Abstract
The first genome of Vitis vinifera vinifera (PN40024), published in 2007, boosted grapevine related studies. While this reference genome is a suitable tool for the overall studies in the field, it lacks the ability to unveil changes accumulated during V. v. vinifera domestication. The subspecies V. v. sylvestris preserves wild characteristics, making it a good material to provide insights into V. v. vinifera domestication. The difference in the reproductive strategy between both subspecies is one of the characteristics that set them apart. While V. v. vinifera flowers are hermaphrodite, V. v. sylvestris is mostly dioecious. In this paper, we compare the re-sequencing of the genomes from a male and a female individual of the wild sylvestris, against the reference vinifera genome (PN40024). Variant analysis reveals a low number but with high impact modifications in coding regions, essentially non-synonymous single nucleotide polymorphisms and frame shifts caused by insertions and deletions. The sex-locus was manually inspected, and the results obtained are in line with the most recent works related with wild grapevine sex. In this paper we also describe for the first time RNA editing in transcripts of 14 genes in the sex-determining region, including VviYABBY and VviPLATZ.
Highlights
The first genome of Vitis vinifera vinifera (PN40024), published in 2007, boosted grapevine related studies
As transitions over transversions (Ti/Tv) ration has been reported dependent of the genomic context of the SNPs27, we have evaluated Ti/Tv on introns, exons with synonymous Single Nucleotide Polymorphisms (SNPs) (1.9), exons with non-synonymous SNPs (1.4) and intergenic regions (2.2) (Fig. 2c)
We found RNA editing in the 3′ UTR transcripts of VviYABBY, in female flower at developmental stage D, where a thymine was replaced by an adenosine in some transcripts (Supplementary Figure S8a)
Summary
The first genome of Vitis vinifera vinifera (PN40024), published in 2007, boosted grapevine related studies. We compare the re-sequencing of the genomes from a male and a female individual of the wild sylvestris, against the reference vinifera genome (PN40024). Sylvestris, free from human selection, may provide clues to explain vinifera domestication This human intervention was an economically important step for grapevine, responsible for morphological changes that include larger berry and bunch size, higher sugar content, altered seed morphology, and a shift from dioecy to a hermaphroditic mating s ystem[13]. In the Vitis genus, several studies have contributed to partially uncover the genomic regions that may be responsible for the differences in flower development between hermaphrodites and dioecious p lants[15,16,17]. RNA editing, defined as post-transcriptional alterations of RNA molecules by insertion, deletion or modification, not including processes as splicing, capping or polyadenylation[20], may contribute to sex differentiation in V. v. sylvestris
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