TAT-like or Twin-peaked rhodopsins

This repository contains code and analysis results used in the paper Mannen et al (2023) Multiple roles of a conserved glutamate residue for unique biophysical properties in a new group of microbial rhodopsins homologous to TAT rhodopsin.

The workflow is divided into two parts: most of the analyses are covered by the default snakemake file workflow/Snakefile while the beast2 analysis is in workflow/Beast2.snakefile.

Dependencies

Most of the dependencies of the main workflow pipilene are taken care of with conda, but in addition to snakemake and conda, the following dependencies have to be installed manually:

• usearch is expected to be available from the PATH;
• RootAnnotator is expected to be in the directory named RootAnnotator in the current directory;
• mad is expected to be available from the PATH.

Files in this repository

The protein fasta file with the expressed TwRs is provided in the file Expressed_TwRs.faa.

The workflow files are located in workflow/.

Input files to run the pipeline(s) from scratch are in input/. They include:

• input/ingroup.fna -- ORF sequences for the representative TwRs
• input/ingroup.tsv -- metadata for the representivatie TwRs
• input/beast2/beast_linked_models.xml -- input for beast2 including the CDS alignment

Final output files are in the folder output. Immediate analysis results needed to produce them are included as well:

• analysis/TAT/rhodopsins.mafft -- fasta files with alignment of all of the collected and reference rhodopsins
• analysis/IIIa_phylophlan/IIIa.tre.treefile -- results of phylogenetic analysis of Pelagibacterales subclade IIIa
• analysis/diamond_collect/{gtdb,lanclos,oceandna}.tsv -- tsv files summarizing presence of rhodopsins in Pelagibacterales genomes obtained from three sources
• analysis/metadata/{gtdb_filtered,lanclos,oceandna_filtered}.tsv -- metadata for the analyzed Pelagibacterales genomes
• analysis/metadata/gtdb_clade.nwk -- tree in newick format corresponding to the o__Pelagibacterales clade in GTDB r. 214.1
• analysis/beast2/{beast_linked_models-codon12.trees,beast_linked_models.xml.state,beast_linked_models.log} -- results of the beast2 run
• analysis/beast2/beast_linked_models-rootAnnotator_annotatedMCCTree.nexus_fixed -- (fixed) output of rootAnnotator, tree in nexus format
• analysis/lazarus -- lazarus analysis

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