DOMINO for biologists: the new app that allows to reconstruct the evolution of all the species.

Researchers from the University of Barcelona have developed an App to select genomic biomarkers at different levels of taxonomic resolution and with either Next Generation Sequencing NGS data or Multiple Sequence Alignments MSA as input.

Here we introduce you to DOMINO (Development Of Molecular markers In Non-model Organisms). Are you ready to play?

 

“Somewhere, something incredible is waiting to be known.” Carl Sagan, astrophysicist and science writer.

 

Tree of life. Source: Pixabay.

 

How are evolutionary processes studied?

One of the great challenges in phylogenetics/genomics (study of evolutionary relationships between several species), phylogeography (study of selection and demographic factors responsible for the distribution of species) and population genetics and genomics (definition of genes and genomic areas affected by various evolutionary processes) is the discovery of new molecular markers. In addition, this process is hindered if the study focused on organisms considered as non-model (those not usually employed in science), since their genome has not yet been sequenced and is therefore unknown.

 

Study of evolutionary processes. a) Phylogenetic tree of life showing its 3 main domains.  b) Phylogeography of different species of Rhagoletis neotropical fluit flies in South America, according to their wing pattern and shape. c)  Population genetics/genomics. Allele frequency changes along 50 generations. Sources: a) Wikimedia. b) BrasilTotal. c)  Wikimedia

 

What has next generation sequencing technologies contributed to the development of evolutionary molecular markers? Traditionally, phylogenetic inferences  (generation of phylogenetic trees  have been made based on a single or a few biomarkers, leading to erroneous results and conclusions. Fortunately, with the advent of Next-Generation Sequencing technologies or NGS, researchers are able to obtain a large number of genetic/genomic markers as ecological and evolutionary indicators. However, not all markers found are informative at all taxonomic or phylogenetic levels.

In this sense, current biomarker selection tools have certain limitations, such as the impossibility of using raw genomic data (new biomarkers discovery) or the lack of flexibility.

 

Why is DOMINO better than traditional marker selection methods?

DOMINO, on the other hand, is designed to identify and select molecular markers distributed throughout the genome of organisms, both models and non-models, and from either NGS raw data (454 / Illumina, .sff or .fasta formats) or pre-calculated multiple alignments (MSA), in various formats. In addition, this tool can be executed via command line or through a user-friendly interface (GUI) that does not require previous bioinformatics knowledge, allowing the customization of multiple parameters.

 

“DOMINO is a new bioinformatic tool to develop on-demand molecular markers from genomic data.” Source, University of Barcelona – News.

 

Furthermore, this application allows scientists to obtain a customized selection of molecular markers with their coordinates (Excel file) and their MSA (in .fasta format), after preprocessing, quality control, assembly and mapping/alignment of the input data. From them, the researcher can: a) To employ them directly as markers with a specific taxonomic depth; b) To use them for downstream amplification by PCR in a wider taxonomic scope; or c) To take them as suitable templates to optimized bait design for target DNA enrichment techniques.

 

DOMINO workflow for developing new molecular markers. Source: DOMINO.

 

DOMINO is freely available for MacOS and Linux (coming soon in Windows) and, as it is an open platform, it allows adaptation to other pipelines. In addition, the types of input files that it accepts are currently being increased. Among those responsible for its development are staff from various departments and institutes of the University of Barcelona, ​​namely: the Department of Genetics, Microbiology and Statistics; the Biodiversity Research Institute; and the Department of Evolutionary Biology, Ecology and Environmental Sciences. Its implementation and testing were published in Bioinformatics last December 2016. Read the article here. Download DOMINO here.

 

References

  1. Frías-López C, Sánchez-Herrero S, Mora E, Arnedo MA, Sánchez-García A, Rozas J. DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms. Bioinformatics 2016;32(24):3753-9.
  2. DOMINO Website.
  3. University of Barcelona – News.

Almudena Devesa Peiró

Contact by: equipoinspira@inspirabiotech.com

almudena-devesa-peiro has 11 posts and counting.See all posts by almudena-devesa-peiro

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