Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris)

• Published in: Scientific reports Vol. 10; no. 1; p. 18993
• Main Authors: Ramos, Miguel J. N., Coito, João L., Faísca-Silva, David, Cunha, Jorge, Costa, M. Manuela R., Amâncio, Sara, Rocheta, Margarida
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 04.11.2020; Nature Publishing Group
• Subjects: 631/449; 631/449/2491; 631/449/2492; Domestication; Flowers; Frameshift Mutation; Gene Expression Regulation, Plant; Genomes; Hermaphrodites; Humanities and Social Sciences; multidisciplinary; Plant Proteins - genetics; Polymorphism, Single Nucleotide; Portugal; Reproductive strategy; RNA Editing; Science; Science (multidisciplinary); Sex; Single-nucleotide polymorphism; Vitis - classification; Vitis - genetics; Vitis - growth & development; Vitis vinifera sylvestris; Vitis vinifera vinifera; Whole Genome Sequencing - methods; Portugal
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-76012-6

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 .