Genome assemblies of the daisy Gorteria diffusa elucidate the molecular-genomic basis of pollination by sexual deception

Genome assemblies:gzip-compressed .fasta files containing the original assembled reference genomes of the Gorteria diffusa morphotypes Springbok, Naries and Okiep without the alterations required by the NCBI. Repetitive regions are softmasked. The raw reads are deposited on NCBI SRA under project PRJNA1181622.Gorteria_diffusa_Springbok.fa.gz: 40× PacBio CLR reads assembled with canu, polished with 100× Illumina PE150 reads using gcpp and NextPolish, scaffolded with Dovetail Omni-C data (gaps are represented by stretches of 100 N). Scaffold 1-4 represent chromosomes 1-4, Scaffold 6 represents the first part of chromosome 5, and Scaffold 5 the second part of chromosome 5.Gorteria_diffusa_Naries.fa.gz: 20× PacBio HiFi reads assembled with hifiasm.Gorteria_diffusa_Okiep.fa.gz: 20× PacBio HiFi reads assembled with hifiasm.Transposable element annotation:gzip-compressed .gff3 files containing the EDTA de-novo transposable element annotations for the three genomes.Gorteria_diffusa_Springbok_EDTA.gff3.gzGorteria_diffusa_Naries_EDTA.gff3.gzGorteria_diffusa_Okiep_EDTA.gff3.gzGene annotation:gzip-compressed .gff3 / .gtf / .fa / .tsv files containing the de-novo structural and functional gene annotations for the Gorteria diffusa Springbok genome.Gorteria_diffusa_Springbok_BRAKER.gff3.gz: Structural gene annotations from BRAKER2Gorteria_diffusa_Springbok_BRAKER_cds.fa.gz: Predicted coding sequences from BRAKER2Gorteria_diffusa_Springbok_BRAKER_aa.fa.gz: Predicted amino acid sequences from BRAKER2Gorteria_diffusa_Springbok_EnTAP_lvl0.tsv.gz: Functional gene annotations (level 0) from EnTAPGorteria_diffusa_Springbok_EnTAP_lvl1.tsv.gz: Functional gene annotations (level 1) from EnTAPGorteria_diffusa_Springbok_genes.gtf.gz: Structural and functional annotations combined.Structural variant analysis:gzip-compressed .vcf files containing the raw and filtered structural genomic variants called with Sniffles2 between Gorteria diffusa Springbok vs. Naries, and Springbok vs. Okiep respectively (Filter criteria: Structural variants larger than 1 Mbp, with a minor allele frequency of less than 0.3, with fewer than 5 supporting reads, imprecise breakpoints and/or overlap with assembly gaps were excluded).Sniffles2_Springbok_Naries_raw.vcf.gzSniffles2_Springbok_Naries_filtered.vcf.gzSniffles2_Springbok_Okiep_raw.vcf.gzSniffles2_Springbok_Okiep_filtered.vcf.gzVariant calling from GBS data:gzip-compressed .vcf files containing the raw and filtered variants (SNPs and indels) called from the genotyping-by-sequencing (GBS) data of the G. diffusa hybrid zones mapped to the Springbok genome assembly (Filter criteria: no indels, minor allele frequency 0.05, max 20% missing data, min quality phred score 20, read depth min 10 max 200). The raw GBS data is deposited on NCBI SRA under project PRJNA1181622. The .tsv file contains the corresponding sample phenotypes (pure morphotype or hybrid) and petal colour for the Soeb-Garies hybrid zone (0=yellow, 1=yellow-orange, 2=orange-yellow, 3=orange).GBS_to_Springbok_raw.vcf.gzGBS_to_Springbok_filtered.vcf.gzGBS_morphotypes.tsv