TABLE 1

Comparison of the genome features among the sulfur-oxidizing bacterium (SOB) in the cold seep sponge (Gsub) and reference genomes^a

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.