Abstract
Xanthomonas arboricola pv. juglandis is an important pathogen responsible for walnut blight outbreaks globally. Here, we report four draft genome sequences of X. arboricola pv. juglandis strains isolated from Chilean walnut trees.
GENOME ANNOUNCEMENT
The Persian or English (Juglans regia L.) walnut tree is a species widely cultivated worldwide. Walnut blight is the main disease affecting walnut production; if not controlled, yield losses can exceed 50% (1, 2). It is caused by the bacterium Xanthomonas arboricola pv. juglandis (Xaj); Xaj is especially important in locations that have warm and rainy springs, because they are favorable conditions for rapid proliferation (2, 3). In Chile, walnuts tree are planted from the Copiapó (latitude 27°30′S) down to Temuco (38°45′S), with Xaj affecting the southern areas of the country.
Agrochemicals based on copper in its various formulations are the principal tools used in controlling Xaj in walnut trees (4). Despite its widespread use, its efficiency has decreased, which could be explained by the ability of bacteria to acquire resistance mechanisms (4–6). This situation is aggravated by evidence suggesting the transfer of copper resistance genes between bacteria (5). The analysis of the four genomes of Xaj presented here could help researchers understand the mechanisms involved in copper resistance in this pathogen.
Genomic DNA of each Xaj strain was extracted using the QIAamp DNA minikit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. Libraries were prepared using 1 ng of genomic DNA with the Nextera XT kit (Illumina, San Diego, CA), and the genomes were sequenced using MiSeq Illumina with the V2 kit (2 × 250 bp) according to the manufacturer’s instructions at 90× to 160× coverage. Genomic sequence contigs for each strain were de novo assembled using CLC Genomics Workbench version 8.2 (Qiagen). The genomic analysis was performed using the RAST server (7). The assembled sequences were annotated by the National Center for Biotechnology Information (NCBI) Prokariyotic Genomes Annotation Pipeline (PGAP, http://www.ncbi.nlm.nih.gov/genome/annotation_prok). The summary report for the 4 genomes sequenced in this study (genome size, G+C content, contigs number, and the number of RNA coding genes) are in Genes related to copper resistance mechanisms (copA, copB, copD, copG, cusA, cusC, cusF, cutA, and cutC) were detected in the four draft genomes, their similarity in nucleotide-based comparison ranged 86 to 100%. A detailed report of genomic features will be addressed in a future publication.
Nucleotide sequence accession numbers.
Genomes were deposited DDBJ/EMBL/GenBank under the accession numbers listed in Table 1. The assembly versions described in this paper are the first version of the assemblies.
TABLE 1.
Summary report of the de novo assembly of the four Chilean Xanthomonas arboricola pv. juglandis strains from this study
| Strain | CFSAN no. | GenBank accession no. | % G+C content | Genome size (bp) | No. of contigs | Avg coverage | No. of tRNAs | No. of rRNAs |
|---|---|---|---|---|---|---|---|---|
| Xaj2 | CFSAN033077 | LHBK00000000 | 65.4 | 5,101,226 | 197 | 150× | 51 | 3 |
| Xaj43a | CFSAN033086 | LHBT00000000 | 65.4 | 5,144,142 | 205 | 90× | 51 | 3 |
| XajA3 | CFSAN033085 | LHBS00000000 | 65.6 | 5,118,988 | 196 | 168× | 51 | 3 |
| Xaj4.1 | CFSAN033078 | LHBL00000000 | 65.6 | 5,116,263 | 215 | 107× | 49 | 3 |
ACKNOWLEDGMENT
This work was supported by FONDEF iDeA CA13I10117 from CONICYT Chile.
Footnotes
Citation Higuera G, González-Escalona N, Véliz C, Vera F, Romero J. 2015. Draft genome sequences of four Xanthomonas arboricola pv. juglandis strains associated with walnut blight in Chile. Genome Announc 3(5):e01160-15. doi:10.1128/genomeA.01160-15.
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