Complex genomes of early nucleocytoviruses revealed by ancient origins of viral aminoacyl-tRNA synthetases

Soichiro Kijima, Hiroyuki Hikida, Tom O. Delmont, Morgan Gaïa, Hiroyuki Ogata*

*Correspondence: ogata[at]kuicr.kyoto-u-ac.jp

1_Phylogenetic_tree_of_nucleocytoviral_maker_genes: Information used for the species tree of Nucleocytoviruses (Figure 1).

2_Phylogenetic_trees_of_viral_and_cellular_aaRSs: Information used for aaRS trees (Figure 2–6, S2, S4–S7, S9).

3_Subsection_trees_of_seleted_aaRSs: Information used for subsection of the aaRS trees (Figure 4, S3, S4).

Each directory listed above contains following directories:
	1_sequences: Amino-acid sequences
	2_multiple_alignment_sequences: Sequences aligned by MAFFT
	3_trimmed_multiple_alignment_sequences: Alignments trimmed by TrimAl
	*For aaRS trees, it was divided into two sub-directroies with corresponding trimming criteria.
	4_phylognetic_trees: Phylogenetic trees constructed by IQ-TREE
	*For aaRS trees, it was divided into sub-directroies with corresponding trimming criteria and statistical tests.

4_Phylogenetic_trees_of_viral_clades: Phylogenetic trees of viral clades (Figure 7–9, S8, S10, S11)
*The trees were constructed from the same data used for whole phylogenetic trees.

5_Tree_annotations: Species name and taxonomic information for each branch, which can be used in iTOL.
*Each file contains the following information:
	1_Species_names.txt: Convert IDs to Species names or MAG identifiers (Figure 2–6, S2–7, S9).
	2_Taxonomic_information.txt: Information of taxonomy of each branch (Figure 2–6, S2–7, S9)
	3_Taxonomic_information_viral_tree.txt: Information of taxonomy of each branch for phylogenetic trees of viral aaRS (Figure 7–9, S8, S10, S11)

6_AU_test: Data used for AU test (Table S1, S2)
*Each directory contains the following information:
	1_Selected_alignments: Subsection of multiple alignments for each aaRS
	2_Tested_trees: Collection of trees tested by IQ-TREE

Nucleocytoviruses_aaRS_phylogenies.pdf: Phylogenetic trees of aaRS sequences visualized with sequence names, taxonomic information, and bootstrap values.