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. 2015 Dec 11;10(6):1383–1399. doi: 10.1038/ismej.2015.214

Table 1. General features of SAGs from this study relative to the type species (Nitrospina gracilis) and related Candidatus Nitromaritima SAGs.

SAGs/strain SCGC AAA799-A02a SCGC AAA799-C22a SCGC AB-629-B06b,c SCGC AB-629-B18b,c SCGC AAA288-L16b,d N. gracilisb
Draft size (bp) 1 404 272 1 678 166 708 914 2 139 866 2 077 614 3 067 213
No. of contigs/N50 (bp) 97/708 347 88/864 303 90/354 767 73/1 137 313 136/1 084 788 109/1 571 461
% GC content 49.4 50.5 39.6 39.7 39.5 56.2
% Coding regions 87.6 88.2 83.1 85.8 87.5 89.6
Predicted ORFs 1379 1639 766 2206 2182 2965
% ORFs predicted functional 74.2 76.7 61.9 60.7 72.5 78.8
ORF density (ORF/kb) 1.14 1.13 1.20 1.17 1.14 1.12
Average ORF size 892 903 769 832 833 927
No. of tRNAse 24 (13) 18 (14) 4 (3) 37 (19) 32 (15) 45 (20)
No. of rRNA operons (16S-23S-5S) 1 1 None 1f 1 1
% Genome overlap with N. gracilisg 11 14 5 15 13 100
% ANI of overlapping genome with N. gracilisg 67 67 63 64 63 100
% ORFs shared with N. gracilish 51 57 44 56 58 100
% AAI of shared ORFs with N. gracilish 58 59 58 58 58 100
% Genome completenessi 20 40 30 73 75 97

Abbreviations: AAI, average amino-acid identity; ANI, average nucleotide identity; INDIGO, INtegrated Data Warehouse of MIcrobial GenOmes; ORF, open-reading frames; SAGs, single-cell-amplified genomes.

a

Assembly statistics: longest contig size are 66 004 bp (AA799-A02) and 123 650 bp (AAA799-C22), whereas the minimum size is 2 kbp for both.

b

Based on annotations via our INDIGO pipeline (Alam et al., 2013) using the published draft assemblies.

c

SAGs from the North Altantic Ocean (Station Archimedes 4, 511 m).

d

SAG from the North Pacific Ocean (Station ALOHA, 770 m; Swan et al., 2011).

e

Brackets indicate the number of unique amino acids encoded by the tRNAs.

f

This SAGs carries an rRNA operon with a partial 16S rRNA gene (849 bp) that is 99.5%, 96.7% and 92% identical to AAA288-L16, AAA799-A02/C22 and N. gracilis, respectively.

g

Based on whole-genome blastn alignment of the assembled nucleotide bases.

h

Based on reciprocal best blast hits of their protein-coding genes.

i

Estimated using 104 single-copy genes common in bacterial genomes using CheckM (Parks et al., 2015). For more details see Supplementary Table S3.