SOMmelier—Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks

Abstract

Background: Whole-genome studies of vine cultivars have brought novel knowledge about the diversity, geographical relatedness, historical origin and dissemination, phenotype associations and genetic markers. Method: We applied SOM (self-organizing maps) portrayal, a neural network-based machine learning method, to re-analyze the genome-wide Single Nucleotide Polymorphism (SNP) data of nearly eight hundred grapevine cultivars. The method generates genome-specific data landscapes. Their topology reflects the geographical distribution of cultivars, indicates paths of cultivar dissemination in history and genome-phenotype associations about grape utilization. Results: The landscape of vine genomes resembles the geographic map of the Mediterranean world, reflecting two major dissemination paths from South Caucasus along a northern route via Balkan towards Western Europe and along a southern route via Palestine and Maghreb towards Iberian Peninsula. The Mediterranean and Black Sea, as well as the Pyrenees, constitute barriers for genetic exchange. On the coarsest level of stratification, cultivars divide into three major groups: Western Europe and Italian grapes, Iberian grapes and vine cultivars from Near East and Maghreb regions. Genetic landmarks were associated with agronomic traits, referring to their utilization as table and wine grapes. Pseudotime analysis describes the dissemination of grapevines in an East to West direction in different waves of cultivation. Conclusion: In analogy to the tasks of the wine waiter in gastronomy, the sommelier, our ‘SOMmelier’-approach supports understanding the diversity of grapevine genomes in the context of their geographic and historical background, using SOM portrayal. It offers an option to supplement vine cultivar passports by genome fingerprint portraits.

Genetic Diversity of Armenian Grapevine (Vitis vinifera L.) Germplasm: Molecular Characterization and Parentage Analysis

“…According to SOM analysis, cultivated grapes occurred initially in South Caucasus and Fertile Crescent (South East Anatolia, North Lebanon and Syria) and then disseminated towards the Mediterranean world to the West and into the East towards Iran and the Middle East (Tajikistan, Uzbekistan), Afghanistan, and India. The northern and southern ways into the west agree with the distribution of settlements of Greeks and Phoenicians, respectively [ 15 ].…”

“…After that, the migration of cultivars took place along with the spreading of wine culture from their primary domestication center in the Near East to Mesopotamia, Levant, Africa, and Europe [ 10 , 11 , 12 , 13 ]. Recently, researchers applied SOM (self-organizing maps) portrayal, a neural network-based machine learning method, with the aim of re-analyzing the genome-wide single nucleotide polymorphism (SNP) data of 783 grapevine cultivars collected from Middle Asia to the Iberian Peninsula and from overseas regions [ 14 , 15 ]. Based on the obtained results, genomic landscape and the different sample similarity plots were consistent with the historical knowledge and mirror the geographical distribution of grape varieties, indicated main pathways of grape dissemination and genome-phenotype associations about grape usage.…”

The Evolving Faces of the SARS-CoV-2 Genome

“…We recently adjusted the method to infer developmental trajectories in sample and gene state space to describe tissue differentiation [ 16 ]. Application of SOM portrayal to large worldwide collections of genomic data, namely of humans [ 17 ] and vine accessions [ 18 ], deciphered genomic footprints of human migration and of dissemination vine cultivation over geographic regions during the last thousands of years. In continuation of this concept, we aimed at characterizing footprints of the spread and evolution in the SARS-CoV-2 genome since its emergence in late 2019 by means of SOM portrayal.…”

Special Issue “Disentangling Mechanisms of Genomic Regulation of Cell Functions at the Gene Level”

“…This Special Issue collects seven publications addressing different topics around genomic regulation of cell functions at the gene level as examples illustrating various aspects of this field of discovery. Two original research publications deal with temporal aspects stored in the genome on completely different timescales; one on the scale of thousands of years and the other on the scale of minutes to hours [2,3]. Both works make use of similarity relations, with one considering the genomes of vine accessions [2] and the other considering the transcriptomes of single cells extracted from the flatworm [3].…”

“…Two original research publications deal with temporal aspects stored in the genome on completely different timescales; one on the scale of thousands of years and the other on the scale of minutes to hours [2,3]. Both works make use of similarity relations, with one considering the genomes of vine accessions [2] and the other considering the transcriptomes of single cells extracted from the flatworm [3]. The vine genome reveals "slow" mutational modifications, which enable reconstructing paths of distribution of wine agriculture and usage from the Middle East towards Western Europe on a long time-scale over many centuries.…”