The genomic diversification of grapevine clones.

BACKGROUND:Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fifteen Zinfandel winegrape clone genomes were sequenced and compared to one another using a highly contiguous genome reference produced from one of the clones, Zinfandel 03. RESULTS:Though most heterozygous variants were shared, somatic mutations accumulated in individual and subsets of clones. Overall, heterozygous mutations were most frequent in intergenic space and more frequent in introns than exons. A significantly larger percentage of CpG, CHG, and CHH sites in repetitive intergenic space experienced transition mutations than in genic and non-repetitive intergenic spaces, likely because of higher levels of methylation in the region and because methylated cytosines often spontaneously deaminate. Of the minority of mutations that occurred in exons, larger proportions of these were putatively deleterious when they occurred in relatively few clones. CONCLUSIONS:These data support three major conclusions. First, repetitive intergenic space is a major driver of clone genome diversification. Second, clones accumulate putatively deleterious mutations. Third, the data suggest selection against deleterious variants in coding regions or some mechanism by which mutations are less frequent in coding than noncoding regions of the genome

Identification of grapevine clones via high-throughput amplicon sequencing: a proof-of-concept study

Wine cultivars are available to growers in multiple clonal selections with agronomic and enological differences. Phenotypic differences between clones originated from somatic mutations that accrued over thousands of asexual propagation cycles. Genetic diversity between grape cultivars remains unexplored, and tools to discriminate unequivocally clones have been lacking. This study aimed to uncover genetic variations among a group of clonal selections of 4 important Vitis vinifera cultivars: Cabernet sauvignon, Sauvignon blanc, Chardonnay, and Merlot, and use this information to develop genetic markers to discriminate the clones of these cultivars. We sequenced with short-read sequencing technology the genomes of 18 clones, including biological replicates for a total of 46 genomes. Sequences were aligned to their respective cultivar's reference genome for variant calling. We used reference genomes of Cabernet sauvignon, Chardonnay, and Merlot and developed a de novo genome assembly of Sauvignon blanc using long-read sequencing. On average, 4 million variants were detected for each clone, with 74.2% being single nucleotide variants and 25.8% being small insertions or deletions (InDel). The frequency of these variants was consistent across all clones. From these variants, we validated 46 clonal markers using high-throughput amplicon sequencing for 77.7% of the evaluated clones, most of them small InDel. These results represent an advance in grapevine genotyping strategies and will benefit the viticulture industry for the characterization and identification of the plant material

Monitoring extreme meteo-marine events in the Mediterranean area using the microseism (Medicane Apollo case study)

Microseism is the continuous background seismic signal caused by the interaction between the atmosphere, the hydrosphere and the solid Earth. Several studies have dealt with the relationship between microseisms and the tropical cyclones, but none focused on the small-scale tropical cyclones that occur in the Mediterranean Sea, called Medicanes. In this work, we analysed the Medicane Apollo which impacted the eastern part of Sicily during the period 25 October–5 November 2021 causing heavy rainfall, strong wind gusts and violent sea waves. We investigated the microseism accompanying this extreme Mediterranean weather event, and its relationship with the sea state retrieved from hindcast maps and wave buoys. The spectral and amplitude analyses showed the space–time variation of the microseism amplitude. In addition, we tracked the position of Apollo during the time using two different methods: (i) a grid search method; (ii) an array analysis. We obtained a good match between the real position of Apollo and the location constraint by both methods. This work shows that it is possible to extract information on Medicanes from microseisms for both research and monitoring purposes.peer-reviewe

Microseism and medicane Apollo : a new approach to investigate the Mediterranean extreme weather events

Microseism is the most continuous and ubiquitous seismic signal on the Earth and is caused by the interaction between the atmosphere, the hydrosphere and the Solid Earth. In literature, there are several studies that deal with the relationship between microseism and cyclonic activity considering in particular hurricanes, tropical cyclones and typhoons. However, the relationships between microseism and the small-scale tropical cyclones that occur in the Mediterranean Sea, called Medicanes, have never been analysed. For this reason, we considered the Medicane Apollo, which developed in the Ionian Sea and impacted the eastern part of Sicily during the period 25th October to 5th November 2021 causing heavy rainfall (> 400 mm/48h), strong wind gusts (104 km/h) and violent sea waves (significant wave height > 3.5 m). Furthermore, the heavy rainfall induced by the presence of Apollo, caused damage to infrastructure and agriculture forcing the Sicilian regional government to declare a state of emergency for 32 municipalities (in the provinces of Catania, Messina, Siracusa and Ragusa) that were mostly affected by the Medicane Apollo.peer-reviewe

Whole-genome sequencing and SNV genotyping of 'Nebbiolo' (Vitis vinifera L.) clones

'Nebbiolo' (Vitis vinifera) is among the most ancient and prestigious wine grape varieties characterised by a wide genetic variability exhibited by a high number of clones (vegetatively propagated lines of selected mother plants). However, limited information is available for this cultivar at the molecular and genomic levels. The whole-genomes of three 'Nebbiolo' clones (CVT 71, CVT 185 and CVT 423) were re-sequenced and a de novo transcriptome assembly was produced. Important remarks about the genetic peculiarities of 'Nebbiolo' and its intra-varietal variability useful for clonal identification were reported. In particular, several varietal transcripts identified for the first time in 'Nebbiolo' were disease resistance genes and single-nucleotide variants (SNVs) identified in 'Nebbiolo', but not in other cultivars, were associated with genes involved in the stress response. Ten newly discovered SNVs were successfully employed to identify some periclinal chimeras and to classify 98 'Nebbiolo' clones in seven main genotypes, which resulted to be linked to the geographical origin of accessions. In addition, for the first time it was possible to discriminate some 'Nebbiolo' clones from the others

Analisi bioinformatica di genomi e di trascrittomi utilizzando dati ottenuti con tecnologia Next Generation Sequencing

Report dell\u2019attivit\ue0 di ricerca svolta nell'ambito dell\u2019impiego di tecnologie Next Generation Sequencing per analizzare le caratteristiche genetiche di diverse specieReport of research activity performed in the aim of applying Next Generation Sequencing technologies to characterise at genenomic level different specie