Last change: 30.June.2023

# This directory contains files used for the analyses.

Existing files:

# Source Data
# Fig1 
A total of 928 epipelagic metagenomes from 143 Tara Oceans stations are included in this study. Each pie chart represents the contributions to richness by six taxonomic main groups, and the size of the pie chart is proportional to the total richness at the station. The table of the richness for each station is provided.
Fig1_Viral_Richness_Tara_Stations.csv

A virus–plankton interaction network. The network is integrated from five individual networks corresponding to eukaryotic MAGs from five cellular size fractions (Piconano, Nano, Micro, Macro, and Broad).
Fig1_Virus-Eukaryote_Cooccurrence.edgelist

The distribution of pairwise sequence similarity of proteins (one protein from the eukaryotic genome and one from the viral genome). 
Fig1_Virus-Euk_Protein_BlastP.txt

# Fig2
Ancestral “Polar” and “Nonpolar” states were estimated using the phylogenetic tree based on a one-parameter equal rates model. The phylogenetic tree used in the analysis is:
Fig2_RED_Normalized_Tree.txt

# Fig3
Distribution of the temperature optima and latitude optima for KEGG Orthologs (KOs) found in viral genomes.
Fig3_KO_env.csv

A boxplot with jitter of ratio of Polar KOs in each pathway is made by:
Fig3_Pathway_5obs_KOs_10per.tsv

# Fig4
The tree shown in the plot is one clade of
Fig2_RED_Normalized_Tree.txt

Three of them (K01627, K00979, K06041) co-occurred in the same genomes and formed a near-complete CMP−KDO biosynthesis module in the lipopolysaccharide biosynthesis pathway. These three KOs could be found statistically enriched in Meso_clade_II:
Fig4_Genus_level_enriched_KO.tsv

The proportion of polar GCCs and eukaryotic KOs is calculated based on the robust ecological optima tables:
Fig4S10_Euk_KO_env.csv
Fig4S10_GCC_env.csv

# Source Data of ExFigs
FigS1_Cumulated_RPKM_along_latitude.csv
FigS3_Size_Index.csv
FigS4_NMDS_Coverage_10_richness_5.csv
FigS4_NMDS_binary_Coverage_10_richness_5.csv
FigS7_Viralrecall.csv
FigS7_Virsorter2.txt
FigS9_A-rich.tsv
FigS9_Phylogent_diversity.csv
FigS9_Polar_KO_proportion.tsv
FigS9_Temperature_optima_lineage_enrichment.csv
Fig4S10_Euk_KO_env.csv
Fig4S10_GCC_env.csv

Before merging to the final network, we inferred five networks by using the relative abundance matrix for the virus MAGs from the Pico size fractions and relative abundance matrices for eukaryotic MAGs from five cellular size fractions (Piconano, Nano, Micro, Macro, and Broad). Five networks are stored in Cooccurrence_networks
Virus-BroadEukaryote_Cooccurrence.edgelist
Virus-MacroEukaryote_Cooccurrence.edgelist
Virus-MicroEukaryote_Cooccurrence.edgelist
Virus-NanoEukaryote_Cooccurrence.edgelist
Virus-PiconanoEukaryote_Cooccurrence.edgelist

Main diversity tables, including the Shannon's index, richness and pielou index of viruses and eukaryotes, are provided in the folder.
Diversity


Reference:
Meng, Lingjie, Tom O. Delmont, Morgan Gaia, Eric Pelletier, Antonio Fernandez-Guerra, Samuel Chaffron, Russell Y. Neches et al. "Genomic adaptation of giant viruses in polar oceans." bioRxiv (2023): 2023-02.

If any question please contact: lingjie@kuicr.kyoto-u.ac.jp