Abstract
Here, we report the draft genome sequence of the Xanthomonas bromi type strain LMG 947, an important pathogen of bromegrasses (Bromus spp.). Comparative analysis with other Xanthomonas spp. that are pathogenic on forage grasses will assist the analysis of host-plant adaptation at the genome level.
GENOME ANNOUNCEMENT
Two Xanthomonas spp. (X. translucens and X. bromi) are known as grassland pathogens (1). While both species cause bacterial wilt on forage grasses, DNA-DNA hybridization assays and analysis of both protein and fatty acid methyl ester profiles have revealed distinct interspecies differences (2). Phylogenetic analysis of Xanthomonas spp. using multilocus sequence analysis of various housekeeping genes (i.e., gyrB, rpoD, dnaK, and fyuA) divided the analyzed 119 strains into two major groups (3). These two groups have been found to separate the two forage grass–affecting Xanthomonas spp. and thus suggest a high genetic distance for both X. bromi and X. translucens. Several studies on the pathogenesis (4, 5) and genome mining of virulence-related traits (6) have contributed to an understanding of the underlying mechanisms of bacterial wilt caused by X. translucens pathovars; however, no genome information was available for X. bromi. Reports on bacterial wilt caused by X. bromi indicate a wide distribution of this pathogen throughout New Zealand and France among a variety of different Bromus spp. (7, 8). The type strain LMG 947 (BCCM/LMG culture collection of the Laboratory of Microbiology, Ghent University, Belgium) was isolated in 1980 in France from the species Bromus carinatus, which shows high susceptibility for bacterial wilt caused by X. bromi (2, 7).
In this study, the X. bromi LMG 947 genome was sequenced to get the first insights into its gene content. The paired-end (2 × 300-bp) sequencing run on the Illumina MiSeq platform (Illumina Inc, San Diego, California, USA) resulted in 4,880,586 reads yielding approximately 1.4 Gb of sequence data. A de novo assembly of the obtained Illumina sequence reads applying Newbler Assembly version 2.8 software (Roche, Basel, Switzerland) resulted in 84 scaffolds and 134 contigs. The software platform GenDB (9) was applied to annotate the X. bromi LMG 947 draft genome. The X. bromi LMG 947 draft genome features a 4,843,951-bp chromosome harboring an average GC content of 64.05%. A total of 4,190 protein coding sequences, 53 tRNAs, and three rRNAs were predicted. Xanthomonas spp. share a variety of common virulence-related traits like the type III secretion system (T3SS) encoded by the hypersensitive response and pathogenicity gene cluster (10), as well as type III secreted effector proteins (11). The LMG 947 genome was found to harbor a canonical T3SS (12), as well as 28 putative type III effector proteins identified by BLASTp analysis against the effectors listed in the online database of Xanthomonas effector proteins (http://xanthomonas.org/t3e.html). A homology search revealed that the putative effector proteins belong to 22 different effector classes (i.e., AvrBs2, XopA, XopAD, XopAE, XopAF, XopAG, XopAH, XopAJ, XopAM, XopE, XopF, XopH, XopI, XopK, XopL, XopN, XopP, XopQ, XopR, XopV, XopX, and XopZ). Moreover, the genome data of LMG 947 indicate the presence of a transcription activator–like effector class AvrBs3 homologue (13). With respect to the high genetic and phenotypic differences between forage grass–affecting Xanthomonas spp., the X. bromi type strain LMG 947 will complement genomic information of forage grass–affecting X. translucens pathovars and may facilitate the identification of conserved traits linked to host adaptation.
Accession number(s).
This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession numbers FLTX01000001 to FLTX01000134. The version described in this paper is the first version, FLTX01000000.
ACKNOWLEDGMENTS
We thank Frank-Jörg Vorhölter and Anika Winkler for their assistance in handling the sequencing project.
Footnotes
Citation Hersemann L, Wibberg D, Blom J, Widmer F, Kölliker R. 2016. Draft genome sequence of the Xanthomonas bromi type strain LMG 947. Genome Announc 4(5):e00961-16. doi:10.1128/genomeA.00961-16.
REFERENCES
- 1.Vauterin L, Hoste B, Kersters K, Swings J. 1995. Reclassification of Xanthomonas. Int J Syst Bacteriol 45:472–489. doi: 10.1099/00207713-45-3-472. [DOI] [Google Scholar]
- 2.Vauterin L, Yang P, Hoste B, Pot B, Swings J, Kersters K. 1992. Taxonomy of xanthomonads from cereals and grasses based on SDS-page of proteins, fatty acid analysis and DNA hybridization. J Gen Microbiol 138:1467–1477. doi: 10.1099/00221287-138-7-1467. [DOI] [Google Scholar]
- 3.Young JM, Park DC, Shearman HM, Fargier E. 2008. A multilocus sequence analysis of the genus Xanthomonas. Syst Appl Microbiol 31:366–377. doi: 10.1016/j.syapm.2008.06.004. [DOI] [PubMed] [Google Scholar]
- 4.Leyns F, De Cleene M, Van Bogaert G, Van de Wiele A, De Ley J. 1988. Preliminary investigations about the mode of transmission and spread of Xanthomonas campestris pv. graminis on forage grasses. J Phytopathol 122:76–88. doi: 10.1111/j.1439-0434.1988.tb00992.x. [DOI] [Google Scholar]
- 5.Schmidt D. 1989. Epidemiological aspects of bacterial wilt of fodder grasses. Bull OEPP/EPPO Bull 19:89–95. [Google Scholar]
- 6.Wichmann F, Vorhölter FJ, Hersemann L, Widmer F, Blom J, Niehaus K, Reinhard S, Conradin C, Kölliker R. 2013. The noncanonical type III secretion system of Xanthomonas translucens pv. graminis is essential for forage grass infection. Mol Plant Pathol 14:576–588. doi: 10.1111/mpp.12030. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Stewart AV. 1996. Potential value of some Bromus species of the section Ceratochloa. New Zeal J Agr Res 39:611–618. doi: 10.1080/00288233.1996.9513220. [DOI] [Google Scholar]
- 8.Schmidt D. 1995. Le flétrissement bactérien des graminées fourragères. Rev Suisse Agric 27:325–328. [Google Scholar]
- 9.Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Pühler A. 2003. GenDB—an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31:2187–2195. doi: 10.1093/nar/gkg312. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Bonas U, Schulte R, Fenselau S, Minsavage GV, Staskawicz BJ, Stall RE. 1991. Isolation of a gene cluster from Xanthomonas campestris pv. vesicatoria that determines pathogenicity and the hypersensitive response on pepper and tomato. Mol Plant Microbe Interact 4:81–88. doi: 10.1094/MPMI-4-081. [DOI] [Google Scholar]
- 11.White FF, Potnis N, Jones JB, Koebnik R. 2009. The type III effectors of Xanthomonas. Mol Plant Pathol 10:749–766. doi: 10.1111/j.1364-3703.2009.00590.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Weber E, Ojanen-Reuhs T, Huguet E, Hause G, Romantschuk M, Korhonen TK, Bonas U, Koebnik R. 2005. The type III-dependent Hrp pilus is required for productive interaction of Xanthomonas campestris pv. vesicatoria with pepper host plants. J Bacteriol 187:2458–2468. doi: 10.1128/JB.187.7.2458-2468.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Boch J, Bonas U. 2010. Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu Rev Phytopathol 48:419–436. doi: 10.1146/annurev-phyto-080508-081936. [DOI] [PubMed] [Google Scholar]