DOI: 10.6084/m9.figshare.31333204
title: Datasets for L. Hambücken (2026) From Early-Diverging SQR Enzyme in Antarctic Gloeobacterales Indicates Sulfide Tolerance in Thylakoid-Lacking Cyanobacteria

description: # Supplementary Material — README<br>## Article information- **Title:** Early-Diverging SQR Enzyme in Antarctic Gloeobacterales Indicates Sulfide Tolerance in Thylakoid-Lacking Cyanobacteria- **Authors:** Louise Hambücken, Edi Sudianto, Jimmy H. Saw, Denis Baurain, Luc Cornet*- **Corresponding author:** Luc Cornet (luc.cornet@uliege.be)<br>---<br>## Overview<br>This repository contains supplementary data used to generatethe analyses presented in the associated manuscript. The files includeprotein sequence datasets, multiple sequence alignments and phylogenetic trees.<br>---<br>## Directory structure and file descriptions<br>### `Terrabacteria_dereplication/`- **`genome_selection.ods`** All Terrabacteria accessions of representative species recovered from GTDB release r220 (Parks et al., 2022), together with the dereplicated list of Terrabacteria accessions.<br>### `Inference_SQRI_ortho_sequences/`- **`SqrI-ortho-sequences.fasta`** FASTA file containing all protein sequences from the 950 Terrabacteria accessions assigned to the Sqr type I orthologous group.<br>- **`sqrI-cyanos.fasta`** FASTA file containing all protein sequences from the 432 cyanobacterial genome accessions that matched the HMM search based on the Sqr type I orthologous group. The alignment has 74 sequences, corresponding to 506 unambiguously aligned positions. - **`Supp_Fig2.fasta`** FASTA file containing all protein sequences from the GTDB database release r220 that matched the HMM search based on the Sqr type I orthologous group. The protein alignment has 19,081 sequences, corresponding to 453 unambiguously aligned positions.<br>- **`Supp_Fig2.nwk`** Phylogenetic tree of Sqr type I inferred from the protein alignment file `Supp_Fig2.fasta`. The tree was constructed from 19,081 sequences, corresponding to 453 unambiguously aligned positions, using FastTree with default parameters. The node support values are based on the Shimodaira-Hasegawa (SH) test (Gascuel, 1997). - **`Fig1.fasta`** FASTA file containing all cyanobacterial protein sequences of the SQR type I region of the `Supp_Fig2.nwk` file. The alignment has 192 sequences, corresponding to 438 unambiguously aligned positions. - **`Fig1.nwk`** Phylogenetic tree of Sqr type I inferred from the protein alignment file `Fig1.fasta`. The phylogenetic tree was performed using IQ-TREE with the best-fit substitution model (Q.PFAM+I+R8) and 1,000 ultrafast bootstrap replicates. The tree was constructed from 192 sequences, corresponding to 438 unambiguously aligned positions. ### `Inference_D1_ortho_sequences/`<br>- **`D1-ortho-sequences.fasta`** FASTA file containing all protein sequences from the 950 Terrabacteria accessions assigned to the D1 (PsbA) orthologous group. - **`Fig3.fasta`** FASTA file containing all protein sequences from the 432 cyanobacterial genome accessions that matched the HMM search based on the PsbA orthologous group. The alignment has 726 sequences, corresponding to 360 unambiguously aligned positions.<br>- **`Fig3.nwk`** Phylogenetic tree of D1 inferred from the protein alignment file `Fig3.fasta`. The tree was constructed from 726 sequences, corresponding to 360 unambiguously aligned positions. The phylogenetic tree was performed using IQ-TREE with the best-fit substitution model (LG+R9) and 1,000 ultrafast bootstrap replicates.<br>- **`D1-consensus.fasta`** Consensus sequences retrieved from Sheridan et al. (2020) used to annotate the D1 phylogenetic tree (Fig. 3).<br> ---<br>## Methods summaryMultiple sequence alignments were generated using **MAFFT v7.520** with defaultparameters.<br>---<br>## Software requirements- MAFFT v7.520 - IQ-TREE v3.0.0 - HMMER v3.3.2 - BLAST+ v2.8.1 - FastTree v2.1.11<br>---<br>## Notes and limitations- All sequence identifiers correspond to GTDB release r220.- Rooted trees depending on the presence or absence of the following taxa : Patescibacteria, Chloroflexota, Margulisbacteria, Sericytochromatia, Vampirovibrionia, Gloeobacterales, Thermostichales.<br>---<br>## CitationIf you use these data, please cite the associated publication:<br>- Gascuel, O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution 14, 685–695 (1997).- GTDB: Parks, D. H. et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research 50, D785–D794 (2022).- HMMER: Finn, R. D., Clements, J. & Eddy, S. R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Research 39, W29–W37 (2011).- IQ-TREE: ong, T. K. F. et al. IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models. EcoEvoRxiv https://doi.org/10.32942/X2P62N (2025) doi:https://doi.org/10.32942/X2P62N.- MAFFT: Katoh, K. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30, 3059–3066 (2002).- Parks, D. H., Chuvochina, M., Rinke, C., Mussig, A. J., Chaumeil, P.-A., & Hugenholtz, P. (2022). GTDB: An ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research, 50(D1), D785–D794. https://doi.org/10.1093/nar/gkab776- Price, M. N., Dehal, P. S., & Arkin, A. P. (2010). FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, 5(3), e9490. https://doi.org/10.1371/journal.pone.0009490- Sheridan, K. J., Duncan, E. J., Eaton-Rye, J. J., & Summerfield, T. C. (2020). The diversity and distribution of D1 proteins in cyanobacteria. Photosynthesis Research, 145(2), 111–128. https://doi.org/10.1007/s11120-020-00762-7