Comparative Genome Analysis of Rathayibacter tritici NCPPB 1953 with Rathayibacter toxicus Strains Can Facilitate Studies on Mechanisms of Nematode Association and Host Infection

Abstract

Rathayibacter tritici, which is a Gram positive, plant pathogenic, non-motile, and rod-shaped bacterium, causes spike blight in wheat and barley. For successful pathogenesis, R. tritici is associated with Anguina tritici, a nematode, which produces seed galls (ear cockles) in certain plant varieties and facilitates spread of infection. Despite significant efforts, little research is available on the mechanism of disease or bacteria-nematode association of this bacterium due to lack of genomic information. Here, we report the first complete genome sequence of R. tritici NCPPB 1953 with diverse features of this strain. The whole genome consists of one circular chromosome of 3,354,681 bp with a GC content of 69.48%. A total of 2,979 genes were predicted, comprising 2,866 protein coding genes and 49 RNA genes. The comparative genomic analyses between R. tritici NCPPB 1953 and R. toxicus strains identified 1,052 specific genes in R. tritici NCPPB 1953. Using the BlastKOALA database, we revealed that the flexible genome of R. tritici NCPPB 1953 is highly enriched in ‘Environmental Information Processing’ system and metabolic processes for diverse substrates. Furthermore, many specific genes of R. tritici NCPPB 1953 are distributed in substrate-binding proteins for extracellular signals including saccharides, lipids, phosphates, amino acids and metallic cations. These data provides clues on rapid and stable colonization of R. tritici for disease mechanism and nematode association.

Earthworms and cadmium – Heavy metal resistant gut bacteria as indicators for heavy metal pollution in soils?

“…Furthermore, Streptomyces caeruleus has been found to help earthworms in organic matter metabolism and plant material decomposition (60). Rathayibacter is a known genus of soil bacteria and contains plant pathogens (61). Nocardioides has been associated with the cast of the earthworm E. andrei (62) and Agromyces bacteria and the Rhodococcus strain has been isolated from the earthworm gut (63,64).…”

Specific and Sensitive Primers Developed by Comparative Genomics to Detect Bacterial Pathogens in Grains

“…Since Rt was previously classified as a species of Clavibacter and separated from Clavibacter ( Zgurskaya et al, 1993 ), we tested the primer pairs with Clavibacter species. Most of primer pairs designed by Rt genome information ( Park et al, 2017 ) seem specific and neither detect the Clavibacter species nor the closely related Rathayibacter species such as R. toxicus , R. iranicus and R. rathayi ( Fig. 3 ).…”

“…To search for pathogen-specific genes of target bacterial pathogens, whole genome information of target bacteria and their closely related species was retrieved from National Center for Biotechnology Information (NCBI) database ( ftp://ftp.ncbi.nlm.nih.gov/genomes/bacteria/ ) at completed or scaffold level of assembly except for contig level and is listed in Table 2 . We also used whole genome sequence information of Rt previously studied ( Park et al, 2017 ). Based on the acquired genomic information, BLASTN searches were initially performed using 2,801 coding sequences (CDS) of Cmn , 4,942 CDS of Pss and 2,995 CDS of Rt as query against the constructed subject nucleotide sequences consisting of CDS of closely related species to the target bacterial pathogen.…”

“…Rt infection and rapid spread is frequently associated with Anguina tritici , a nematode, producing seed galls (ear cockles) in certain plant varieties ( Paruthi and Bhatti, 1985 ). Despite the wide distribution of this bacterial pathogen ( Park et al, 2017 ), no reliable detection method has been reported so far.…”