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. 2020 Mar 2;86(6):e02873-19. doi: 10.1128/AEM.02873-19

TABLE 4.

Genomic characteristics of Clavibacter sp. strains used in this studya

Parameter or subsystem feature C. michiganensis sensu stricto (NCPPB 382) C. capsici (PF008T) Clavibacter sp. (CFBP 8615) Clavibacter sp. (CFBP 8616) C. michiganensis subsp. californiensis (CFBP 8216T) Clavibacter sp. (CFBP 7491) Clavibacter sp. (CFBP 7493) Clavibacter sp. (CFBP 7494) Clavibacter sp. (CFBP 8019) Clavibacter sp. (CFBP 8017) Clavibacter sp. (DOAB 609) Clavibacter sp. (CF11) Clavibacter sp. (LMG 26808) C. michiganensis subsp. phaseoli (CFBP 8627T) C. michiganensis subsp. chilensis (CFBP 8217T) Clavibacter sp. (CASJ009) C. insidiosus (LMG 3663T) C. nebraskensis (NCPPB 2581T) C. sepedonicus (ATCC 33113T) C. tessellarius (ATCC 33566T)
Genome size (bp) 3,297 3,056 3,129 3,094 3,193 3,288 3,275 3,313 3,024 3,172 3,296 3,118 3,420 3,052 3,044 3,268 3,387 3,063 3,258 3,318
GC content (%) 72.7 73.6 73.2 73.2 72.7 73.0 72.9 73.3 73.5 73.5 73.2 73.6 72.0 73.5 73.5 73.6 72.7 73.0 72.6 73.7
No. of CDS 2,979 2,725 2,807 2,730 2,784 2,917 2,897 2,956 2,676 3,014 3,181 3,002 3,097 2,642 2,629 3,054 3,091 2,739 3,047 2,956
No. of subsystems 345 326 323 319 338 316 342 330 326 263 266 260 340 315 311 341 332 325 345 317
No. of RNAs 51 51 47 47 48 50 48 50 48 48 53 49 57 50 49 51 52 51 51 52
No. of CDS for:
    Cofactors, vitamins, pigments 177 158 169 157 165 139 173 161 158 107 116 99 175 167 130 181 165 139 169 176
    Virulence, disease, defense 34 38 37 36 38 36 36 32 38 26 25 25 40 35 34 42 36 30 33 22
    Resistance to antibiotics/toxic compounds 19 23 22 21 23 21 21 17 24 17 16 15 25 21 19 27 21 17 20 18
    Invasion and intracellular resistance 15 15 15 15 15 15 15 15 14 9 9 10 15 14 15 15 15 13 13 4
    Potassium metabolism 13 12 12 12 13 12 13 13 16 5 5 5 9 9 13 8 13 9 10 11
    Phages, prophages, transposable elements 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
    Iron acquisition and metabolism 16 17 13 25 16 8 19 18 13 5 10 5 17 10 10 12 15 14 17 16
    Siderophoresb
        Yersiniabactin 2 0 0 0 2 0 2 0 0 0 5 0 2 0 0 0 2 2 0 0
        Aerobactin 3 3 3 3 3 3 4 3 3 0 0 0 3 3 3 3 3 3 3 3
    Nucleosides and nucleotides 87 72 93 92 89 76 100 76 81 80 79 75 74 98 68 90 79 80 99 65
    Protein metabolism 211 201 209 192 189 185 209 204 208 166 162 167 205 178 198 192 205 178 213 185
    Cell division and cell cycle 26 21 8 8 23 24 24 23 21 0 0 0 8 23 8 22 24 20 22 23
    Motility and chemotaxis 1 2 2 2 2 3 1 2 2 0 0 0 3 3 3 3 2 1 2 2
    Regulation and cell signaling 33 30 19 20 22 22 25 30 33 14 17 18 36 28 17 29 31 33 35 24
    Secondary metabolism 6 18 5 5 4 5 11 12 11 9 9 9 12 0 1 11 5 5 13 11
    Fatty acids, lipids, and isoprenoids 88 78 84 103 82 108 78 88 59 44 44 42 79 85 76 82 65 65 80 101
    Nitrogen metabolism 7 10 6 6 10 6 7 6 6 6 6 6 7 6 6 11 7 7 6 11
    Stress response 67 73 76 69 74 67 64 70 78 27 27 28 68 71 61 82 74 71 78 64
    Metabolism of aromatic compounds 10 8 9 8 9 14 10 10 8 4 3 3 10 10 10 18 10 9 10 10
    Amino acids and derivatives 224 190 223 212 233 221 210 192 199 217 221 203 236 193 195 224 219 229 232 220
    Sulfur metabolism 20 16 16 11 9 12 10 16 17 6 5 5 13 10 11 26 17 9 22 18
    Phosphorus metabolism 38 26 25 27 28 26 27 23 25 28 27 27 36 25 26 25 23 23 25 24
    Carbohydrates 285 266 255 268 267 283 247 268 237 181 194 175 278 263 261 382 266 266 269 281
a

Individual genomes were analyzed using the online annotating service RAST, and protein-encoding sequences (CDS), functions of the genes, and subsystems represented in the genomes were determined for each genome using the SEED-Viewer comparative environment. Features corresponding to cell wall and capsule, DNA metabolism, dormancy and sporulation, membrane transport, respiration, RNA metabolism, and miscellaneous groups are not included since they were common among all the evaluated taxa.

b

The siderophore assembly kit was detected only in Clavibacter sp. strain CFBP 8616.