Table 2. Nucleotide polymorphisms in the sequences of putative virulence factors found in the genome of Clavibacter michiganensis subsp. nebraskensis strains GIL1 and HF4. PCR primers flanking each locus were used in sequencing reactions to obtain the complete sequence of each gene.

Locus in Cmn genome (Isolate NCPPB 2581)	Putative function	Nucleotide differences
Cmn 00734	Chloride anion channel	No difference
Cmn 00144	Secreted cellulase A	Indel (18 nucleotides)
Cmn 02650	Endoglucanase	3 SNPs
Cmn 02651	Endoglucanase	Indel (66 nucleotides)
Cmn 00792	Translocase glycosyl hydrolase	No difference
Cmn 01115	Polysaccharide deacetylase	No difference
Xys A	Endo-1, 4-beta xylanase A	No difference
Xys B	Endo-1, 4-beta xylanase B	6 SNPs
Pga A	Polygalacturonase A	No difference
Cmn 01173	Secreted serine peptidase	No difference
Cmn ppaF	Secreted serine peptidase	No difference
Cmn 457	Secreted serine peptidase	No difference
Cmn sbtC	Serine peptidase	No difference
Cmn sbtB	Serine peptidase	No difference
Cmn 2417	Secreted serine peptidase	No difference
Cmn 2381	Secreted serine peptidase	No difference
Cmn 2235	Secreted serine peptidase	No difference
Cmn 1337	Secreted serine peptidase	No difference
Cmn 1248	Secreted serine peptidase	No difference
Cmn 00106	Toxin-antitoxin system	No difference
Cmn 00626	Toxin-antitoxin system	No difference
Cmn 00771	Toxin-antitoxin system	No difference
Cmn 01077	Toxin-antitoxin system	No difference
Cmn 01078	Toxin-antitoxin system	No difference
Cmn 02136	RTX toxin	No difference
Cmn 02626	Toxin component	No difference
Cmn 02669	Toxin component	No difference
Cmn 02707	Toxin gene	No difference
Cmn 00414	Protein kinase	No difference
Cmn 0118	Exported toxin	No difference
Cmn 02101	TetR lipase/esterase	No difference
Cmn 00283	Glycosyl transferase	No difference
Cmn 02654	Pectate lyase	I SNP

Sequences were aligned and examined for nucleotide sequence differences. Primers were designed from reference strain NCPPB 2581 genomic sequence.