Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot on foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onions. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onions and millets or on millets only, respectively. In the current study, we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n = 4) and pv. setariae (n = 13)]. The full spectrum of the pan-genome contained 7030 genes. Among these, 3546 (present in genomes of all 17 strains) were the core genes that were a subset of 3682 soft-core genes (present in ≥16 strains). The accessory genome included 1308 shell genes and 2040 cloud genes (present in ≤2 strains). The pan-genome showed a clear linear progression with &gt;6000 genes, suggesting that the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison with core genome SNPs-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study using Psi strains from both pathovars along with strains from other Pantoea species, namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfer events occurring between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes, including seven gene-clusters, which were associated with the pathogenicity phenotype (necrosis on seedling) on onions. One of the gene-clusters contained 11 genes with known functions and was found to be chromosomally located.</jats:p

Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot on foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onions. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onions and millets or on millets only, respectively. In the current study, we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n = 4) and pv. setariae (n = 13)]. The full spectrum of the pan-genome contained 7030 genes. Among these, 3546 (present in genomes of all 17 strains) were the core genes that were a subset of 3682 soft-core genes (present in ≥16 strains). The accessory genome included 1308 shell genes and 2040 cloud genes (present in ≤2 strains). The pan-genome showed a clear linear progression with &gt;6000 genes, suggesting that the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison with core genome SNPs-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study using Psi strains from both pathovars along with strains from other Pantoea species, namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfer events occurring between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes, including seven gene-clusters, which were associated with the pathogenicity phenotype (necrosis on seedling) on onions. One of the gene-clusters contained 11 genes with known functions and was found to be chromosomally located

Pan-genome of Novel &lt;em&gt;Pantoea stewartii&lt;/em&gt; subsp. &lt;em&gt;indologenes&lt;/em&gt; Reveal Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot of foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onion. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onion and millets or on millets only, respectively. In the current study we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n= 4) and pv. setariae (n=13)]. The full spectrum of the pan-genome contained 7,030 genes. Among these, 3,546 (present in genomes of all 17 strains) were the core genes that were a subset of 3,682 soft-core genes (present in &amp;ge;16 strains). The accessory genome included 1,308 shell genes and 2,040 cloud genes (present in &amp;le; 2 strains). The pan-genome showed a clear liner progression with &amp;gt;6,000 genes, suggesting the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison to core genome SNP-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study including four other Pantoea species namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfers observed between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes including seven cluster of genes associated with the pathogenicity phenotype on onion. One of the clusters contain 11 genes with known functions and are found to be chromosomally located.</jats:p

Epiphytic Survival of <i>Pantoea ananatis</i> on <i>Richardia scabra</i> L. in Georgia

Pantoea ananatis, the causal organism of center rot of onion (Allium cepa L.), can survive on different weeds but, in a previous survey, it was most commonly found on Florida pusley (Richardia scabra L.). The epiphytic survival of P. ananatis on R. scabra under different temperature and moisture regimes was investigated. Weed seedlings were spray inoculated with rifampicin-resistant strain PNA 97-1rif at either 103 or 108 CFU/ml and incubated in a growth chamber at 15.5 or 21.1°C at 65% relative humidity for 96 h postinoculation (hpi), which represented the mean environmental conditions during mid-March to mid-May in Vidalia, GA when onion production and R. scabra presence overlap. For plants inoculated with P. ananatis at 103 CFU/ml, the bacterium survived for 96 hpi when incubated at 21.1°C, with mean populations of 1.7 × 102 CFU/g of leaf tissue. In contrast, no viable bacteria were detected after 72 hpi at 15.5°C. For plants inoculated with P. ananatis at 108 CFU/ml, the bacterium survived for 96 hpi at 21.1°C (3.8 × 105 CFU/g) whereas, during the sample time period, viable bacterial populations were not detected at 15.5°C. Survival of P. ananatis on R. scabra was also monitored during alternating 12 h wet and 12 h dry periods, or continuous wet or dry periods for 96 hpi at 15.5 or 21.1°C. Compared with initial or continuous dry periods, P. ananatis survived significantly better with a 12 h wet/12 h dry cycle or a continuous 96 hpi wet period at both 15.5 and 21.1°C. Unlike at 15.5°C, P. ananatis populations (7.4 × 102 CFU/g) survived for 96 hpi at 21.1°C under a cycle of 12 h dry and 12 h wet. These results demonstrate that P. ananatis can survive on R. scabra leaves under conditions of 21.1°C and prolonged leaf wetness and may potentially serve as a source of inoculum to onion. </jats:p

Characterization of a Peanut Leaf Spot of Unknown Etiology

Irregular leaf spot (ILS) of peanut was first noticed in Florida during the late 1990s. By 2000, ILS was apparent throughout much of the southeastern peanut growing region of the United States. Experiments were conducted to identify the cause of ILS, characterize ILS development over time, and evaluate the effect of genotype, tillage, and applications of fungicides and bactericides on ILS. Severities of ILS were near maximum levels at 33 to 42 days after planting (DAP) and in decline by 56 DAP. Incidence of ILS was greater in the lower canopy than the upper canopy. In most cases, ILS intensities were greater in strip-tilled plantings than conventional-tilled plantings and in the peanut breeding line UF-99325 than the cultivar Georgia Green. No fungicide or bactericide treatment suppressed ILS intensity. Attempts to isolate pathogenic fungi or bacteria from ILS lesions were unsuccessful. Although a pathogen cannot be totally dismissed as the cause of ILS, it is likely that ILS is caused by an abiotic factor. Accepted for publication 17 May 2010. Published 27 July 2010. </jats:p

An Epidemic of Downy Mildew caused by <i>Peronospora destructor</i> on Vidalia Sweet Onions in Georgia in 2012

The first reported occurrence of onion downy mildew (ODM) on Vidalia sweet onions in Georgia was in 1999. Although the disease is not common every year, two epidemics have occurred since 1999. The authors report here on the impact of a recent outbreak of ODM on the $100-million Vidalia onion crop in 2012. Accepted for publication 29 January 2013. Published 28 March 2013. </jats:p

Development of an Improved Isolation Approach and Simple Sequence Repeat Markers To Characterize Phytophthora capsici Populations in Irrigation Ponds in Southern Georgia▿

Phytophthora capsici, the causal agent of Phytophthora blight, is a major concern in vegetable production in Georgia and many other states in the United States. Contamination of irrigation water sources by P. capsici may be an important source of inoculum for the pathogen. A simple method was developed in this study to improve the efficiency of recovering P. capsici from fruits used as baits in irrigation ponds. In contrast to direct isolation on agar plates, infected fruit tissues were used to inoculate stems of pepper seedlings, and the infected pepper stems were used for isolation on agar plates. With isolation through inoculation of pepper stems, the frequency of recovering P. capsici from infected eggplant and pear fruits increased from 13.9% to 77.7% and 8.1% to 53.5%, respectively, compared with direct isolation on agar plates. P. capsici was isolated from seven out of nine irrigation ponds evaluated, with most of the ponds containing both A1 and A2 mating types and a 4:5 ratio of A1 to A2 when isolates from all ponds were calculated. All P. capsici isolates were pathogenic on squash plants, and only a small proportion (8.2%) of the isolates were resistant or intermediately sensitive to mefenoxam. Simple sequence repeats (SSRs) were identified through bioinformatics mining of 55,848 publicly available expressed sequence tags of P. capsici in dbEST GenBank. Thirty-one pairs of SSR primers were designed, and SSR analysis indicated that the 61 P. capsici isolates from irrigation ponds were genetically distinct. Cluster analysis separated the isolates into five genetic clusters with no more than two genetic groups in one pond, indicating relatively low P. capsici genetic diversity in each pond. The isolation method and SSR markers developed for P. capsici in this study could contribute to a more comprehensive understanding of the genetic diversity of this important pathogen