Genomic adaptation of giant viruses in polar oceans

1.

KO enrichment in Polar viral genomes and pathways

“Polar”, “Nonpolar”, or “Unknown” biome niche was assigned to each

viral genome based on presence/absence and overrepresentation

(“Biome and size niche” section). For individual lineages at four taxonomic levels (root, main group, family, and genus), the enrichment of a

given KO in Polar genomes assessed using Fisher’s exact test in SciPy

v.1.7.190. Adjustments for multiple testing were performed using the

Benjamini-Hochberg (BH). The significance threshold was set to a

corrected P value of 0.05.

Polar-specific KOs were defined as those with a temperature

optimum below 10 °C and a latitude optimum above 50°. For pathways

with at least half of the detected KOs as polar-specific KOs, we compared the fraction of components (i.e., enzymes) defined as polarspecific KOs with the fraction of all other pathways. This fraction was

tested by the Fisher’s exact test and adjusted by the BenjaminiHochberg (BH). This analysis excluded rare KOs (observed in fewer

than five genomes). To avoid the enrichment of pathways led by sparse

KOs, the pathways were exhibited only if the number of detected viral

KOs in a given pathway constituted more than 10% of the total number

of KOs in the pathway.

Phylogenetic signal of functions

We hypothesized that the phylogenetic distributions of some polar

specific functions (i.e., “trait distribution”) could be better explained in

part by environment selection rather than only by speciation history.

We therefore compared two models, (i) the Brownian motion model

(Pagel’s lambda = 1, used as the null hypothesis in which the distribution of a trait is simply explained by species tree) and (ii) the Lambda

model (0 ≤ Pagel’s lambda ≤ 1; lambda = 0 corresponds to the lack of

phylogenetic signal in the distribution of a trait), by the likelihood ratio

test using the function “fitContinuous” in an R package “geiger”91. The

p values to reject the null hypothesis were calculated by assuming chisquared distribution with 1 d.f. for the likelihood-ratio test statistic and

adjusted using the BH procedure. The threshold was set to a corrected

p value of 0.05

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Reporting summary

Further information on research design is available in the Nature

Portfolio Reporting Summary linked to this article.

Nature Communications | (2023)14:6233

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Acknowledgements

This work was supported by JSPS/KAKENHI (18H02279 and 22H00384,

to H.O.), and the Collaborative International Joint Research Program of

the Institute for Chemical Research, Kyoto University (No. 2021-29, 202226 to T.O.D.; No. 2022-27, to S.C.), and the H2020 European Commission

project AtlantECO (award number 862923, to S.C.). Computational time

was provided by the SuperComputer System, Institute for Chemical

Research, Kyoto University. We further thank the Tara Oceans consortium, and the people and sponsors who supported Tara Oceans. Tara

Oceans (including both the Tara Oceans and Tara Oceans Polar Circle

expeditions) would not exist without the leadership of the Tara Expeditions Foundation and the continuous support of 23 institutes (https://

oceans.taraexpeditions.org). This article is contribution number 147 of

Tara Oceans. We thank Gabe Yedid, PhD, from Edanz (http://jp.edanz.

com) for editing a draft of this manuscript.

Author contributions

L.M. and H.O. designed the study. L.M. performed the primary biogeographical analysis. T.O.D completed the genome-resolved metagenomic analysis. M.G. performed phylogenomic analyses. E.P. generated

the reads mapping data. A.F.-G. provided de novo clusters of viral genes.

S.C., R.Y.N., J.W., H.K., H.E. contributed to the bioinformatics analysis. All

the authors contributed to interpreting the data and writing the

manuscript.

Competing interests

The authors declare no competing interests.

Additional information

Supplementary information The online version contains

supplementary material available at

https://doi.org/10.1038/s41467-023-41910-6.

Correspondence and requests for materials should be addressed to

Hiroyuki Ogata.

Peer review information Nature Communications thanks Frank Aylward,

Chuan Ku and the other, anonymous, reviewer(s) for their contribution to

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