DOI: 10.4119/unibi/2963492
title: Supplementary material related to MBS analysis of seed quality parameters in Brassica napus

description: The data comprises the supplementary materials of the MBS analysis of seed quality parameters in Brassica napus. File S1: Data sets used for phylogenetic and genomic analysis. File S2: Schematic illustration of the workflow for the generation of the gold standard and follow up delta allele frequency calculation. File S3: Variants of the reconstituted F1. File S4: Variants of the gold standard. File S5: Seed GSL content SNVs left after filtered for the gold standard. File S6: SPC SNVs left after filtered for the gold standard. File S7: dARCs of seed GSL content pools. File S8: dARCs of SPC pools. File S9: ZCRs of seed GSL content pools. File S10: ZCRs of SPC pools. File S11: Genome-wide delta allele frequency plots of seed GSL content pools. File S12: Genome-wide delta allele frequency plots of SPC pools. File S13: PAVs of GSL pool analysis. File S14: PAVs of SPC pool analysis. File S15: IGV screenshot of GSL MYB homologs expression and genomic coverage in the GSL pools and the parental genotypes, as well as transcriptomic coverage of Janetzkis Schlesischer (JS) leaves and seeds RNA-Seq data. File S16: CDS sequences from B. napus Lorenz. File S17: Peptide sequences from B. napus Lorenz. File S18: CDS sequences from B. napus Janetzkis Schlesischer. File S19: Peptide sequences from B. napus Janetzkis Schlesischer. File S20: Frame-corrected gff3 file for SnpEff analysis. File S21: Predicted high impact variants of genes located within +/- 5 kbp of the borders of the genomic intervals associated with seed GSL content. File S22: Predicted high impact variants of genes located within +/- 5 kbp of the borders of the genomic intervals associated with SPC content. File S23: SRA IDs of the used public available RNA-Seq data sets from B. napus. File S24: RNA-Seq mapping statistics. File S25: Genes located in genomic intervals associated with seed GSL content. File S26: Genes located in genomic intervals associated with SPC content. File S27: CDS sequences from B. napus SGDH14. File S28: Peptide sequences from B. napus SGDH14. File S29: GSL MYB transcription factors homologs. File S30: MYB amino acid sequences used for phylogenetic analysis. File S31: GSL transcription factors‘coding sequences of B. napus Janetzkis Schlesischer. File S32: GSL transcription factors‘coding sequences of B. napus Lorenz. File S33: GSL transcription factors‘coding sequences of B. napus SGDH14. File S34: Phylogenetic tree based on the amino acid sequences of all MYB homologs identified in Brassica species marking the key GSL MYB transcription factor clade. File S35: Phylogenetic tree based on the amino acid sequences of the key GSL transcription factors identified in Brassica species. File S36: Oligonucleotide sequences. File S37: Genomic read mapping statistics. File S38: Gene located in the deleted region of B. napus Janetzkis Schlesischer. File S39: Expression of GSL transcription factors based on public available B. napus RNA-Seq data sets. File S40: Genomic and transcriptomic read mappings of GSL pools, parental genotypes, and Ja-netzkis Schlesischer (JS) leaves and seeds RNA-Seq data vs the Darmor-bzh genome sequence. (A) Whole gene view is presented, while (B) shows a close up of the position of the 4 bp InDel. File S41: The C09 BnaMYB28_2 and A09 BnaMYB28_4 alleles association with seed GSL pheno-type across various B. napus genotypes. File S42: IGV screenshot of the ~25 kbp deletion located within A09_GSL_13 in B. napus Janetzkis Schlesischer. Note: Files with the extension .7z need to be de-compressed before use.