Additional file 1 of Growth rate determines prokaryote-provirus network modulated by temperature and host genetic traits
Creators: name: Liu, Zhenghua
name: Yan, Qingyun
name: Jiang, Chengying
name: Li, Juan
name: Jian, Huahua
name: Fan, Lu
name: Zhang, Rui
name: Xiao, Xiang
name: Meng, Delong
name: Liu, Xueduan
name: Wang, Jianjun
name: Yin, Huaqun
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology
subject: Virology

description: Additional file 1: Table S1. Model default parameters. Table S2. Model initial conditions. Table S3. Linear regression model for host growth rate and their virus specificity across different phyla. Table S4. Phylogenetic linear regression model for host growth rate and their virus specificity across different phyla. Table S5. Effects of the host surface receptors on the GrSRs estimated by linear regression analyses. Figure S1. Schematic diagram of modeling host-virus population dynamic. There are five compartments including susceptible cell (B−, $${B}_0^{-}$$ B 0 - ), non-susceptible cell (B+), infected host in lysogeny ( $${B}_i^{-},i\ne 0$$ B i - , i ≠ 0 ) and lytic state (Li) states, virus (P). Arrows denote the transitions between compartments. More details can be saw in the Methods. Figure S2. Distribution of the viral cluster number across all species genomes. Such distribution follows the Poisson distribution with an expect value of 1.55. Bar plot are observed values and blue points are predicted values. Figure S3. The proportions of proviruses with unavailable genome completeness after the removal of the nodes with low network degrees in the bipartite networks. We considered only the proviruses with unavailable genome completeness for all proviruses or the proviruses of host-provirus networks, and found that the proportion of these proviruses decreased until the network degree ≥ 3. The degrees of 1 and 2 are referring the nodes of singletons and doubletons, respectively. Figure S4. The distribution of interaction specialization d’ for host in the whole host-provirus network (A) and the host-provirus network without singletons and doubletons (B), and the skewness and kurtosis of frequency distribution in the panel B (C) and the panel A (D). Notably, the skewness and kurtosis of frequency distribution indicate the distribution in the panel B is closer to normal distribution than that in the panel A. Figure S5. The pairwise correlations among variables. The diagonal plots are the frequency distributions of variables. The plots in upper triangular matrix show the Pearson’s correlation between variables. d’: interaction specialization for host. GS: genome size (Mb). GC: GC-content %. CDS: the number of gene coding sequences. 5S rRNA: the number of 5S ribosome RNA. 16S rRNA: the number of 16S ribosome RNA. 23S rRNA: the number of 23S ribosome RNA. 1/NVC: the reverse of number of viral clusters. Gr: host growth rate (doublings/day). OGT: optimal growth temperature (°C). *: P &lt; 0.05. **: P &lt; 0.01. ***: P &lt; 0.001. Figure S6. Slopes of the GrSRs across different ecosystems. The slope of GrSR for all environments was estimated by a mixed effect model: d’ ~ log10(1/DT) + (1 + log10(1/DT) | ecosystem). The slope of GrSR for each environment was estimated by linear model: d’ ~ log10(1/DT). Black points denote significant linear relationships (all Padj &lt; 0.05), while white points are nonsignificant. Point size represents adjust R-square. Figure S7. The GrSRs across phyla. Solid lines are significant linear relationships (Padj &lt; 0.05), while dashed lines are nonsignificant. Figure S8. Effects of the genes encoding heat shock proteins (HSP) on GrSRs. Solid lines denote significant linear relationships (Padj &lt; 0.05), while dashed lines are nonsignificant. Figure S9. The GrSR slopes across the number of genes encoding heat shock proteins (HSP). Numerical labels represent the number of genomes for analyses. Black points denote significant linear relationships (Padj &lt; 0.05), while grey points are nonsignificant. Error lines denote standard error. Figure S10. Effects of the genes encoding cold shock proteins (CSP) on GrSRs. Solid lines denote significant linear relationships (Padj &lt; 0.05), while dashed lines are nonsignificant. Figure S11. Effects of the csp7 genes on GrSRs across main orders. Dashed lines denote nonsignificant linear relationships (all P &gt; 0.1). Figure S12. Effects of the scoF genes on GrSRs across various orders. Solid lines denote significant linear relationships (Padj &lt; 0.05), while dashed lines are nonsignificant. Figure S13. Effects of the RM systems on GrSRs. Solid lines denote significant linear relationships (Padj &lt; 0.05), while dashed lines are nonsignificant. Figure S14. Effects of the CRISPR-Cas systems on GrSRs. Solid lines denote significant linear relationships (Padj &lt; 0.05), while dashed lines are nonsignificant. Figure S15. Effects of the anti-CRISPR systems on GrSRs. Solid lines denote significant linear relationships (Padj &lt; 0.05), while dashed lines are nonsignificant. Figure S16. Effects of the temperature-dependent lytic switches on GrSRs. Solid lines denote significant linear relationships (Padj &lt; 0.05), while dashed lines are nonsignificant. Figure S17. GrSRs for those species harboring the genes involving in the molecular processes in promoting the infection cycle at the stages of adsorption, establishment and viral release (R2adj = 0.182, P &lt; 0.001, df = 154). Those species harbor at least one gene encoding heat shock protein (hsp20, hsp40, hsp70 or hsp100), at least two genes encoding cold shock protein (cspC, cspD, or cspLA), at least one gene encoding receptor protein (fliC, fljB or mshA), at least one pair of genes encoding heat lytic switch (cI and cro) and at least one gene encoding cold lytic switch (fpsR). Figure S18. Temperature-dependent induction. It is controlled by two lytic switches including the repressors of CI/Cro (for high temperature at 37°C) and FpsR (for low temperature at 4 °C), which is simulated by a Sigmond function. Figure S19. Significant linear GrSRs of the potential psychrophiles harboring at least three CSP genes and the thermophiles with OGT larger than 40°C. All Padj &lt; 0.05.