Comparative Genomic Analysis of Xanthomonas axonopodis pv. citrumelo F1, Which Causes Citrus Bacterial Spot Disease, and Related Strains Provides Insights into Virulence and Host Specificit

Abstract

Xanthomonas axonopodis pv. citrumelo is a citrus pathogen causing citrus bacterial spot disease that is geographically restricted within the state of Florida. Illumina, 454 sequencing, and optical mapping were used to obtain a complete genome sequence of X. axonopodis pv. citrumelo strain F1, 4.9 Mb in size. The strain lacks plasmids, in contrast to other citrus Xanthomonas pathogens. Phylogenetic analysis revealed that this pathogen is very close to the tomato bacterial spot pathogen X. campestris pv. vesicatoria 85-10, with a completely different host range. We also compared X. axonopodis pv. citrumelo to the genome of citrus canker pathogen X. axonopodis pv. citri 306. Comparative genomic analysis showed differences in several gene clusters, like those for type III effectors, the type IV secretion system, lipopolysaccharide synthesis, and others. In addition to pthA, effectors such as xopE3, xopAI, and hrpW were absent from X. axonopodis pv. citrumelo while present in X. axonopodis pv. citri. These effectors might be responsible for survival and the low virulence of this pathogen on citrus compared to that of X. axonopodis pv. citri. We also identified unique effectors in X. axonopodis pv. citrumelo that may be related to the different host range as compared to that of X. axonopodis pv. citri. X. axonopodis pv. citrumelo also lacks various genes, such as syrE1, syrE2, and RTX toxin family genes, which were present in X. axonopodis pv. citri. These may be associated with the distinct virulences of X. axonopodis pv. citrumelo and X. axonopodis pv. citri. Comparison of the complete genome sequence of X. axonopodis pv. citrumelo to those of X. axonopodis pv. citri and X. campestris pv. vesicatoria provides valuable insights into the mechanism of bacterial virulence and host specificity.Xanthomonas is an important genus of plant pathogenic bacteria (87). These Gram-negative rod-shaped pathogens belong to the class Gammaproteobacteria and can infect over 350 species of plants (12). Among the diseases on citrus, citrus bacterial canker (CBC) and citrus bacterial spot (CBS) are caused by distinct pathovars of Xanthomonas species. Citrus canker is caused by several pathogenic variants of X. axonopodis pv. citri (synonyms Xanthomonas citri, Xanthomonas campestris pv. citri, or Xanthomonas citri subsp. citri) (90, 109), whereas CBS is caused by X. axonopodis pv. citrumelo. X. axonopodis pv. citri strain 306 with a suspected origin in southeastern Asia causes Asiatic type A canker and is the most widespread and virulent form of CBC. It produces hyperplasic and hypertrophic (corky) lesions surrounded by oily or watersoaked margins and a yellow halo on leaves, stems, and fruits.In 1984, a disease similar to citrus canker was discovered in citrus nurseries in central Florida, leading to the destruction of millions of seedlings (98). This new form of citrus canker was described as the "E-strain" group, also known as nursery strain canker. Leaf spots of this strain are irregular to round, 3 to 5 mm in diameter, flat, water so...

Positive selection is the main driving force for evolution of citrus canker-causing Xanthomonas

“…A de novo BamHI optical map of the genome of XacA*270 was generated by OpGen Technologies (Madison, WI, USA). The draft genome of XacA*270 was closed using the method described in our previous study (Jalan et al, 2011).…”

“…The reads from XacA and XacA w strains were reference assembled against XacA306 and XacA w 12879 genome (da Silva et al, 2002; Jalan et al, 2013b), respectively. As no XacA* genome was publically available, De Novo assembly was conducted for the genome of XacA*270 (Supplementary Table S2) using previously described methodology (Jalan et al, 2011), and the two remaining XacA* strains were reference assembled based on the XacA*270 genome. The comparison of our reads and assemblies (Supplementary Table S3) with other published assemblies for Xanthomonas (Bart et al, 2012) indicated that our assemblies are of high quality.…”

HrcT Is a Key Component of the Type III Secretion System in Xanthomonas spp. and Also Regulates the Expression of the Key hrp Transcriptional Activator HrpX

“…3B). In addition to the numerous regulatory loci that map elsewhere in the Xanthomonas genomes (16)(17)(18)(19)(20), our findings highlight the existence of key regulatory loci that map within the hrp-hrc-hpa genes in X. oryzae pv. oryzicola.…”

“…In xanthomonads, the hrp-hrc-hpa genes are highly conserved and clustered within several sequenced genomes (16)(17)(18)(19)(20). Our previous studies revealed that the hrp cluster in X. oryzae pv.…”

Identification of New Genes Related to Virulence of <i>Xanthomonas axonopodis</i> Pv. <i>Citri</i> during Citrus Host Interactions

“…citrumelonis (X. axonopodis pv. citrumelo), which specifically attacks rootstocks of the 'Swingle' citrumelo (Citrus paradisi x Poncirus trifoliata) [28], and the fifth ortholog was found in X. campestris pv. ve-sicatoria, which causes disease in peppers and tomatoes [29].…”