ORPER: A Workflow for Constrained SSU rRNA Phylogenies

Luc Cornet; Anne-Catherine Ahn; Annick Wilmotte; Denis Baurain

doi:10.3390/genes12111741

ORPER: A Workflow for Constrained SSU rRNA Phylogenies

Genes (Basel). 2021 Oct 29;12(11):1741. doi: 10.3390/genes12111741.

Authors

Luc Cornet¹, Anne-Catherine Ahn², Annick Wilmotte², Denis Baurain³

Affiliations

¹ BCCM/IHEM, Mycology and Aerobiology, Sciensano, 1050 Bruxelles, Belgium.
² BCCM/ULC Collection, InBioS-Centre for Protein Engineering, University of Liège, 4000 Liège, Belgium.
³ InBioS-PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, University of Liège, 4000 Liège, Belgium.

Abstract

The continuous increase in sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects ever more complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed the Nextflow workflow "ORPER", for "ORganism PlacER", containerized in Singularity, which allows the determination the phylogenetic position of a collection of organisms in the genomic landscape. ORPER constrains the phylogenetic placement of SSU (16S) rRNA sequences in a multilocus reference tree based on ribosomal protein genes extracted from public genomes. We demonstrate the utility of ORPER on the Cyanobacteria phylum, by placing 152 strains of the BCCM/ULC collection.

Keywords: SSU (16S) rRNA; cyanobacteria; phylogenomics; ribosomal proteins; sequencing; workflow.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Automation / methods*
Cyanobacteria / genetics*
DNA, Bacterial
Electronic Data Processing / methods
Phylogeny*
RNA, Ribosomal, 16S / genetics*
Ribosomal Proteins / genetics*
Ribotyping / methods*
Sequence Analysis, DNA / methods*
Workflow

Substances

DNA, Bacterial
RNA, Ribosomal, 16S
Ribosomal Proteins