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

Abstract

Vitis is a relevant genus worldwide. The genome of a Vitis vinifera representative (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. vinifera domestication. Considering that grapevines for wine production (V. v. vinifera, hereafter vinifera) have evolved from V. v. sylvestris (hereafter sylvestris), or from a shared no-longer existing ancestor, both subspecies are quite close, but sylvestris has not been domesticated and still exist nowadays, preserving wild characteristics, making it a good material to provide insights into vinifera domestication. The difference in the reproductive strategy between both subspecies is one of the characteristics that sets them apart. While vinifera flowers are hermaphrodite with functional male and female organs, sylvestris is mostly dioecious. Male plants present flowers lacking functional carpels unable to produce grapes and female individuals have flowers with reflexed stamens producing infertile pollen but able to exhibit small and acidic grapes.In this paper, we describe the re-sequencing of the genomes from a male and a female individual of the wild sylvestris and its comparison against the reference vinifera genome.Vitis vinifera vinifera (hereafter vinifera) is a worldwide important crop, mainly due to wine production. Vinifera has already two sequenced genome versions 1,2 , obtained from PN40024 genotype, a Pinot Noir 1 variety back crossed to reach 93% homozygosity. The contribution of these vinifera genomes knowledge is unquestionable, however, they are limited in providing information on particular changes that occurred during domestication. One of the most relevant subspecies of V. vinifera history is Vitis vinifera sylvestris (hereafter sylvestris), which some authors have referred as vinifera 3,4 . 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 system 5 . The dioecious sylvestris, produce female individuals with reflexed stamens, where infertile pollen is produced, whereas male individuals are unable to produce grapes as flowers lacks a functional carpel 6 .In the Vitis genus, a number of studies have contributed to partially uncover the genomic regions that may be responsible for the differences in flower development between hermaphrodites and dioecious plants 7-9 . However, the identified regions (chr2:4,907,434..5,050,616) 7,8 are poorly sequenced, assembled and annotated in the canonical reference genome 1-3,5,9 . Recently, two new studies 10,11 suggested the possible players involved in sylvestris sex specification by uncovering INAPERTURATE POLLEN1 (INP1) as a male sterility gene and proposing a set of genes resp...

RNA editing in inflorescences of wild grapevine unveils association to sex and development

“…Although the full Vitis genome is available (Jaillon et al, 2007) it could not be used to establish a precise comparison between DNA-RNA, since the subject of the present research concerns the wild dioecious subspecies V. v. sylvestris. Thus, to accurately determine editing sites in both male (Ma1_2014) and female (Fe1_2014) plants, the genomes of these plants were re-sequenced (Ramos et al, 2020). (Figures 2A and S1).…”

“…In-depth analysis revealed that male inflorescences are heterozygous in 33% of female exclusive events (27716), contrasting with male specific RNA editing events (6301) where the female inflorescences are heterozygous in 8% (483) (Ramos et al, 2020). By being heterozygous, male flowers do not need RNA editing to translate the same proteins as female flowers.…”

“…Filters set to the SNP calling were SnpCluster (more than 2 SNPs found in cluster of size=10), LowQual (SNP with quality score < 30), LowCov (SNP with coverage < 20) and Mask (SNP is at least 10 base near to indel location). For more details, refer to Ramos et al, 2020.…”