Here, we report the complete genome sequence of Xanthomonas arboricola pv. juglandis 417, a copper-resistant strain isolated from a blighted walnut fruit (Juglans regia L. cv. Chandler). The genome consists of a single chromosome (5,218 kb)

Adaskaveg, James E

Dandekar, Abhaya M

Goulart, Luiz Ricardo

Gouran, Hossein

Nascimento, Rafael

Pereira, Ulisses P

eScholarship - University of California

UC DavisUC Davis Previously Published WorksTitleComplete Genome Sequence of Xanthomonas arboricola pv. juglandis 417, a Copper-Resistant Strain Isolated from Juglans regia L.Permalinkhttps://escholarship.org/uc/item/7x4448n0JournalMicrobiology Resource Announcements, 3(5)ISSN2576-098XAuthorsPereira, Ulisses PGouran, HosseinNascimento, Rafaelet al.Publication Date2015-10-29DOI10.1128/genomea.01126-15 Peer reviewedeScholarship.org Powered by the California Digital LibraryUniversity of CaliforniaComplete Genome Sequence of Xanthomonas arboricola pv. juglandis417, a Copper-Resistant Strain Isolated from Juglans regia L.Ulisses P. Pereira,a Hossein Gouran,b Rafael Nascimento,c James E. Adaskaveg,d Luiz Ricardo Goulart,c Abhaya M. DandekarbPreventive Veterinary Medicine Department, State University of Londrina, Campus UEL, Londrina, PR, Brazila; Plant Sciences Department, University of California Davis,Davis, California, USAb; Institute of Genetics and Biochemistry, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazilc; Department of PlantPathology and Microbiology, University of California Riverside, California, USAdHere, we report the complete genome sequence of Xanthomonas arboricola pv. juglandis 417, a copper-resistant strain isolatedfrom a blighted walnut fruit (Juglans regia L. cv. Chandler). The genome consists of a single chromosome (5,218 kb).Received 17 August 2015 Accepted 19 August 2015 Published 1 October 2015Citation Pereira UP, Gouran H, Nascimento R, Adaskaveg JE, Goulart LR, Dandekar AM. 2015. Complete genome sequence of Xanthomonas arboricola pv. juglandis 417, acopper-resistant strain isolated from Juglans regia L. Genome Announc 3(5):e01126-15. doi:10.1128/genomeA.01126-15.Copyright © 2015 Pereira et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Abhaya M. Dandekar, amdandekar@ucdavis.edu.The Gram-negative gammaproteobacterium Xanthomonas ar-boricola pv. juglandis, the causal agent of walnut blight, is themost important disease of Persian (English) walnut (Juglans regiaL.) in California and many other production areas worldwide (1–3). The disease can occur on seedlings and mature walnut treesand is considered a major cause of yield reductions. The bacteriaattacks leaves, buds, catkins, and young twigs, but fruits are gen-erally most susceptible to infection. Symptoms begin as smalldark-brown spots with a yellowish halo that develop into largerareas of dark, dead tissue. Most of the economic loss due to walnutblight is associated with fruit infection, which can lead to theirpremature drop and reduction in nut quality of fruit that remainon the tree (4–6). The disease is most severe in climates with rainsthroughout the growing season, however, in California the diseasedevelops during spring rains. Host susceptibility differs amongcultivars (7); however, all commercially grown walnut varietiesare considered susceptible to walnut blight (8).The current management strategy for walnut blight is mostlybased on multiple applications of copper-based bactericides forprotecting susceptible plant tissue, but efficacy is often variable(9). Extensive copper usage for the past decades has caused selec-tion for copper-resistant strains (10, 11). We describe here thegenome sequence of X. arboricola pv. juglandis strain 417, acopper-resistant strain isolated from a blighted cv. Chandler wal-nut fruit in Chico, California, in 2012.The genome sequence was obtained using the MiSeq (IlluminaInc., San Diego, CA) system with two paired-end libraries, whichgenerated 10,403,000 and 9,233,152 (both with reads of 100 bp insize) and insert size of 500 bp and 2,000 bp, respectively. Theestimated genome coverage with these two libraries was ~385-fold. After sequencing, reads were assembled using Mira 4.0 soft-ware (12) resulting in 59 contigs, N50 of 171,731 bp, and the small-est contig of 1,102 bp. These contigs were ordered using theContiguator software (13) against many genomes of the same ge-nus. The genome of X. campestris strain 17 (GenBank accessionnumber CP011256) was used as a reference due to better syntenyand number of contigs mapped. The initial scaffold was later sub-jected to a finishing process using CLC Genomics Workbenchsoftware, and gaps were removed with recursive rounds of shortreads mapped against the scaffold (14). The annotation step wasperformed using NCBI Prokaryotic Genome Annotation Pipe-line.The final genome had five large contigs separated by four gaps,the total size was 5,218,943 nucleotides with 4,178 putative openreading frames. The GC content was 65.41%, there were threerRNA genes, 52 tRNA genes, and 133 predicted pseudogenes. Fur-ther analysis of the genome is now under way. It will allow us toidentify specific factors that might explain the differences in thepathobiology of X. arboricola pv. juglandis when compared toother members of the Xanthomonadaceae family.Nucleotide sequence accession number. The Xanthomonasarboricola pv. juglandis strain 417 genome sequence and annota-tion data have been deposited at DDBJ/EMBL/GenBank under theaccession number CP012251.ACKNOWLEDGMENTJ.E.A. and A.M.D. wish to acknowledge the support of the CaliforniaWalnut Board for this research.REFERENCES1. Du Plessis HJ, Van der Westhuizen TJ. 1995. Identification of Xan-thomonas campestris pv. juglandis from (Persian) English walnut nurserytrees in South Africa. J Phytopathol 143:449 – 454. http://dx.doi.org/10.1111/j.1439-0434.1995.tb04552.x.2. Lang MD, Evans KJ. 2010. Epidemiology and status of walnut blight inAustralia. J Plant Pathol 92:S1.35–S1.48.3. Mulrean EN, Schroth MN. 1982. Ecology of Xanthomonas campestris pv.juglandis on Persian (English) walnuts. Phytopathology 72:434 – 438.http://dx.doi.org/10.1094/Phyto-72-434.4. Belisario BA, Zoina A, Pezza L, Luongo L. 1999. Susceptibility of speciesof Juglans to pathovars of Xanthomonas campestris. Eur J Forest Pathol29:75– 80. http://dx.doi.org/10.1046/j.1439-0329.1999.00132.x.5. Esterio MA, Latorre BA. 1982. Potential sources of inoculum of Xan-thomonas juglandis in walnut blight outbreaks. J Hort Sci 57:69 –72.6. Olson WH, Moller WJ, Fitch LB, Jeter RB. 1976. Walnut blight control.Calif Agric 30:10 –13.crossmarkGenome AnnouncementsSeptember/October 2015 Volume 3 Issue 5 e01126-15 genomea.asm.org 17. Woeste KE, McGranahan GH, Schroth MN. 1992. Variation amongPersian walnuts in response to inoculation with Xanthomonas campestrispv. juglandis. J Am Soc Hort Sci 117:527–531.8. Lindow S, Olson W, Buchner R. 2014. Colonization of dormant walnutbuds by Xanthomonas arboricola pv. juglandis is predictive of subsequentdisease. Phytopathology 104:1163–1174. http://dx.doi.org/10.1094/PHYTO-01-14-0001-R.9. Ninot A, Aletà N, Moragrega C, Montesinos E. 2002. Evaluation of areduced copper spraying program to control bacterial blight of walnut.Plant Dis 86:583–587. http://dx.doi.org/10.1094/PDIS.2002.86.6.583.10. Gardan L, Brault T, Germain E. 1993. Copper resistance of Xanthomonascampestris pv. juglandis in French walnut orchards and its association withconjugative plasmids. Acta Hort 311:259 –265. http://dx.doi.org/10.17660/ActaHortic.1993.311.33.11. Lee Y-A, Schroth MN, Hendson M, Lindow SE, Wang X-L, Olson B,Buchner RP, Teviotdale B. 1993. Increased toxicity of iron-amendedcopper-containing bactericides to the walnut blight pathogen Xanthomo-nas campestris pv. juglandis. Phytopathology 83:1460 –1465. http://dx.doi.org/10.1094/Phyto-83-1460.12. Chevreux B, Wetter T, Suhai S. 1999. Genome sequence assembly usingtrace signals and additional sequence information, p 45–56. In Computerscience and biology. Proceedings of the German Conference on Bioinfor-matics, GCB ’99. GCB, Hannover, Germany.13. Galardini M, Biondi EG, Bazzicalupo M, Mengoni A. 2011.CONTIGuator: a bacterial genomes finishing tool for structural insightson draft genomes. Source Code Biol Med 6:11. http://dx.doi.org/10.1186/1751-0473-6-11.14. Tsai IJ, Otto TD, Berriman M. 2010. Improving draft assemblies byiterative mapping and assembly of short reads to eliminate gaps. GenomeBiol 11:R41. http://dx.doi.org/10.1186/gb-2010-11-4-r41.Pereira et al.Genome Announcements2 genomea.asm.org September/October 2015 Volume 3 Issue 5 e01126-15

Complete Genome Sequence of Xanthomonas arboricola pv. juglandis 417, a Copper-Resistant Strain Isolated from Juglans regia L.

Abstract

Similar works

Full text

Available Versions

eScholarship - University of California