Hybridity has a greater effect than paternal genome dosage on heterosis in Sugar Beet

The x-axis shows the base position within a sequencing read, and the y-axis shows the average error rate of all reads at each position. Pair-end sequencing data are plotted together, with the first 144 bp representing read 1 and the following 144 bp for read 2. 3. Classification of the sequence reads.

Raw sequencing data must undergo quality control steps. Reads are classified as either clean, low quality, containing uncertain nucleotides, or adapter related. 4. Statistics of the sequence data.

The details of each sequencing run are displayed herein including number and length of sequence, number and length of valid sequences following quality control, the ratio of clean data to raw data, the overall error rate, the percentage of bases with higher Phred score than 20 and 30, and percentage GC content. 5. Statistics of the reference genome. The details of the sugar beet reference genome used for alignment are displayed herein including the total number of the assembled genomic sequences, the total length of the assembled genomic sequence, the percentage GC content, the proportion of unknown sequence, the length of the scaffold N50 and scaffold N90. 6.

Statistics of mapping rate, depth and coverage, plus tag-related statistics. The mapping statistics are displayed herein including the number of clean reads mapped to the reference genome assembly, the total effective reads in clean data, the number of unique tags, the number of tags with depth > 4, the ratio of the reference genome assembly mapped reads to the total sequenced clean reads, the average depth of mapped reads at each site, the percentage coverage with more than one read at each site and ≥4X coverage at each site. 7.

Statistics of enzymatic digestion. The details of enzymatic digestion among clean reads, including the number of pair-ended clean reads, the number of enzyme-catched reads, the number of completely cut reads, the ratio of enzyme-catched reads to total clean reads, and the ratio to completely cut reads to total clean reads. 8. Statistics of SNP detection and annotation.

The details of the detected SNPs using SAMtools and subsequent annotation using ANNOVAR are displayed herein, including upstream, exonic, intronic, splicing, downstream, and intergenic SNPs, point mutations, and genome-wide heterozygosity rate. Funding: Irish Research Council (IRC Grant number GOIPG/2014/1021) and Science Foundation Ireland (SFI Grant number 13/IA/1820).