolution, suggesting that the majority
 of deletions were not under any types of selection. Clustering
 results based on SNPs separated the deletions of the genotypes into eight
 clusters which largely corresponded with geographic origins. Even though
 most deletions appeared to be neutral, a handful of cluster-specific
 deletions were found in genes related to biotic (plant defense and
 bacterial resistance) and abiotic stress (drought and temperature)
 responses, supporting the possibility that at least some
 deletions contribute to local adaptation in sorghum.
description: The pipeline for calling SVs in the BAP was adopted from
 the svtools pipeline (Larson <i>et al.</i> 2019). Briefly,
 de-multiplexed sequences reads in FASTQ format for each individual were
 aligned to version 3.0.1 of the BTx623 reference genome (as downloaded
 from Phytozome v12.1.6: https://phytozome.jgi.doe.gov/pz/portal.html) using the program speedseq (Chiang <i>et al.</i> 2015). Structural variations were identified in each individual aligned BAM file using LUMPY (Layer <i>et al.</i> 2014) with default parameters. The resulting 347 structural variation files were then sorted and merged with svtools (Larson <i>et al.</i> 2019). A full tutorial of this process has been delineated by the authors of svtools, and can be found at https://github.com/hall-lab/svtools/blob/master/Tutorial.md. The merged vcf was then used to calculate a genotype for each individual at the variant positions resulting in a fully genotyped vcf file of each individual. CNVnator(Abyzov <i>et al.</i> 2011) was run within svtools in order to annotate the called variants based on copy number. Subsequently, svtools merged the genotyped and CNV-annotated vcf files to remove any redundant variants that were called by both programs. 
description: The VCF file was the product of LUMPY pipeline integrating with
 genotyping and CNV detecting step to generate a merge SV