## 2 Results  
### Isolated VviTPS04 and -10-Like Paralogues  
The PN40024 genome showed that the forward strand of the _VviTPS04_ locus had a start codon 27 bp upstream of the start codon for the _VviTPS10_ locus [1, 7]. These two loci had high homology with a total of 28 _VviTPS_-like loci from the three phased diploid genomes (8 in CH, 9 in CR, and 11 in CS), predicted by [PERSON] et al. (2020). The 28 phased diploid and two PN40024 gDNA models (hereafter referred to as reference sequences) were subsequently used to map short reads from 11 different genotypes that were used in the WGRS effort by reference [37]. This resulted in 112/330 consensus sequences with near-complete coverage, with a further 35 that lacked coverage at the 5\({}^{\prime}\) terminal region, relative to the reference sequence. Only a single reference sequence (_CRTPS105_) did not result in the recovery of at least a single consensus sequence from the 11 WGRS genotypes selected for this analysis. This resulted in 147 consensus and 30 reference sequences that were subsequently aligned and their phylogenetic relationships assessed, as shown in Figure 1 (a higher-resolution version of the complete tree is available in Supplementary Figure S1). The lowest pairwise identity in this alignment was 89.2%, with the highest being 99.5%, indicating that all sequences in the multiple sequence alignment (MSA) were highly similar. The phylogenetic tree revealed that _VviTPS04_ and _VviTPS10_-like sequences were grouped into a distinct clade, coloured in grey in Figure 1. Eight of the sequences in this grey clade lacked coverage at the terminal end. The _VviTPS04_-like sequences (containing the additional 27 bp at the 5\({}^{\prime}\) terminal end) could be separated further from the _VviTPS10_-like sequences, forming distinct subclades. The _VviTPS10_ gDNA-containing subclade had an orthologous gDNA model from CS (_CSTPS086_) with eight gDNA models predicted from the WGRS data. The subclade containing _VviTPS04_-like sequences had two near-identical reference sequences (_CSTPS051_ and _CHTPS062_) to _VviTPS04_. Ten gene models in this clade were predicted from the WGRS mapping. Incongruence between the PN40024 _VviTPS04_ gene model and the gene model predicted for the Pinot nori TA-379 WGRS genotype was observed. The short branch lengths indicated high homology for sequences within the grey clade, despite the bifurcation for the _VviTPS04_-like and _VviTPS10_-like subclades. The remaining sequences were grouped into five distinct clades (Supplementary Figure S1). These sequences were near-identical at the 5\({}^{\prime}\)-region, with 24 lacking coverage. All 175 sequences in the MSA had a near-identical 3\({}^{\prime}\)-region. The high homology in the terminal ends meant that three primers could be designed to target 112/175 sequences: Primer A and B targeted the 27-bp difference at the 5\({}^{\prime}\) region, while a single conserved 3\({}^{\prime}\) primer was designed. These results are shown in Table 1, where groups A and B correspond to the binding of their respective forward primers, whereas group C reflects the sequences that lack coverage at these primer-binding regions. The primer-binding circles in the phylogenetic tree (Figure 1) use the same bin colours used in Table 1. Nucleotide sequences for the reference genes and those predicted by mapping of the WGRS data is available is Supplementary File S1. It should be noted that the 27-bp difference results in two start codons being in frame, shown in Figure 2C. The primers were validated through PCR amplification using gDNA from nine genotypes, as shown in Figure 2A,B. The expected gDNA band of \(\pm\)2260 bp was present in all genotypes, with certain genotypes showing a second band at \(\pm\)1700 bp for primer set B (Figure 2B). A second band was notably absent for CH using either primer combination. For primer set A, a 2000-bp amplicon was observed in PN, with this band also faintly visible in six other genotypes (Figure 2A). Primer set A resulted in a unique second amplicon for CS.