Looking at evolution's genealogy from home

Date:
September 28, 2020
Source:
University of Mu"nster
Summary:
Evolution leaves its traces -- in particular -- in
genomes. Researchers used '2-n-way' software to determine the
relationships between species or individuals and compare any genome
of and for anyone.



FULL STORY ========================================================================== Evolution leaves its traces -- in particular -- in genomes. Pinpointing
its influence is a laborious process -- but one in which Dr. Ju"rgen
Schmitz and his team at the University of Mu"nster are at home. Five
years ago, the team made public a web app which can compare the genomes
of humans and animals and thus help to provide an understanding of
evolutionary developments. The Mu"nster researchers are now going
one step further: their new software -- "2- n-way" -- can compare any
genomes from and for anyone and systematically search for regions which
are characterized by the presence or absence of certain sequences -- or,
to put it simply, what is missing and where in the genome and when it
got lost or when it newly emerged. This makes it possible to recognize relationships among species or individuals. The Mu"nster researchers
have now published details of their new development -- which, like its predecessor -- is freely available on the internet -- in the journal
Genome Research.


========================================================================== Ju"rgen Schmitz, a biologist and zoologist at the Institute of
Experimental Pathology at Mu"nster University's Faculty of Medicine, led
the study together with Dr. Gennady Churakov and for him it represents
a "unique, forward-pointing opportunity to take a close look at the
mutability of multiple genomes." It means that not only genome evolutions
can be analysed, but also the occurrence of genetic diseases as a result
of deletions or insertions -- i.e. the loss of a DNA segment or the
insertion of a new one. The decisive difference between the new model
and its predecessor, GPAC -- which has been used hundreds of thousands
of times since it was activated -- is that 2-n-way can sequence any
number of genomes. "The tool is a response to the modern genomic era --
and it is a piece of software which, despite the complexity behind it,
can be used by anyone, whether a non-medical layperson, a student or a professor. Last but not least, the tool links up a very wide range of
areas, such as evolution, population genetics and medicine" says Schmitz.

The term "2-n-way" is derived from two abbreviations used by specialists:
"2- way" stands for the linear alignment of sequences to be compared;
and "n-way" means the combination of individual components and the
subsequent multiple comparison. But users do not need to know such
background information. "They only have to download on the internet the
genomes they want to compare. One source, for example, is the website
of the National Center for Biotechnology Information (NCBI) in the
USA. The genomes fed into 2-n-way are then aligned with each other by
the software. The genes which are of particular interest are selected
from the genomic "coordinates" -- or "loci," to give them their proper technical term. "The search can be geared for example to some or all of
the so- called jumping genes, i.e. those genes which have changed their position in the genome," Schmitz explains.

If for example a search is made for certain jumping genes in humans, chimpanzees or rhesus monkeys, the results are given in a table with
"plus" and "minus." If the evaluation contains two finds and an exact
gap in the rhesus monkey, then the conclusion is that humans and
chimpanzees have inherited the jumping gene from a common ancestor
and are therefore closely related -- while the rhesus monkey still
displays the original locus without any insertion and is therefore only distantly related. However, the software not only indicates whether a
certain insertion is present, but also the region in which it is to be
found. In addition to the table of correlations, 2-n-way also provides
the user with a list of DNA sequences for all loci.

Although the new tool has only just been made public, the team of
researchers is already looking ahead -- working on the simplification
of the individual creation of 2-ways, i.e. the alignment. "This is a
process which, at the moment, can take up a lot of time -- which is a
bit annoying," says Schmitz.

Otherwise, he comments, the tool "has been tested intensively and is
absolutely perfect."

========================================================================== Story Source: Materials provided by University_of_Mu"nster. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Gennady Churakov, Fengjun Zhang, Norbert Grundmann, Wojciech
Makalowski,
Angela Noll, Liliya Doronina, Ju"rgen Schmitz. The
multicomparative 2-n- way genome suite. Genome Research, 2020;
DOI: 10.1101/gr.262261.120 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/09/200928133145.htm

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