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.

Keywords: Rathayibacter toxicus; Rathayibacter tritici NCPPB 1953; comparative genome.

Fig. 1

Image of transmission electron microscope (TEM) photomicrograph (A–C) and the appearance of colony morphology on solid media (D) of Rathayibacter tritici NCPPB 1953. Cells were grown in NBY agar plate for 96 h. The magnification rates of TEM for A–C were 15,000×, 25,000×, and 10,000×, respectively. Bacterial capsules with extracellular outer layer were observed (black arrows).

Fig. 2

16S rRNA phylogenetic tree showing the relationships of Rathayibacter tritici NCPPB 1953 (shown in bold print) with other members in the genus Rathayibacter. Sequences were aligned using ClustalW and the phylogeny was inferred from the alignment of 1,267 bp of 16S rRNA using the Maximum Likelihood method based on the Tamura-Nei model with MEGA 7.0 software. The bootstrap consensus tree from 1,000 replicates was performed to assess the support of the clusters. The scale bar indicates 0.01 nucleotide change per nucleotide position. The GenBank accession numbers are shown in parentheses.

Fig. 3

Graphical circular map of Rathayibacter tritici NCPPB 1953 chromosome displaying relevant genetic features. From centre to outside: 1, positive (green) and negative (yellow) of GC skew; 2, GC content (black); 3, CDSs on reverse strand (blue); 4, CDSs on forward strand (red); 5, pseudogenes (grey); 6, tRNAs (brown); 7, rRNAs (pink). This figure was built using the CGView tool.

Fig. 4

Whole genome alignment of Rathayibacter tritici NCPPB 1953, Rathayibacter toxicus WAC3373, and Rathayibacter toxicus 70137. The top, middle, and bottom sequences represent each genomic sequence of R. tritici NCPPB 1953, R. toxicus WAC3373, and R. toxicus 70137, respectively. Identically coloured boxes by same lines are locally collinear blocks, indicating homologous and conservative regions in both genomes. Coloured bars inside boxes are related to the level of sequence similarities. Numbers above the map show nucleotide positions.

Fig. 5

Summary of biological systems in Rathayibacter tritici NCPPB 1953-specific genes. A distribution of the KEGG systems is displayed as a pie-chart. The number of gene counts is shown inside each pie of categories. Total 11 KEGG terms are displayed.

Fig. 6

The network of Rathayibacter tritici NCPPB 1953 in KEGG transporter. Pathway maps of KEGG transporter system were constructed by the Cytoscape tool. The KEGG database was used to download the data source. There are two color types in the rectangle node: red, genes belonging to flexible genome of R. tritici NCPPB 1953; green, genes belonging to the core genome among R. tritici NCPPB 1953, R. toxicus WAC3373, and R. toxicus 70137.