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Computomics: unlocking the secrets of plant genome sequences

Thanks to the latest generation of sequencing technology, the deciphering of the complete genome of organisms is becoming faster and cheaper. The challenge is to compile the book of life from millions of DNA fragments and unlock the secrets of the human and other organisms. The young bioinformatics company Computomics in Tübingen is doing just this for crops. In contrast to the human genome, the genome of the majority of plants is still a book with seven seals.

Dr. Tobias Dezulian (l.) and Dr. Sebastian J. Schultheiß, co-founders and managing directors of Computomics, are pleased with the successful start of the company. © Computomics

Computomics – the company name is a combination of the word computer and the suffix omics, commonly used by biologists to refer to different fields of study. Examples of such fields include genomics, which deals with the complete DNA set in an organism, and transcriptomics, which examines the expression level of mRNAs. The term computomics could not be more appropriate for the service the company from Tübingen offers. The managing directors and company co-founders Dr. Sebastian J. Schultheiß and Dr. Tobias Dezulian analyse the sequencing data of crops such as maize (corn), wheat and melons for their clients in the agricultural industry (seed producers and plant breeders). A fully sequenced crop genome results in several terabytes of data. Using state-of-the-art computer algorithms, bioinformaticians assemble the entire genome from several million fragments of around 100 nucleotides. It is quite a challenge to arrange the nucleotides in the correct order due to the many repetitions. The bioinformaticians reveal the location of the sense-conveying “sentences” and “words” within the DNA sequence, i.e. the genes and exons that contain the construction plan for proteins. They can also identify epigenetic markers (short methyl residues attached to bases which are induced by environmental signals and regulate the activity of genes) and the sequence differences between individual plants. 

A view into the genome with the aim of producing more resistant crops

Computomics is specialised in the genetic analysis of crops, rice and maize. © Computomics

“We provide our clients with the information they need to grow high-yield plants, plants that are resistant to drought, nutrient deficiency or high salt concentrations. We also give tips on how to experimentally proceed further, or suggest other sequencing methods if there is insufficient data,” said Schultheiß. “Plant breeders can of course learn themselves how to analyse their sequencing data themselves,” says the 31-year-old. “However, documentation of the software is usually not available. It is easier for us to understand how bioinformatics software works as we usually have direct contact with the software developers, or have been involved in software development,” said Schultheiß, also pointing out that their scientific background and routine enables him and his team to analyse the data a lot faster. Schultheiß knows what he is talking about as his doctoral thesis, which he finished a few months ago at the Friedrich Miescher Laboratory of the Max Planck Society in Tübingen, dealt with the analysis of plant genomes using different analysis programmes. Plant breeders from around the world have regularly enquired about the possibility of applying such scientific studies for their plants. “We realized that there was a market for such analyses,” said the young entrepreneur who gained initial experience as an entrepreneur when he was at university and he provided computer services to clients. 

Plant knowledge – an ace up their sleeve

In 2011, Schultheiß and his former principal supervisor, Professor Gunnar Rätsch, joined forces with three professors from the Max Planck Institutes and the University of Tübingen who also worked in the field of plant bioinformatics. Tobias Dezulian joined them shortly after. The idea for the new company was born. In October 2012, the six scientists established Computomics, which now employs two consultants and twelve freelance scientists. Orders keep coming in and the team is expecting that the trend will continue and enable them to hire three more people in 2013.

The Computomics team holds a trump card, which is their specific knowledge of plants. “We therefore do not need to participate in the highly competitive bioinformatics services market,” said Schultheiß. Although the genomes of plants, animals and humans consist of the same letters, and the sequencing technology used to decipher them is the same, this knowledge alone is not enough. “One needs to know how plants are crossbred, how resistance genes are integrated or breeding markers identified. And this is what distinguishes us from other bioinformatics service providers,” said Schultheiß.

Further information:
Computomics GmbH & Co. KG
Dr. Sebastian J. Schultheiß (Managing Director)
Sand 14
72076 Tübingen
Tel.: +49 (0)7071/ 568 – 3995
E-mail: sebastian.schultheiss(at)computomics.com

Website address: https://www.biooekonomie-bw.de/en/articles/news/computomics-unlocking-the-secrets-of-plant-genome-sequences