Casting Light on the Evolution of Nightshades

With the participation of Helmholtz Zentrum München, the Tomato Genome Consortium, a group of more than 300 scientists from 14 countries, has sequenced the tomato genome with its approximately 35 000 genes. The Department of Plant Genome and Systems Biology manages a range of several plant genome databases, provided important infrastructure for the data management and carried out gene family and comparative genome analyses. 

The Tomato Genome Consortium (TGC), a group of more than 300 scientists from 14 countries, has sequenced the genome of the domesticated tomato and its closest wild relative (Solanum pimpinellifolium). Together with other research centers in Germany, Helmholtz Zentrum München was involved in the bioinformatics analysis and annotation of the genome sequences.

The research group led by Klaus Mayer at the Department of Plant Genome and Systems Biology was responsible for data management, database infrastructure and dissemination as well as gene family and comparative genome analyses. The sequences provide the most detailed insights to date into the tomato genome. Thus, the approximately 35 000 genes of the tomato with their genomic position and a large portion of their likely functions are now known.

The tomato is a member of the Solanaceae or nightshade family. The Solanaceae family includes potatoes, bell peppers and eggplant. Worldwide, it is the most important family of vegetable plants – both with regard to its economic significance and the quantity produced. Members of the Solanaceae family are used as food, spices and as medicinal plants. The new sequences provide a reference to identify important genes in related species.The sequences also open up insights into the diversification of the tomato and the adaptation to new environmental conditions.

They reveal that 60 million years ago triplication of the tomato genome occurred. After that, a large part of the triplicated genes were lost. However, some exist even until today and control the most important breeding traits of the tomato including strength, fleshiness and fruit coloring.

The results are an important basis for further research to optimize the production of tomatoes and other crops. The resistance to pests, diseases and drought, which in part have been lost during the domestication of the plant, is of particular importance.

In gene sequence annotation, the position of exons and introns, protein-encoding regions including the encoded protein and its possible functions, promoter elements and repetitive DNA elements is attached (annotated) to the actual DNA sequence.