Supplementary Files

Data from the manuscript "De novo biosynthesis of omega-3 polyunsaturated fatty acids in animals" by Kabeya et al.

It contains eight files: two figures, two tables and four text files.

1) Fig_1-PhyloBayes_tree

Complete view of the 50% majority-rule phylogenetic tree inferred with PhyloBayes software under CAT+GTR model of evolution. The outgroup was defined as the most divergent monophyletic clade within ωx desaturase protein sequences and includes representatives of Cyanobacteria and Viridiplantae. Major metazoan taxonomic clades are coloured as in Figure 2 of the manuscript. Additional colours are assigned for non-Metazoan taxonomic units, which are not represented in detail in Figure 2. Generally, sequences are named with, generally, three major taxonomic ranks plus the species name and the accession number. Posterior probability values are displayed next to each node. This tree is available in nexus format as "TextFile_3-tree_PhyloBayes.nexus".

2) Fig_2-RAxML_tree

Complete view of the 50% majority-rule phylogenetic tree inferred with RAxML software under LG+G+I model of evolution. The outgroup was defined as the most divergent monophyletic clade within ωx desaturase protein sequences and includes representatives of Cyanobacteria and Viridiplantae. Major metazoan taxonomic clades are coloured as in Figure 2 of the main manuscript. Additional colours are assigned for non-Metazoan taxonomic units, which are not represented in detail in Figure 1b. Generally, sequences are named with, generally, three major taxonomic ranks plus the species name and the accession number. Posterior probability values are displayed next to each node. This tree is available in nexus format as "TextFile_4-tree_RAxML.nexus".

3) Table_1-WGS_TSA_projects

List of animal Whole Genome Shotgun (WGS) and Transcriptome Shotgun Assemblies (TSA) projects blasted to expand the number of distinct metazoan ωx desaturase sequences in the final dataset. WGS sequences are incomplete genomes that have been sequenced by a whole genome shotgun strategy. TSA sequences are transcript sequences that have been computationally assembled from primary RNA sequence data. All sequencing projects are accessible through the NCBI Sequence Set Browser (https://www.ncbi.nlm.nih.gov/Traces/wgs/).

4) Table_2-finalSequences

Accession numbers, histidine boxes, clade location in Figures 2 and 3 and URL for all ωx desaturase sequences included in the final dataset. Sequences functionally characterised in this study are indicated with "*" and sequences (or nearly identical ones) that were part of the initial queries used to search ωx desaturase homologues are indicated with "**".

5) TextFile_1-Protein_Alignment

ωx desaturase protein alignment used for inferring all phylogenetic trees presented in this study. The final sequences were aligned with MAFFT (parameters: --genafpair --maxiterate 1000) and filtered with GUIDANCE v.2.0 with the following parameters: 100 bootstrap replicates, sequence, column and site masking cut-off threshold < 0.5. The resultant MSA was then filtered with TrimAl v.1.4.rev9 to remove columns with gaps in 95% or more of the sequences.

6) TextFile_2-tree_MrBayes.nexus

Bayesian (MrBayes) phylogenetic tree on ωx desaturase protein alignment, basis for Figures 2,3 and Supplementary Figures 1, in nexus format.

7) TextFile_3-tree_PhyloBayes.nexus

Bayesian (PhyloBayes) phylogenetic tree on ωx desaturase protein alignment, basis for figure "Fig_1-PhyloBayes_tree".

8) TextFile_4-tree_RAxML.nexus

Maximum likelihood (RAxML) phylogenetic tree on ωx desaturase protein alignment, basis for figure "Fig_2-RAxML_tree".