Abstract
Compared to those of dicot-infecting bacteria, the available genome sequences of bacteria that infect wheat and barley are limited. Herein, we report the draft genome sequences of four pseudomonads originally isolated from these cereals. These genome sequences provide a useful resource for comparative analyses within the genus and for cross-kingdom analyses of plant pathogenesis.
GENOME ANNOUNCEMENT
Recent comparative genomics analyses of fungi have revealed the importance of cross-kingdom lateral gene transfers in the evolution of the virulence of eukaryotic microbes (1–3). For example, we have identified virulence-associated genes specific to cereal fungal pathogens where phylogenetic analysis strongly indicates that they have been acquired by horizontal gene transfer from bacteria (2). Moreover, in some cases, the most similar sequences available in public repositories to the fungal genes are from plant-associated bacteria. However, the availability of genome sequences of cereal-associated bacteria, particularly those associated with wheat and barley, is limited compared to the availability of genome sequences of dicot-associated bacteria. Herein, we report the genome sequences of four Pseudomonas spp. isolated from cereals in Australia to augment the availability of cereal-associated bacterial genomes for comparative analyses.
Cultures of Pseudomonas associated with wheat or barley were selected from the Queensland Plant Pathology Herbarium (BRIP). The isolates Pseudomonas syringae BRIP 34876 and BRIP 34881 and Pseudomonas fluorescens BRIP 34879 were originally isolated from barley glumes showing rot symptoms in September 1971 near Warwick, Queensland, Australia. P. syringae isolate BRIP 39023 was isolated from wheat glumes in September 1988 near Bauhinia Downs, Queensland, Australia. In reinoculation experiments on barley and wheat leaves, the P. syringae isolates BRIP 34876 and BRIP 34881 resulted in symptom development in both hosts, while P. fluorescens BRIP 34879 and P. syringae BRIP 39023 did not induce symptoms.
DNA for genome sequencing was prepared from bacteria grown in liquid culture using a Qiagen blood and tissue kit, according to the manufacturer’s instructions. Illumina library preparation and sequencing were performed by the Australian Genome Research Facility, Melbourne, Australia, using one-fifth of a HiSeq 2000 lane for each library. Following quality filtering (with a low-quality threshold of 0.05, the maximum number of ambiguities set at 2, removal of 2 terminal nucleotides, and a minimum length of 50 bases) of paired-end Illumina reads, the genome sequences were assembled from a minimum of 5.2 × 107 reads using the CLC Genomics Workbench version 5.1 with the scaffolding option selected (minimum contig size, 200 bp). Coverage of the genomes ranged from 836- to 1,208-fold. Total genome size ranged from 5.5 to 6 Mbp. Details of the genome assemblies are presented in Table 1. Scaffolds were split into component contigs at any site of sequence ambiguity (i.e., even a single N) using custom Perl scripts to allow gene annotation using the NCBI Prokaryote Genomes Automatic Annotation Pipeline (PGAAP). Contig relationships were maintained in the GenBank submission by the inclusion of A Golden Path (AGP) file. The output of the PGAAP was manually curated to correct the nomenclature of the type III secretion system effectors in the P. syringae genomes.
TABLE 1.
Genome assembly statistics and accession numbers
| Isolate | Assembly size (Mbp) |
Scaffold no. (contigs) |
N50a | L50 (kbp)a | Accession no. |
|---|---|---|---|---|---|
|
P. syringae BRIP 34876 |
6.02 | 99 (148) | 7 | 232 | AMXK00000000 |
|
P. fluorescens BRIP 34879 |
5.53 | 110 (261) | 13 | 150 | AMZW00000000 |
|
P. syringae BRIP 34881 |
6.12 | 96 (157) | 6 | 300 | AMXL00000000 |
|
P. syringae BRIP 39023 |
5.94 | 35 (71) | 6 | 356 | AMZX00000000 |
N50 and L50 statistics refer to scaffold sequences.
Nucleotide sequence accession numbers.
These Whole-Genome Shotgun projects have been deposited at DDBJ/EMBL/GenBank under the following accession no.: AMXK00000000 for P. syringae isolate BRIP 34876, AMXL00000000 for P. syringae isolate BRIP 34881, AMZW00000000 for P. fluorescens isolate BRIP 34879, and AMZX00000000 for P. syringae isolate BRIP 39023.
ACKNOWLEDGMENTS
The sequencing work presented in this paper was supported by the BioPlatforms Australia Wheat Pathogenomics Initiative. D.M.G. was partially supported by the Australian Grains Industry Research and Development Corporation.
Footnotes
Citation Gardiner DM, Stiller J, Covarelli L, Lindeberg M, Shivas RG, Manners JM. 2013. Genome sequences of Pseudomonas spp. isolated from cereal crops. Genome Announc. 1(3):e00209-13. doi:10.1128/genomeA.00209-13.
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