Cyanobacteriochromes from Gloeobacterales provide new insight into the diversification of cyanobacterial photoreceptors

The phytochrome superfamily comprises three groups of photoreceptors sharing a conserved GAF (cGMP-specific phosphodiesterases, cyanobacterial adenylate cyclases, and formate hydrogen lyase transcription activator FhlA) domain that uses a covalently attached linear tetrapyrrole (bilin) chromophore to sense light. Knotted red/far-red phytochromes are widespread in both bacteria and eukaryotes, but cyanobacteria also contain knotless red/far-red phytochromes and cyanobacteriochromes (CBCRs). Unlike phytochromes, CBCRs require only the GAF domain for bilin binding, chromophore ligation, and full, reversible photoconversion. CBCRs can sense a wide range of wavelengths (ca. 330-750 nm) and can regulate phototaxis, second messenger metabolism, and optimization of the cyanobacterial light-harvesting apparatus. However, the origin and diversification of CBCRs are not well understood. In the current work, we use the increasing availability of genomes and metagenome-assembled-genomes from early-b..., Data are deposited as a gzipped tarball containing three types of data, each in its own directory: Phylogenies, Genome Analysis, and Spectroscopic data. Deposited data are all flat text files with UNIX newlines.
1. Phylogenies are presented for the CBCR (cyanobacteriochrome) domain, the histidine kinase bi-domain, for a catenation of taxis proteins, and for a catenation of translation proteins (ribosomal proteins + elongation factor 4). In each case, the initial sequence alignment was generated using MAFFT v7.450 with the following command-line settings:
 --genafpair --maxiterate 16 --clustalout –reorder
The resulting alignments are deposited in CLUSTAL format (indicated by the .aln extension). For phylogenetic analysis, each alignment was processed with an in-house script to remove positions having ≥5% gaps. The resulting alignments are deposited in PHYLIP format (indicated by the .phy extension) and were used to infer maximum-likelihood phylogenies in PhyML-3.1 with 100 bootstraps, us..., All files are flat text files.
Alignments can be opened in text editors or word processors.
Newick-format tree files were examined using FigTree.
All other data can be examined using spreadsheet/plotting software such as xmgrace, Excel, etc. For this work, data were analyzed and plotted using Kaleidagraph., ## Title: Underlying data for \"Cyanobacteriochromes from Gloeobacterales provide new insight into the diversification of cyanobacterial photoreceptors\"

## Description of the Data and file structure

Deposited data are in three folders:

Phylogenies
Genome_Analysis
Spectroscopic_data

Phylogenies:
For each phylogeny, three files are deposited: the original multiple sequence alignment in CLUSTAL format, the input file for PHYML in PHYLIP format after removal of gap-enriched columns, and the final tree with transfer bootstrap expectation values in Newick format.

As an example, files for the CBCR phylogeny are the original alignment (CBCR_domain.aln), the PHYLIP format input file (CBCR_domain.phy), and the
final output tree (CBCR_domain.TBE.txt).

The different phylogenetic analyses are described as follows:

CBCR_domain files are for analysis of the CBCR domain.
HisKinase files are for analysis of histidine kinase bidomains.
Taxis_catenation files are f...