DOI: 10.5281/zenodo.14597767
title: Supplementary data for: "Drastic genome reduction driven by parasitic lifestyle: Two complete genomes of endosymbiotic bacteria possibly hosted by a dinoflagellate"

description: Supplementary data for phylogenomic analysis in "Drastic genome reduction driven by parasitic lifestyle: Two complete genomes of endosymbiotic bacteria possibly hosted by a dinoflagellate" by Nakayama, T., Harada, R., Yabuki, A., Nomura, M., Shiba, K., Inaba, K., & Inagaki, Y.

The compressed file supplementary_datasets.tar.gz contains the following directories and files.





supplementary_datasets/ATPADP_transporter_tree/: This directory contains data related to the phylogenetic analysis of ADP:ATP antiporters.





ATPADP.fasta: This file contains the amino acid sequences of ADP:ATP antiporters used for phylogenetic analysis in multi-FASTA format.




ATPADP_linsi_gt85.fasta: This file contains the aligned amino acid sequences of ADP:ATP antiporters. The sequences in ATPADP.fasta were aligned using MAFFT and trimmed using trimAl. The resulting alignment is in FASTA format.




ATPADP_linsi_gt85.fasta_LG+C60+F+G.treefile: This file contains the phylogenetic tree data inferred from the ATPADP_linsi_gt85.fasta alignment using IQ-TREE. The tree is in Newick format.






supplementary_datasets/Orthofinder_Outputs/: This directory contains the results of the orthologous protein analysis using OrthoFinder.





Orthogroup_Sequences/: This directory contains the amino acid sequences of proteins belonging to each orthogroup. Each file corresponds to a single orthogroup and contains the sequences in FASTA format.




Orthogroups.tsv: This file contains the orthogroup information obtained from OrthoFinder analysis in tab-separated value (TSV) format. Each row represents an orthogroup, and each column contains information about the orthologous genes in each species.






supplementary_datasets/Phylogenomics_Fig2/: This directory contains data related to the phylogenomic tree of 46 OTUs shown in Figure 2.





105gene_46otu.fasta: This file contains the concatenated amino acid sequences of 105 genes from 46 species (trimmed alignment) in FASTA format.




105gene_46otu.fasta_LG+C60+F+I+G.treefile: This file contains the phylogenetic tree data inferred from the 105gene_46otu.fasta alignment using IQ-TREE. The tree is in Newick format.




105gene_46otu.fasta_LG+C60+F+I+G_fullname.treefile: This file contains the same phylogenetic tree data as 105gene_46otu.fasta_LG+C60+F+I+G.treefile, but with taxonomic information added to the OTU names. The tree is in Newick format.




fasta/: This directory contains the amino acid sequences of each of the 105 genes from 46 species. Each file corresponds to a single gene and contains the sequences in FASTA format.




trimmed_alignments/: This directory contains the trimmed alignments of the amino acid sequences in the 'fasta' directory. The sequences were aligned using MAFFT and trimmed using BMGE. Each file contains a trimmed alignment in FASTA format.






supplementary_datasets/Phylogenomics_FigS2/: This directory contains data related to the phylogenomic tree of 203 OTUs shown in Supplementary Figure S2.





105gene_203otu.fasta: This file contains the concatenated amino acid sequences of 105 genes from 203 species (trimmed alignment) in FASTA format.




105gene_203otu.fasta_LG+C10+F+I+G.treefile: This file contains the phylogenetic tree data inferred from the 105gene_203otu.fasta alignment using IQ-TREE. The tree is in Newick format.




105gene_203otu.fasta_LG+C10+F+I+G_fullname.treefile: This file contains the same phylogenetic tree data as 105gene_203otu.fasta_LG+C10+F+I+G.treefile, but with taxonomic information added to the OTU names. The tree is in Newick format.




fasta/: This directory contains the amino acid sequences of each of the 105 genes from 203 species. Each file corresponds to a single gene and contains the sequences in FASTA format.




trimmed_alignments/: This directory contains the trimmed alignments of the amino acid sequences in the 'fasta' directory. The sequences were aligned using MAFFT and trimmed using BMGE. Each file contains a trimmed alignment in FASTA format.