Article Figures & Data
- FIG 1
Neighbor-joining phylogenetic tree of strain SH4 and closely related cyanobacterial strains based on partial 16S rRNA genes (1,100 bp). CSS, cluster of “Ca. Synechococcus spongiarum.” Bootstrap values based on 1,000 replications are shown as percentages at branch angles. Scale bar indicates 1% estimated sequence divergence.
- FIG 2
Phylogenomic inference of “Ca. Synechococcus spongiarum” SH4. (a) Maximum-likelihood phylogenomic tree using 31 concatenated conserved proteins of SH4 and cyanobacterial strains. The branches were colored according to the bootstrap values, ranging from purple (80%) to red (100%). Scale bar indicates 10% estimated sequence divergence. (b) ANI values plus correlation indexes of tetranucleotide frequency between SH4 and closely related Synechococcus, Prochlorococcus, Cyanobium cluster Synechococcus, and other cyanobacterial strains revealed differences in their genome composition. (c) GC content and genome size of SH4 and other cyanobacterial strains.
- FIG 3
Schematic overview of the methionine metabolism pathway in “Ca. Synechococcus spongiarum” SH4. Red and green labels indicate the absence and presence, respectively, of that enzyme in SH4.
- FIG 4
Abundance of photosynthetic genes in “Ca. Synechococcus spongiarum” SH4 and related cyanobacteria strains based on KEGG orthology annotation. The identities of the cyanobacterial strains are described in Table 1.
- FIG 5
Genes of “Ca. Synechococcus spongiarum” SH4 and related cyanobacterial strains important for resistance to oxidative stress, antibiotics, and environmental toxins based on SEED/Subsystems annotation. See details in Tables S1 and S2. The identities of the cyanobacterial strains are described in Table 1.
- FIG 6
Schematic of mode of life of the sponge symbiont “Ca. Synechococcus spongiarum.” The schematic figure was deduced from the genomic analysis of the draft genome of strain SH4.
- TABLE 1
General features and functional comparison of “Candidatus Synechococcus spongiarum” SH4 and related picocyanobacterial strains
Genome feature or gene function Value for indicated taxona 1 2 3 4 5 6 7 8 Genome recovery ~90% F D D F F D F Genome size (Mbp) 1.66 2.22 2.58 3.04 2.61 1.75 2.83 3.34 No. of essential genes 96 106 104 106 105 106 105 106 % GC content 63.4 60.8 64.5 65.4 52.5 36.4 68.7 68.7 % Coding density 87.5 94.2 92.7 88.4 87.2 89.3 87.6 89.5 No. of genes in KEGG pathways Photosynthesis 47 60 64 61 64 53 57 59 Antenna proteins 24 28 18 23 28 8 21 17 TCA cycles 10 9 8 11 8 11 11 11 DNA replication 13 13 13 14 13 13 15 14 DNA repair 31 38 41 47 38 36 40 41 Cysteine/methionine metabolism 10 21 22 24 19 17 21 24 No. of genes in SEED/subsystems Response to oxidative stress 12 28 26 32 26 21 29 31 Resistance to antibiotics and toxins 8 22 22 28 23 9 30 36 CPS and EPS biosynthesis 3 13 13 16 10 8 19 17 Gram-negative cell wall 7 14 12 14 9 10 20 17 Peptidoglycan biosynthesis 16 15 15 17 15 15 17 16 Eukaryotic-like domain Fibronectin type III domain 2 0 0 1 0 0 0 0 AR 17 0 0 0 0 0 0 0 TPR 3 9 7 17 1 6 12 14 LRR 9 0 0 0 0 2 0 0 ↵a Taxa: 1, “Ca. Synechococcus spongiarum” SH4; 2, Synechococcus sp. strain RCC307; 3, Synechococcus sp. strain RS9917; 4, Synechococcus sp. strain WH 5701; 5, Synechococcus sp. strain CC9311; 6, P. marinus CCMP137; 7, Cyanobium sp. strain PCC 7001; 8, Cyanobium gracile PCC 6307. Genome recovery: F, finished genome; D, draft genome.
Supplemental Material
Figure S1
High abundance of “Ca. Synechococcus spongiarum” (represented by OTU1691) in the sponge C. foliascens according to the percentage of 16S rRNA gene amplicons analyzed by tag pyrosequencing. Download Figure S1, TIF file, 2.7 MB.
Copyright © 2014 Gao et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S2
Microbial community compositions in the sponge C. foliascens revealed by 16S rRNA genes predicted from the metagenome in this study and (a) and tag pyrosequencing of 16S rRNA gene amplicons (b). Download Figure S2, TIF file, 2.1 MB.
Copyright © 2014 Gao et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S3
Genome binning of “Ca. Synechococcus spongiarum” SH4. Each circle represents a metagenomic contig with size proportional to length and colored by GC content (a) or taxonomic affiliation (b). Only contigs greater than 2 kbp in length are shown. (c) Sequence composition-independent binning of metagenomic contigs based on the coverage. (d) Principal component analysis clustering on tetranucleotide frequencies for further genome binning. Download Figure S3, TIF file, 2.8 MB.
Copyright © 2014 Gao et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S4
Abundance of genes involved in amino acid metabolism pathways in “Ca. Synechococcus spongiarum” SH4 and closely related free-living cyanobacterial strains. Functional pathways are referred to the KEGG database. Download Figure S4, TIF file, 2.3 MB.
Copyright © 2014 Gao et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Table S1
Number of genes important for resistance to oxidative stress in SH4 and related cyanobacterial strains. Taxa: 1, “Ca. Synechococcus spongiarum” SH4; 2, Synechococcus sp. RCC307; 3, Synechococcus sp. RS9917; 4, Synechococcus sp. WH 5701; 5, Synechococcus sp. CC9311; 6, P. marinus CCMP137; 7, Cyanobium sp. PCC 7001; 8, Cyanobium gracile PCC 6307. Table S1, PDF file, 0.1 MB.
Copyright © 2014 Gao et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Table S2
Number of genes important for resistance to antibiotics and environmental toxins in SH4 and related cyanobacterial strains. Taxa: 1, “Ca. Synechococcus spongiarum” SH4; 2, Synechococcus sp. RCC307; 3, Synechococcus sp. RS9917; 4, Synechococcus sp. WH 5701; 5, Synechococcus sp. CC9311; 6, P. marinus CCMP137; 7, Cyanobium sp. PCC 7001; 8, C. gracile PCC 6307. Table S2, PDF file, 0.1 MB.
Copyright © 2014 Gao et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Table S3
Number of genes important for DNA replication and repair in SH4 and related cyanobacterial strains. Taxa: 1, “Ca. Synechococcus spongiarum” SH4; 2, Synechococcus sp. RCC307; 3, Synechococcus sp. RS9917; 4, Synechococcus sp. WH 5701; 5, Synechococcus sp. CC9311; 6, P. marinus CCMP137; 7, Cyanobium sp. PCC 7001; 8, C. gracile PCC 6307. Table S3, PDF file, 0.2 MB.
Copyright © 2014 Gao et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Additional Files
Supplementary Data
Supplementary Data
Files in this Data Supplement:
- Table st1, PDF - Table st1, PDF
- Table st2, PDF - Table st2, PDF
- Table st3, PDF - Table st3, PDF
- Figure sf01, TIF - Figure sf01, TIF
- Figure sf02, TIF - Figure sf02, TIF
- Figure sf03, TIF - Figure sf03, TIF
- Figure sf04, TIF - Figure sf04, TIF
