W

WGS

Modules for genotyping and characterisation of bacterial isolates utilizing whole-genome-sequencing data

This repo aims to provide a general pipeline for WGS processing.

In this project, we question the origin of two popular grape varieties in France and Argentina named respectively Cot and Malbec. According to the literature, Cot's original cuttings were brought from France (Cot) to Argentina (Malbec) before the phylloxera epidemic destroyed most of the vineyards by the end of the 19th century.

We use whole-genome resequencing (WGS) data from different accessions to track their evolution history and identify new genetic markers that can distinguish them. A stringent variant calling procedure is established to identify reliable single-base variations (SNPs and SNVs). This article demonstrates the diversification process behind the somatic mutation that transformed Cot in a new variety of wines with sweeter tannins and a red fruit expression.

Article: Calderón L, Mauri N, Muñoz C, et al. Whole genome resequencing and custom genotyping unveil clonal lineages in 'Malbec' grapevines (Vitis vinifera L.). Scientific Reports. 2021 Apr;11(1):7775. DOI: 10.1038/s41598-021-87445-y. PMID: 33833358; PMCID: PMC8032709.