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Table 2 Virulence and virulence-associated genes in C. perfringens strain CP1 that were significantly expressed under different conditions

From: Comparative transcriptome analysis by RNAseq of necrotic enteritis Clostridium perfringens during in vivo colonization and in vitro conditions

    in vivo-RM in vivo-PM in vivo-OS PM-RM OS-RM
Feature Locus Tag Predict product (gene name) Fold log2FC FDR Fold log2FC FDR Fold log2FC FDR Fold log2FC FDR Fold log2FC FDR
V CP4_0080 phospholipase C (plc) 9.3 3.2 0.0     7.1 2.8 0.0 6.9 2.8 0.0    
V CP4_0193 peptidoglycan protein (cna) −8.5 −3.1 0.0           −7.5 −2.9 0.0
V CP4_0211 collagenase_kappa toxin (colA) 4.7 2.2 0.0             
V CP4_0212 collagenase_kappa toxin (colA) 4.9 2.3 0.0             
QS CP4_0214 UbiE/COQ5 family methlytransferase (ycgJ) −59.4 −5.9 0.0        −22.5 −4.5 0.0 −112.0 −6.8 0.0
QS CP4_0215 cystathionine beta-lyase (metB) −59.3 −5.9 0.0        −18.6 −4.2 0.0 −40.2 −5.3 0.0
QS CP4_0216 cysteine synthase (cysK) −30.7 −4.9 0.0        −17.8 −4.2 0.0 −31.5 −5.0 0.0
QS CP4_0217 S-ribosylhomocysteinase (luxS) −27.3 −4.8 0.0        −7.2 −2.9 0.0 −29.8 −4.9 0.0
NELoc-2 CP4_0460 putative VTC domain superfamily    0.0     −5.8 −2.5 0.0       
NELoc-2 CP4_0461 putative tubulin/FtsZ, GTPase −6.3 −2.7 0.0 −5.4 −2.4 0.0 −8.3 −3.1 0.0       
VR10B CP4_0572 collagen adhesin (cnaA)    0.0     −7.4 −2.9 0.0       
VR10B CP4_0573 signal peptidase I (lepB) −5.3 −2.4 0.0     −11.0 −3.5 0.0 −4.2 −2.1 0.0    
VR10B CP4_0574 PitB −4.6 −2.2 0.0     −9.2 −3.2 0.0       
VR10B CP4_0575 sortase, SrtB family (srtB) −4.1 −2.0 0.0     −8.7 −3.1 0.0 −4.3 −2.1 0.0    
VR10B CP4_0576 putative streptococcal pilin isopeptide link −4.2 −2.1 0.0     −9.8 −3.3 0.0       
V CP4_0806 sialidase (nanI) 76.1 6.3 0.0     129.2 7.0 0.0 132.8 7.1 0.0    
regulator CP4_0922 VirT (virT) 30.1 4.9 0.0     32.4 5.0 0.0 78.1 6.3 0.0    
regulator CP4_1328 VR-RNA (vrr)    0.0     −16.1 −4.0 0.0 −5.6 −2.5 0.0 4.2 2.1 0.0
V CP4_1570 enterotoxin (entD) 4.0 2.0 0.0             
V CP4_1581 hyaluronidase _mu-toxin (nagJ) 4.9 2.3 0.0     13.0 3.7 0.0 5.0 2.3 0.0    
V CP4_2582 hyaluronidase _mu-toxin (nagA)    0.0        8.2 3.0 0.0    
plasmid CP4_3441 beta2 toxin (cpb2)        8.3 3.1 0.0 6.9 2.8 0.0    
NELoc-1 CP4_3443 beta-lactamase domain-containing protein    0.3 6.7 2.7 0.0     −4.9 −2.3 0.0    
NELoc-1 CP4_3444 M protein trans-regulator −15.7 −4.0 0.0 −4.6 −2.3 0.3 −24.3 −4.6 0.0       
NELoc-1 CP4_3445 SAM domain-containing protein −14.0 −3.8 0.0 −22.7 −4.5 0.0 −14.4 −3.9 0.0       
NELoc-1 CP4_3446 putative internalin −8.5 −3.1 0.1 −8.0 −3.0 0.1 −20.2 −4.3 0.0       
NELoc-1 CP4_3454 chitinase B 19.6 4.3 0.0     70.3 6.1 0.0 26.9 4.8 0.0    
NELoc-1 CP4_3455 chitodextrinase 31.1 5.0 0.0     112.2 6.8 0.0 39.2 5.3 0.0    
NELoc-1 CP4_3458 pore-forming toxin_NetB (part)    0.0 28.2 4.8 0.0     −8.5 −3.1 0.0    
NELoc-1 CP4_3459 pore-forming toxin_NetB (part) 4.2 2.1 0.0 29.9 4.9 0.0 4.5 2.2 0.0 −7.1 −2.8 0.0    
NELoc-1 CP4_3460 hypothetical protein −12.9 −3.7 0.0           −4.5 −2.2 0.0
NELoc-1 CP4_3461 hypothetical protein −4.2 −2.1 0.0     −6.1 −2.6 0.0       
NELoc-1 CP4_3464 resolvase/recombinase    0.0        −7.7 −3.0 0.0    
NELoc-1 CP4_3465 resolvase/recombinase    0.0        −7.5 −2.9 0.0    
NELoc-1 CP4_3475 ABC transporter    0.0        −5.7 −2.5 0.0    
NELoc-1 CP4_3478 diguanylate cyclase/phosphodiesterase −4.1 −2.0 0.0 −4.9 −2.3 0.0 −6.5 −2.7 0.0       
NELoc-3 CP4_3569 resolvase/recombinase        5.8 2.5 0.0       
NELoc-3 CP4_3570 hypothetical protein −5.8 −2.5 0.1           −4.4 −2.2 0.0
  1. 1Features: V: Virulence factors; QS: Quorum-sensing; VR10B: Variable region; NELoc-1, 2, 3: Pathogenicity locus 1, 2, 3
  2. 2 Locus Tag referent to CP4 genome
  3. 3Differential expression (DE) calculated by edgeR method, significantly expressed genes (fold change ≥ 2 and FDR = false discovery rate p-value ≤ 0.05)