DOI: 10.5061/dryad.mgqnk994n
title: Genomic characterization and gene bank curation of Aegilops using genotyping-by-sequencing

description: In this study, genotyping-by-sequencing (GBS) was performed on 1041
 Aegilops accessions, representing 23 different species. These accessions
 have been maintained by the Wheat Genetics and Resource Center (WGRC) at
 Kansas State University. The GBS FASTQ files have been uploaded to the
 NCBI SRA public repository under the BioProject accession number #
 PRJNA985892. We have provided other files related to data analysis, such
 as the barcode key file, SNP matrices, and taxonomic information of the
 accessions in this Dryad repository, which can be accessed through the
 provided link.  The aim of the study was to explore the genetic
 and genomic characteristics of wild wheat relatives, Aegilops, using a
 larger number of SNP markers. Here, we also curated the WGRC gene
 bank Aegilops collection via the identification of misclassified
 accessions and genetically identical redundant accessions. Further, we
 explored the genomic relationship between wheat and the different Aegilops
 species. 
description: In this study, <em>Aegilops</em> accessions preserved
 and maintained as single seed descent (SSD) at the Wheat Genetics Resource
 Center at Kansas State University were subjected to
 genotyping-by-sequencing. The DNA was extracted from the seedlings of
 individual plants and GBS library was made as described in the manuscript.
 The GBS data were utilized to detect variants using a reference-based
 pipeline, such as TASSEL GBS, in cases where genome assemblies were
 available. For the accessions without available genome assemblies, the
 sequence FASTQ files were aligned to a mock reference generated from the
 raw GBS data. The accessions with a higher amount of data were chosen to
 generate the mock reference. Variants were called using both GBS-SNP-CROP
 and bcfools pipeline. Subsequently, the SNP matrices were filtered and
 utilized for various analyses. 
description: R and RStudio
description: Genomic Characterization and Gene Bank Curation of Aegilops: The Wild
 Relatives of Wheat Laxman Adhikari*, John Raupp, Shuangye Wu, Dal-Hoe Koo,
 Bernd Friebe, and Jesse Poland* Emails:
 and 
 Data Set In this study, Aegilops accessions preserved and maintained as
 single seed descent (SSD) at the Wheat Genetics Resource Center at Kansas
 State University were subjected to genotyping-by-sequencing. The DNA was
 extracted from the seedlings of individual plants and GBS library was made
 as described in the manuscript. The GBS data were utilized to detect
 variants using a reference-based pipeline, such as TASSEL GBS, in cases
 where genome assemblies were available. For the accessions without
 available genome assemblies, the sequence FASTQ files were aligned to a
 mock reference generated from the raw GBS data. The accessions with a
 higher amount of data were chosen to generate the mock reference. Variants
 were called using both GBS-SNP-CROP and bcfools pipeline. Subsequently,
 the SNP matrices were filtered and utilized for various analyses. Files
 and Descriptions 1. Readme.md This file contains basic information about
 the dataset, software, and the other files uploaded to Dryad. 2.
 barcode.file.all.accessions.AegilopsProject.txt This file contains
 flowcell, lane, sample ID, sequence files name in NCBI SRA and the NCBI
 Project ID. This information is sufficient for demultiplexing the GBS data
 using Tassel GBS [] and Sabre
 []. 3.
 sample.info.after.adjusted.missclassified.txt The file contains
 species-level taxonomy information for all accessions after curating the
 misclassified accessions. The final genetic cluster and PCA plots were
 colored based on this information. Each species was represented by a
 single number, as demonstrated in the
 "All.aegilops.with.mock_Ref.phylogenetic.PCA.Rmd" file.
 Additionally, there are several "line.info" or
 "sample.info" files corresponding to specific analyses and the
 inclusion of species in those particular analyses. 4.
 Ae.all.species.denovo.mockref.SNP.matrix.final.hmp.txt.zip This file
 contains the matrix of 54,667 SNPs generated for all Aegilops accessions.
 We filtered the genotyping information based on minor allele frequency
 (MAF), missing data, and heterozygosity. After applying the following
 filters (MAF &gt; 0.01, missing data &lt; 30%, heterozygosity &lt; 10%),
 we retained 46,879 SNPs for 1,041 individuals. 5.
 filtered.numeric.coded.SNP.matrix.hmp.txt.zip The SNP matrix for all
 accessions is represented numerically as [1, 0, -1]. After filtration, the
 matrix consisted of 46,879 SNPs, which were utilized for phylogenetic
 clustering and PCA analysis. 6. U-genome.clade.SNP.matrix.txt.zip The SNP
 matrix file was used to generate the phylogenetic tree of the U-genome
 clade, as depicted in the manuscript. 7.
 S-genome.and.mutica_SNP.matrix_speltoides-ref.txt.zip The SNP matrix was
 used to cluster the Sitopsis section Aegilops species and Ae. mutica. The
 provided line info file, [S.genome.and.mutica.lineinfo.txt], is essential
 for coloring the NJ phylogenetic tree generated using this matrix. 8.
 crassa.juvenalis.vavilovii.SNP.matrix.txt The SNP matrix was used to
 cluster the hexaploid Aegilops species. 9.
 Neglecta.columnaris.SNP.matrix.txt.zip The SNP matrix was used to cluster
 and distinguish between Ae. neglecta and Ae. columnaris. 10.
 F_MAF0.01_Miss50_Het20-all.diploid.wheat.geno-tags.fastq-all.wheat.D.genome.ref.hmp.txt.zip The SNP matrix includes all diploid Aegilops, including the previously curated Ae. tauschii collection and the CIMMYT wheat lines. Information regarding the GBS data for these Ae. tauschii and CIMMYT lines can be found in Supplementary Table 1. 11. gene.bank.curation.tauschii_F_MAF0.05_Miss50_Het10-tauschii.genome-tags.fastq-all.vcf.hmp.txt.zip The SNP matrix was utilized to curate the Ae. tauschii collection, specifically in identifying and removing duplicates that were not curated in the previous study. 12. gene.bank.curation.data-sharonensis.longissima.0.01maf.0.5miss.0.1het.19Ksnps.hmp.txt.zip The SNP matrix was used to curate the Ae. sharonensis and Ae. lognissima collections, with a specific focus on identifying duplicates. 13. gene.bank.curation.data-searsii.with.Searsii.genome.0.01maf.0.5miss.0.1het.SNPs11663.zip The SNP matrix was used to curate the Ae. searsii collection, with a specific focus on identifying duplicates. R-script 1. All.aegilops.with.mock_Ref.phylogenetic.PCA.Rmd This file has R script used to generate a phylogenetic tree and PCA plot for the whole Aegilops collection 2. All.species.diversity.and.seg.loci.Rmd This file includes the R script used to compute Neis genetic diversity indices and the segregating loci for each of the 23 species. 3. Aegilops.duplicated.accessions.Rmd This file includes the R script used to identify genetically duplicated accessions. The script was specifically executed on diploid Aegilops species for which a reference genome is available. 4. U-genome.clade.Rmd This file contains the R script used to generate the U-genome phylogenetic tree. 5. neglecta-columnaris-de-novo.Rmd The R script file was used to cluster Ae. neglecta and Ae. columnaris, and to study their genomic relations and genome formula. 6. M.genome.loci.in.tetraploids.Rmd The file contains an R script to study genetic variations in tetraploid Aegilops species that share the M genome. The variants in the input file were initially called on the diploid M genome species (Ae. comosa). 7. crassa-vavilovii-juvenalis.Rmd This file contains an R script used to generate a phylogenetic tree of the hexaploid Aegilops group. 8. Genome.vs.snp.plot.sitopsis.seg.loci.Rmd This file contains an R script to generate a bar chart illustrating the number of loci of diploid Aegilops of Sitopsis section that were mapped on different wheat subgenomes. In addition to these files, there are several line info text files that contain taxonomic information about the accessions. These files are essential for coloring the NJ phylogenetic tree and the PCA plots.