A method from the Czech Republic can change global genome research
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More than 15 years of research has produced a major breakthrough that will benefit scientists around the world across disciplines, according to representatives of the Academy of Sciences.

“The method of genome polarization – diem – allows us to quickly and efficiently find places in genomes where there is no gene flow between species. That is, places that are responsible for the emergence of new species,” explained the author of the method, Stuart JE Baird from the Institute of Vertebrate Biology (ÚBO) of the Academy of Sciences of the Czech Republic.

At the same time, the method can also be used to find places where gene flow still occurs. “Such places can have an important role for the organism to adapt to some external conditions,” added his colleague from ÚBO Natália Martínková, who participated in the study in the last two years.

The discovery of “enhancing” genetic exchanges

In practice, “diem” (Diagnostic Index Expectation Maximisation) makes it possible to see, for example, which parts of the Neanderthal genome are still present in the human genome.

“Some Neanderthal genes are known to cause greater susceptibility to various diseases in human carriers,” Martínková noted.

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In the case of mice, for example, researchers using a new method found that two species relatively recently exchanged part of their genetic information. Some populations of the western house mouse have acquired resistance to pesticides through genetic exchange. The Mediterranean mouse has acquired genes that increase its sense of smell.

“Both species of mice thus acquired genes that improve their characteristics, and therefore the ability to survive in an environment altered by humans,” explained Martínková.

Photo: ÚBO archive

Natália Martínková and Stuart JE Baird

According to Baird, archaeologists will especially appreciate the new method when searching for archaic sections in the human or other genome. Evolutionary biologists are said to be excited about the possibility of tracking advantageous sections of genomes that occur across species, and ecologists will have the opportunity to use these sections in genomes as so-called biomarkers of earlier expansions.

Polarization of genomes

Scientists have been interested in the origin of species for centuries. With the discovery of PCR (polymerase chain reaction) in 1983 and the subsequent advent of molecular genetics, they got a tool to study the development of individual species or entire groups.

“Thanks to molecular genetics, we discovered, for example, that there is a hybrid zone of hedgehogs, bats and mice in the Czech Republic. So two different species or subspecies are meeting here,” Baird mentioned. The researchers also calculated when these species diverged from each other and where each particular species is found.

Later, thanks to the methods of “massively parallel sequencing” (next generation sequencing), they received a tool to examine entire genomes – how to obtain even more precise information about the evolution of organisms.

“But the problem with genomes is that they’re huge. The mouse has 2,716,965,481 base pairs, the human genome is only about 10 percent longer,” pointed out Martínková. That’s why scientists sometimes say that a single genome contains as much text as a small town library.

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“Until recently, genome analyzes that took several days or weeks required computers with enormous computing capacity, or the analyzes were run through remote servers,” added Baird.

Thanks to the diem method, analyzes are now more accurate and much faster. “Diem polarized 38 million genetic traits in less than three hours. We have not even attempted such a large amount of data with existing methods. We tried 120,000 characters, which Diem calculated in about three quarters of an hour, while the existing method took 13 hours on the same eight-year-old computer,” explained Martínková.

According to the press release of the Academy of Sciences of the Czech Republic, science is a very competitive environment where the rule “publish or perish” applies and favors quick results. The story of the creation of a new method for genome analysis is therefore non-standard, Baird worked on the method for over 15 years. During his research, he repeatedly asked the Grant Agency of the Czech Republic for research support, but the grant was not awarded.

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