TABLE 1.
Feature | Value(s)a |
---|---|
Sequencing metrics | |
454 (shotgun) platform | |
No. of reads | 177,873 |
No. of bases | 73,714,660 |
Average length (bases) | 414.4 |
Coverage (×) | 26.3 |
454 (paired-end) platform | |
No. of reads | 150,593 |
No. of bases | 46,384,064 |
Average length (bases) | 308.0 |
Coverage (×) | 16.6 |
Illumina HiSeq 2000 platform | |
No. of reads | 25,306,576 |
No. of bases | 2,530,657,600 |
Average length (bases) | 100 |
Coverage (×) | 903.6 |
PacBio platform | |
No. of reads | 129,047 |
No. of bases | 399,548,656 |
Average length (bases) | 3,096.1b |
Coverage (×) | 142.7 |
Newbler metricsc | |
N50ContigSize (454) (bases) | 90,324 |
Q40PlusBases (454) (%) | 99.84 |
N50ContigSize (HiSeq pool 1) (bases) | 78,972 |
Q40PlusBases (HiSeq pool 1) (%) | 99.99 |
N50ContigSize (HiSeq pool 2) (bases) | 90,503 |
Q40PlusBases (HiSeq pool 2) (%) | 99.96 |
N50ContigSize (HiSeq pool 3) (bases) | 79,027 |
Q40PlusBases (HiSeq pool 3) (%) | 99.97 |
Genomic data | |
Chromosome | |
Size (bp) | 2,800,582 |
G+C content (%) | 26.25 |
No. of CDSd | 2,666 |
Assigned function (% CDS) | 1,044 (39.2) |
General function annotation (% CDS) | 995 (37.3) |
Domain/family annotation only (% CDS) | 199 (7.5) |
Hypothetical (% CDS) | 428 (16.1) |
Pseudogenes | 31 |
Genomic islands/CRISPR | |
No. of genetic islands | 3 |
No. of CDS in genetic islands | 71, [1] |
CRISPR-Cas loci | I-B, [III-A] |
Gene content/pathways | |
IS elements, mobile elements, or tranposases | 3 (IS1595); 1, [1] (other) |
Signal transduction | |
Che proteins | cheABDRVW(Y)2 |
No. of methyl-accepting chemotaxis proteins | 26 |
No. of response regulators | 57 |
No. of histidine kinases | 62 |
No. of response regulator/histidine kinase fusions | 7 |
No. of diguanylate cyclases | 17 |
No. of diguanylate phosphodiesterases (HD-GYP, EAL) | 4, 5 |
No. of diguanylate cyclase/phosphodiesterases | 8 |
No. of other | 11 |
Motility | |
Flagellin genes | fla1 to fla6 |
Restriction/modification | |
No. of type I systems (hsd) | 1 |
No. of type II systems | 1, [1] |
No. of type III systems | 0 |
Transcription/translation | |
No. of transcriptional regulatory proteins | 64 |
Non-ECFe σ factors | σ54, σ70 |
No. of ECF σ factors | 0 |
No. of tRNAs | 56 |
No. of ribosomal locif | 3 (A), 3 (B) |
CO dehydrogenase (coxSLF) | Yes |
Ethanolamine utilization (eutBCH) | Yes |
Nitrogen fixation (nif) | Yes |
Osmoprotection | BCCT3, ectABC |
Pyruvate → acetyl-CoA | |
Pyruvate dehydrogenase (E1/E2/E3) | Yes |
Pyruvate:ferredoxin oxidoreductase | por |
Urease | ureAB |
Vitamin B12 biosynthesis | Yes |
Numbers in square brackets indicate pseudogenes or fragments.
Maximum length, 25,747 bases.
Features and values taken from largeContigMetrics within 454NewblerMetrics.txt for each assembly. Large contigs were defined as ≥500 bases. Due to the large number of HiSeq reads, the total reads were split into three pools and assembled independently.
Numbers do not include pseudogenes; CDS, coding sequences.
ECF, extracytoplasmic function.
A: 16S-tRNAIle-tRNAAla-23S-5S; B: 16S-23S-5S.