Genomic Analysis of Xanthomonas oryzae Isolates from Rice Grown in the United States Reveals Substantial Divergence from Known X. oryzae Pathovars

Abstract

The species Xanthomonas oryzae is comprised of two designated pathovars, both of which cause economically significant diseases of rice in Asia and Africa. Although X. oryzae is not considered endemic in the United States, an X. oryzae-like bacterium was isolated from U.S. rice and southern cutgrass in the late 1980s. The U.S. strains were weakly pathogenic and genetically distinct from characterized X. oryzae pathovars. In the current study, a draft genome sequence from two U.S. Xanthomonas strains revealed that the U.S. strains form a novel clade within the X. oryzae species, distinct from all strains known to cause significant yield loss. Comparative genome analysis revealed several putative gene clusters specific to the U.S. strains and supported previous reports that the U.S. strains lack transcriptional activator-like (TAL) effectors. In addition to phylogenetic and comparative analyses, the genome sequence was used for designing robust U.S. strain-specific primers, demonstrating the usefulness of a draft genome sequence in the rapid development of diagnostic tools.The species Xanthomonas oryzae is comprised of pathovars oryzae and oryzicola, the causative agents of bacterial leaf blight (BLB) and bacterial leaf streak (BLS) on rice, respectively (27). Although the two pathovars are closely related, BLB is a vascular disease characterized by marginal leaf lesions, while BLS affects parenchyma cells and results in leaf streaking. Both pathovars can cause substantial losses to rice production (27). X. oryzae has been designated a USDA select agent in the United States, and movement is restricted by several international quarantines (25,29).The finished genomes of three Asian X. oryzae pv. oryzae strains and one X. oryzae pv. oryzicola strain are available, facilitating in-depth comparative genomic analyses (22,28,35) (GenBank accession no. AAQN01000001). Whole-genome alignment revealed that the sequenced X. oryzae pv. oryzae strains, MAFF 311018, KACC 10331, and PXO99A, are very closely related (24, 35). X. oryzae pv. oryzicola clusters with the X. oryzae group, forming a branch distinct from X. oryzae pv. oryzae strains (24, 35). All the X. oryzae genomes are characterized by large numbers of insertion sequence (IS) elements, the major contributors to sequence diversity within the species (28, 35), and by various numbers of secreted transcriptional activator-like (TAL) effectors required for full virulence (35,42). The African X. oryzae pv. oryzae strains are different from Asian strains and more closely related to Asian X. oryzae pv. oryzicola. A specific and intriguing feature of African X. oryzae pv. oryzae strains is that the genome contains a smaller number of TAL effector and IS elements than the Asian strains (8). Bacterial blight has also been observed in South America (12, 23); strains isolated in Colombia are closely related to Asian strains (15,17).Although X. oryzae is not historically considered indigenous to the United States (27), strains of a yellow bacterium causing mild BLB-like symptoms we...

New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae

“…On a global scale, the MLVA-16 scheme confirmed the lineage differentiation that was largely described in previous typing and phylogenetic studies (20,33,34,55). However, on a smaller scale, the MLVA-16 scheme was shown to be more discriminatory than other previously used molecular-typing tools.…”

“…oryzicola (from Asia and Africa). More recently, multilocus sequence typing (MLST) targeting nine housekeeping genes of a few strains of X. oryzae confirmed the designation of the three lineages (33). Other studies combining multilocus sequence analysis (MLSA) with the analysis of the type III effector repertoires of 40 X. oryzae strains belonging to different pathovars and from different geographical origins clearly confirmed that both X. oryzae pv.…”

Sensitive Detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by Loop-Mediated Isothermal Amplification

“…oryzae, 40 strains of X. oryzae pv. oryzicola, and 7 strains of a distinct group of X. oryzae isolates recovered in the United States (13,29). An additional 31 strains representing other plant-pathogenic species and unknown bacteria isolated from rice tissue and seed were tested.…”

“…oryzae and two strains of X. oryzae pv. oryzicola are publicly available (GenBank accession numbers AYSX00000000 and AYSY00000000, respectively) (11)(12)(13)(14). These resources, along with draft genome sequences of another nine X. oryzae strains, provided insights into the genetic diversity among strains within this species, including a unique group of weakly pathogenic X. oryzae strains isolated in the United States (13; V. Verdier, unpublished).…”

“…oryzae, and X. oryzae pv. oryzicola) and differentiated certain groups of strains on the basis of their geographic origin (13,15). Multilocus sequence analysis and restriction fragment polymorphism analysis have shown that X. oryzae pv.…”