Abstract
The Vitis vinifera L. terpene synthase (VviTPS) family was comprehensively annotated on the phased diploid genomes of three closely related cultivars: Cabernet Sauvignon, Carménère and Chardonnay. VviTPS gene regions were grouped to chromosomes, with the haplotig assemblies used to identify allelic variants. Functional predictions of the VviTPS subfamilies were performed using enzyme active site phylogenies resulting in the putative identification of the initial substrate and cyclization mechanism of VviTPS enzymes. Subsequent groupings into conserved catalytic mechanisms was coupled with an analysis of cultivar-specific gene duplications, resulting in the identification of conserved and unique VviTPS clusters. These findings are presented as a collection of interactive networks where any VviTPS of interest can be queried through BLAST, allowing for a rapid identification of VviTPS-subfamily, enzyme mechanism and degree of connectivity (i.e., extent of duplication). The comparative genomic analyses presented expands our understanding of the VviTPS family and provides numerous new gene models from three diploid genomes.
Highlights
Grapevine has an extensive domestication history that includes various non-vinifera hybridizations, resulting in high levels of heterozygosity (Minio et al, 2017)
The results presented for the draft diploid genomes provide new chromosome specific information of the Vitis vinifera L. terpene synthase (VviTPS)-g subfamily
The availability of new genomic resources allowed for a comparative analysis of the VviTPS family, expanding on what the PN40024 genome offered
Summary
Grapevine has an extensive domestication history that includes various non-vinifera hybridizations, resulting in high levels of heterozygosity (Minio et al, 2017). The sequencing of the Vitis vinifera cultivar Pinot Noir resulted in the first genome of a woody crop species (Jaillon et al, 2007; Velasco et al, 2007). Inbreeding of Pinot Noir simplified the genome to near homozygosity (93%) which facilitated sequencing of PN40024 (Jaillon et al, 2007). A heterozygous clone of Pinot Noir, ENTAV115, was sequenced but difficulties in assembly of the heterozygous and highly repetitive regions resulted in a fragmented genome, limiting its usability (Velasco et al, 2007; Figueroa-Balderas et al, 2019). Continuous improvement over the last decade resulted in numerous assemblies and annotations of the PN40024 reference genome with the latest version (12X.v2 assembly and VCost.v3 annotation) improving the contig coverage and orientation by 14% over the previous assembly (12X.v0) and annotation (v1). 2.64 Mbp of contig sequences remain unmapped (chr. 00) while the orientation of numerous mapped contigs remain uncertain (Canaguier et al, 2017)
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