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Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Related Experiment Video

Updated: Oct 12, 2025

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

ORPER: A Workflow for Constrained SSU rRNA Phylogenies.

Luc Cornet¹, Anne-Catherine Ahn², Annick Wilmotte²

¹BCCM/IHEM, Mycology and Aerobiology, Sciensano, 1050 Bruxelles, Belgium.

|November 27, 2021

Summary

Choosing bacterial strains for sequencing is hard due to genome redundancy. We created the ORganism PlacER (ORPER) workflow to determine a strain's phylogenetic position, aiding in selecting unique organisms for future genomic studies.

Keywords:

SSU (16S) rRNA cyanobacteria phylogenomics ribosomal proteins sequencing workflow

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Last Updated: Oct 12, 2025

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

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Published on: July 11, 2025

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

Genomics
Bioinformatics
Phylogenetics

Background:

Public genome repositories are growing rapidly.
Selecting novel bacterial strains for sequencing is challenging due to high redundancy with existing genomes.

Purpose of the Study:

To develop a computational workflow for assessing the phylogenetic placement of bacterial strains.
To aid researchers in identifying unique strains for future sequencing projects and reducing redundancy.

Main Methods:

Developed the Nextflow workflow "ORganism PlacER" (ORPER), containerized in Singularity.
Constrained phylogenetic placement of small subunit (SSU) ribosomal RNA (rRNA) sequences using a multilocus reference tree.
Utilized ribosomal protein genes extracted from public genomes for tree construction.

Main Results:

Demonstrated the utility of the ORPER workflow.
Successfully placed 152 strains from the BCCM/ULC collection within the Cyanobacteria phylum.
Provided a method to estimate the phylogenetic position and redundancy of bacterial strains.

Conclusions:

ORPER is an effective tool for determining the phylogenetic position of bacterial strains within the broader genomic landscape.
This workflow assists in the strategic selection of bacterial strains for sequencing, optimizing resource allocation and scientific discovery.