Comparison of the genome features among the sulfur-oxidizing bacterium (SOB) in the cold seep sponge (Gsub) and reference genomesa
Genome feature | Gsub | Rmag | Voku | Glop | Ghal | Tsul | Tcru |
---|---|---|---|---|---|---|---|
Habitat | Deep-sea sponge | Deep-sea clam | Deep-sea clam | Deep-sea sponge | Shallow-water sponge | Shallow water free-living | Deep-sea free-living |
Accession no. | JYIN01000000 | CP000488 | AP009247 | LFLB01000000 | JFBG01000000 | CP001339 | CP000109 |
Completeness (%) | 98.00 | 94.16 | 94.19 | 94.51 | 99.56 | 99.89 | 99.39 |
Potential contamination (%) | 0 | 0 | 0 | 2.44 | 1.01 | 0.34 | 0 |
Total length (Mbp) | 1.4 | 1.2 | 1.0 | 2.7 | 3.5 | 3.5 | 2.4 |
No. of protein-coding genes | 1,370 | 1,076 | 939 | 2,506 | 2,741 | 3,319 | 2,201 |
No. of tRNA genes | 36 | 36 | 36 | 43 | 44 | 48 | 44 |
Reduced features | |||||||
No. of genes involved in: | |||||||
Monosaccharide metabolism | 4 | 4 | 3 | 10 | 32 | 17 | 12 |
Sugar alcohol metabolism | 2 | 2 | 2 | 17 | 21 | 8 | 3 |
Oligosaccharide metabolism | 2 | 0 | 0 | 7 | 8 | 11 | 11 |
Motility and chemotaxis | 4 | 4 | 3 | 6 | 9 | 65 | 76 |
Resistance to toxic compounds and heavy metals | 14 | 14 | 14 | 17 | 23 | 57 | 55 |
Oxidative stress | 14 | 11 | 13 | 22 | 20 | 27 | 17 |
Osmotic stress | 0 | 0 | 0 | 10 | 14 | 5 | 9 |
DNA repair | 31 | 21 | 16 | 39 | 39 | 46 | 36 |
Retained features | |||||||
No. of type II secretion system genes | 11 | 0 | 0 | 0 | 8 | 12 | 12 |
No. of CRISPR sites | 3 | 0 | 0 | 6 | 0 | 2 | 0 |
No. of CRISPR spacers | 16 | 0 | 0 | 191 | 0 | 71 | 0 |
No. of CRISPR protein | 2 | 0 | 0 | 14 | 4 | 5 | 0 |
↵a The reference genomes include two endosymbionts from vent clams, “Candidatus Ruthia magnifica” strain Cm (Rmag) and “Candidatus Vesicomyosocius okutanii” strain (Voku), two extracellular SOB in sponges, the SOB in the deep-sea glass sponge Lophophysema (Glop) and in the shallow water sponge Haliclona (Ghal), and two free-living relative SOB, Thioalkalivibrio sulfidophilus HL-EbGr7 (Tsul) from shallow water and Thiomicrospira crunogena XCL-2 (Tcru) from the deep sea.