An effective tool for bioinformatics from FST, UD

An article has been published first in a prestigious British scientific journal about the computer software developed at the Faculty of Science and Technology of the University of Debrecen, which can efficiently facilitate certain evolutionary genomics research efforts.

MTA-DE Lendület Evolúciós Filogenomikai Kutatócsoport [“Lendület” Evolutionary Phylogenomics Research Group of the Hungarian Academy of Sciences and the University of Debrecen] at UD’s Faculty of Science and Technology has been recently working on understanding the bio-geographical conditions and evolutionary history of the Eurasian steppe. The members of the research group have taken part in several research trips, with destinations ranging from Mongolia to Ukraine.

The head of the research group, Gábor Sramkó, said that, during the exploration and examination of the local plants there, they carried out genomic testing methods that correspond to the international practice standards of today’s biological research. That is to say, they applied methods based on the entire genetic material – all the DNAs of the cell – and thus gained insight into the development history of this bio-geographical region.

“As our research progressed, more and more genomic information became available to us to sort out the evolutionary descent relationships. During their analysis, the question was raised whether it would be possible to extract more information from the expensive genomic data by separating the DNA extracted from the cells based on its place of origin. The reason for this query was that, since in organisms with a nucleus, not only the nucleus contains genetic material, but also the cell organelles, i.e., mitochondria and plastids. Their evolutionary history may differ from the one preserved in the cell nucleus, so additional information can be obtained from the comparison of the data found in cell organelles and cell nuclei. This information could point to, for example, the mixing of species and hybridization that occurred in the past, and it can also put the results in a wider context,” said Gábor Sramkó.

The head of the research group underlined that he and his colleagues realized that the sorting of DNA according to place of origin from genomic data could also be solved by using information technological or, more specifically, bio-informatics related methods used in the field of biology. Therefore, the bio-informatician of the research group, Levente Laczkó, developed a computer program that can automatically separate DNA from the nucleus and organelles based on the input data, and then reconstruct the sequence information from the latter. Then Sándor Jordán, a doctoral student at Juhász-Nagy Pál Biológiai Doktori Iskola [Pál Juhász-Nagy Doctoral School of Biology], carried out in silico testing and fine-tuning of the software on open access data. The experiments showed that the new software could significantly facilitate supplementing the results of research that does not take DNA origin into account, and the process can be automated using the new open source code. This provided the researchers with a useful tool.

The results and findings were recently published in the prestigious British international journal Methods in Ecology and Evolution. Find the full text of the article, including a summary in Hungarian, by clicking here.

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