4 research outputs found
Additional file 1: of Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
Metadata. Table S1. Metadata from the coastal (H3) and mesotrophic (67-70) sites. Samples for the 16S rRNA amplicons were collected twice at 67-70, 8 days apart (with the 10 Oct. sample being done on the same day as the viral sample). The mesotrophic station is often subject to upwelling. Figure S1. Sea surface temperatures (SST) of the region of the California Cooperative Oceanic Fisheries Investigations (CalCOFI) Line 67 ocean transect on 5 October 2009 (contoured from a single synoptic image, Aqua Modis, NOAA) with the locations of the nearshore (yellow, H3 - coastal) and offshore (red, 67-70 - offshore mesotrophic) stations marked with stars. Gene marker (16S rRNA gene amplicons) analyses using the reference alignments of ref. Sudek et al., 2015 revealed different Synechococcus communities at the two sites (for additional details on sampling details see Additional file 2: Table S1). The Synechococcus community was analyzed twice at 67-70, one day after the coastal sampling and on the same day as the viral 67-70 sample collection. Proportions of different clades varied in the 67-70 Synechococcus amplicon data but the same clades were present on both dates. (DOC 721 kb
Additional file 2: of Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
Lineage information. Figure S2. TEM images of phage isolates from cyanophage (A) lineage I, (B) lineage II, (C) lineage III, (D) lineage IV, (E) lineage V, (F) lineage VI, and (G-J) singleton and duplicon populations confirms myovirus morphology. Table S2. List of 51 core protein clusters shared across all six phylogenetic lineages. Fig. S3. Unrooted phylogenomic maximum likelihood tree of 27 concatenated protein sequences shared across published marine and non-marine T4-like phage genomes and the 142 cyanophage isolate genomes sequenced here. For simplicity, cyanophage isolate names in this tree were shortened from Syn7803* to just *. These analyses show that the 10 cyanophage populations observed here share similar evolutionary histories with other T4-like phages. Table S3. Average ANI of the 51 core genes within and between lineages. Table S4. AGDB groupings correspond with the phylogenetic lineages. Table S5. Average phylogenetic distances within and between lineages. Table S6. Corrected Rand Indices and Malia’s VI values to compare the row and column hierarchical clustering between the original ANI and Shared Gene matrix and a randomized ANI and Shared Gene matrix, respectively. The hierarchical clusters were split into different number of clusters (5,10, 20 and 50) for the analyses. The analyses revealed low correspondence between clustering, indicating that the clustering we observe in the original matrices are not random. (DOC 4227 kb
Additional file 3: of Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
Testing genetic drift, selection, and recombination. Table S7. FST values for genetic differentiation between coastal and offshore populations within each cyanophage lineage. The FST value for lineage II is most likely high due to the low number of representatives and lack of diversity among the offshore lineage II phages. Due to the low number of individuals isolated from the offshore site for some of the clusters, FST could not be calculated. Figure S4. (A) Quantitative host range analyses of 15 Synechococcus host strains against 138 cyanophage isolates testing the efficacy of infection. (B) Analysis of mean infectivity of coastal and upwelling phages in lineage I, II, IV, and VI reveal statistically different infectivity phenotypes at either site with T-test p <0.05 (*). Statistical significance was not assessed for lineages III and V due to low sample size nor on the original isolation host, WH7803 (†). Table S8. Corrected Rand Indices and Malia’s VI values to hierarchical clustering between the original host range matrix and a randomized host range matrix. The hierarchical clusters were split into different number of clusters (5,10, 20 and 50) for the analyses. The analyses revealed low correspondence between clustering, indicating that the clustering we observe in the original shared genes matrix is not random and that there is some correlation with a biological signal. Table S9. Fisher’s exact tests p-values and phi coefficients (for effect size) for genes found under positive selection in comparisons between phylogenomic lineages using the non-polarized McDonald-Kreitman test. Also, the table reflects the corresponding protein clusters in the GOV population dataset [19]. Table S10. Genic versus intergenic recombination breakpoints for each lineage. (DOC 250 kb
Additional file 2: Figure S1. of Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants
Percentage of GC nucleotides along the LGC of CCMP1545 (left top) and RCC299 (left bottom) and a typical non-LGC chromosome of each (right). GC fraction was calculated using a 30 kb sliding scale. Figure S2. Size distribution of prasinophyte predicted proteins. Transcriptome-based proteins are overrepresented in the shorter bins indicating likely assembly issues, especially in D. tenuilepis. Figure S3. PPASP contains a transmembrane domain (yellow box) and a LysM domain (red box), predicted to be on the outside of the membrane. Sequence logo motif generated with 14 input sequences. Figure S4. Phylogenetic analysis of MURA (A), PPASP (B) and MURE (C) protein sequences. Figure S5. Cellular localization of Micromonas RCC299 and CCMP1545 protein families in the Ancestral and Core (essential) sets based on TargetP analysis. Mixed: members of an ortholog group show different targeting signals. (PDF 746 kb