Analyzing Gene Trees With Ease

Scientists in Japan have developed a web-based tool capable of inferring gene function, estimating gene trees and identifying sets of ancestral genes in minutes.

AsianScientist (Dec. 20, 2018) – In a study published in the journal Molecular Biology and Evolution, scientists in Japan have developed a free, web-based tool for analyzing gene trees.

Gene trees, much like family trees, trace the lineage of a particular gene from its deep ancestral roots to its still-growing stems. By comparing gene trees to species trees, which map the evolutionary history of species, scientists can track how genes change over time. The ability to build accurate gene trees relies on having access to adequate genomic data, but it takes time and effort to gather data from disparate online genomic repositories.

To simplify this process, researchers led by Professor Noriyuki Satoh of the Okinawa Institute for Science and Technology (OIST), Japan, compiled data from the NCBI and Ensembl gene banks, as well as a large database built by the Marine Genomics Unit at OIST, to create an analysis tool called ORTHOSCOPE.

ORTHOSCOPE users start an analysis by inputting the coding sequences of protein-coding genes they are interested in. They then select one of four groups of species, namely Protostomia, Deuterostomia, Vertebrata, or Actinopterygii, to focus their search. They can refine their query further by selecting specific species to sample.

Given sequence data, ORTHOSCOPE automatically constructs a new gene tree, allowing researchers to discover whether a gene is present in a species’ genome and how many copies there are. Most importantly, researchers can now rapidly infer the function of a particular gene as well as the functions of earlier versions of that gene in ancestral species.

Using ORTHOSCOPE, Satoh’s team was able to identify genes that evolved as a result of whole genome duplication, a key event in vertebrate evolutionary history. Whole genome duplication essentially quadrupled the size of the ancestral vertebrate genome, opening the door for more random mutations and the introduction of novel gene functions.

“We need to think about species evolution when we think about gene function,” said Dr. Jun Inoue, first author of the study and a staff scientist in the Marine Genomics Unit led by Satoh. “This software makes it possible to compare the phylogenetic relationship of different genes.”

The article can be found at: Inoue & Satoh (2018) ORTHOSCOPE: An Automatic Web Tool for Phylogenetically Inferring Bilaterian Orthogroups With User-selected Tax.


Source: Okinawa Institute of Science and Technology Graduate University; Photo: Pixabay.
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