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Background   Salmonella  is a major bacterial pathogen associated with a large number of outbreaks of foodborne diseases. Many highly virulent serovars that cause human illness belong to  Salmonella  serogroup C1, and  Salmonella  ser. Choleraesuis is a prominent cause of invasive infections in Asia. Comparative genomic analysis in our previous study showed that two homologous genes,  SC0368  and  SC0595  in  Salmonella  ser. Choleraesuis were unique to serogroup C1. In this study, two single-deletion mutants (Δ0368 and Δ0595) and one double-deletion mutant (Δ0368Δ0595) were constructed based on the genome. All these mutants and the wild-type strain were subjected to RNA-Seq analysis to reveal functional relationships of the two serogroup C1-specific genes.    Results  Data from RNA-Seq indicated that deletion of  SC0368  resulted in defects in motility through repression of σ 28  in flagellar regulation Class 3. Consistent with RNA-Seq data, results from transmission electron microcopy (TEM) showed that flagella were not present in △0368 and △0368△0595 mutants resulting in both swimming and swarming defects. Interestingly, the growth rates of two non-motile mutants △0368 and △0368△0595 were significantly greater than the wild-type, which may be associated with up-regulation of genes encoding cytochromes, enhancing bacterial proliferation. Moreover, the △0595 mutant was significantly more invasive in Caco-2 cells as shown by bacterial enumeration assays, and the expression of lipopolysaccharide (LPS) core synthesis-related genes ( rfaB ,  rfaI ,  rfaQ ,  rfaY ,  rfaK ,  rfaZ ) was down-regulated only in the △0368△0595 mutant. In addition, this study also speculated that these two genes might be contributing to serotype conversion for  Salmonella  C1 serogroup based on their apparent roles in biosynthesis of LPS and the flagella.    Conclusion  A combination of biological and transcriptomic (RNA-Seq) analyses has shown that the  SC0368  and  SC0595  genes are involved in biosynthesis of flagella and complete LPS, as well as in bacterial growth and virulence. Such information will aid to revealing the role of these specific genes in bacterial physiology and evolution within the serogroup C1.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07759-z.

Two homologous Salmonella serogroup C1-specific genes are required for flagellar motility and cell invasion