The Genome Assembly of Vitis vinifera cv. Shiraz

Figure 4

The VviTPS24 locus in V. vinifera. (a) Functional annotation of the VviTPS24 locus in the haplotypes of V. vinifera Shiraz. VviGuaS (blue) represents the polymorphic variant of VviTPS24 containing the T414S and V530M amino acid substitutions previously reported [5]. VviTPS24 (red) represents an allele without the T414S and V530M amino acid substitutions. Dotted lines depict the insertion point of a transposable element within exon 5 of VviTPS24. (b) Schematic representation of the VviTPS24 locus in the haplotype phased assemblies of nine additional V. vinifera cultivars. (c) Maximum likelihood phylogenetic tree predicted from the CDS of VviTPS24 for nine V. vinifera cultivars with V. rotundifolia as an outgroup. The CDS for all alleles including retroelement disrupted variants were manually predicted using the VviTPS24 CDS of the pinot noir PN40024 reference genome. Cultivars denoted with an asterisk () contain an insertion/deletion within the CDS of VviTPS24. (d) Presence (orange) and absence (grey) of a retroelement within VviTPS24 for 15 V. vinifera cultivars predicted using publicly available short-read data (Table S1).

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