TABLE 1 

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

Genome featureGsubRmagVokuGlopGhalTsulTcru
HabitatDeep-sea spongeDeep-sea clamDeep-sea clamDeep-sea spongeShallow-water spongeShallow water free-livingDeep-sea free-living
Accession no.JYIN01000000CP000488AP009247LFLB01000000JFBG01000000CP001339CP000109
Completeness (%)98.0094.1694.1994.5199.5699.8999.39
Potential contamination (%)0002.441.010.340
Total length (Mbp)1.41.21.02.73.53.52.4
No. of protein-coding genes1,3701,0769392,5062,7413,3192,201
No. of tRNA genes36363643444844
Reduced features
    No. of genes involved in:
        Monosaccharide metabolism44310321712
        Sugar alcohol metabolism222172183
        Oligosaccharide metabolism200781111
        Motility and chemotaxis443696576
        Resistance to toxic compounds and heavy metals14141417235755
        Oxidative stress14111322202717
        Osmotic stress000101459
        DNA repair31211639394636
Retained features
    No. of type II secretion system genes1100081212
    No. of CRISPR sites3006020
    No. of CRISPR spacers16001910710
    No. of CRISPR protein20014450
  • 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.