@article{oh_ingram_shekasteband_adhikari_louws_dean_2023, title={Tissues and mechanisms associated with Verticillium wilt resistance in tomato using bi-grafted near-isogenic lines}, volume={5}, ISSN={["1460-2431"]}, url={https://doi.org/10.1093/jxb/erad182}, DOI={10.1093/jxb/erad182}, abstractNote={Abstract}, number={15}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Oh, Yeonyee and Ingram, Thomas and Shekasteband, Reza and Adhikari, Tika and Louws, Frank J. and Dean, Ralph A.}, editor={Höfte, MonicaEditor}, year={2023}, month={May} }
 @article{ingram_sharpe_louws_meadows_2021, title={Pruning reduces yields in grafted tomatoes planted in the field}, volume={1302}, ISSN={["2406-6168"]}, url={https://publons.com/wos-op/publon/56007336/}, DOI={10.17660/ActaHortic.2021.1302.9}, journal={II INTERNATIONAL SYMPOSIUM ON VEGETABLE GRAFTING}, author={Ingram, T. and Sharpe, S. and Louws, F. J. and Meadows, I}, year={2021}, pages={65–71} }
 @article{ingram_oh_adhikari_louws_dean_2020, title={Comparative Genome Analyses of 18 Verticillium dahliae Tomato Isolates Reveals Phylogenetic and Race Specific Signatures}, volume={11}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2020.573755}, abstractNote={Host resistance is one of the few strategies available to combat the soil borne pathogenic fungus Verticillium dahliae. Understanding pathogen diversity in populations is key to successfully deploying host resistance. In this study the genomes of 18 V. dahliae isolates of races 1 (n = 2), 2 (n = 4), and 3 (n = 12) from Japan, California, and North Carolina were sequenced and mapped to the reference genome of JR2 (from tomato). The genomes were analyzed for phylogenetic and pathogen specific signatures to classify specific strains or genes for future research. Four highly clonal lineages/groups were discovered, including a lineage unique to North Carolina isolates, which had the rare MAT1-1 mating type. No evidence for recombination between isolates of different mating types was observed, even in isolates of different mating types discovered in the same field. By mapping these 18 isolates genomes to the JR2 reference genome, 193 unique candidate effectors were found using SignalP and EffectorP. Within these effectors, 144 highly conserved effectors, 42 mutable effectors (truncated or present in some isolates but absent in others), and 7 effectors present in highly variable regions of the chromosomes were discovered. Of the 144 core effectors, 21 were highly conserved in V. alfalfae and V. longisporum, 7 of which have no known function. Within the non-core effectors 30 contained large numbers of non-synonymous mutations, while 15 of them contained indels, frameshift mutations, or were present on highly variable regions of the chromosome. Two of these highly variable region effectors (HVREs) were only present in race 2 isolates, but not in race 3 isolates. The race 1 effector Ave1 was also present in a highly variable region. These data may suggest that these highly variable regions are enriched in race determinant genes, consistent with the two-speed genome hypothesis.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Ingram, Thomas W. and Oh, Yeonyee and Adhikari, Tika B. and Louws, Frank J. and Dean, Ralph A.}, year={2020}, month={Nov} }
 @article{adhikari_gao_ingram_louws_2020, title={Pathogenomics Characterization of an Emerging Fungal Pathogen,Fusarium oxysporumf. sp.lycopersiciin Greenhouse Tomato Production Systems}, volume={11}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2020.01995}, abstractNote={In recent years, greenhouse-grown tomato (Solanum lycopersicum) plants showing vascular wilt and yellowing symptoms have been observed between 2015 and 2018 in North Carolina (NC) and considered as an emerging threat to profitability. In total, 38 putative isolates were collected from symptomatic tomatoes in 12 grower greenhouses and characterized to infer pathogenic and genomic diversity, and mating-type (MAT) idiomorphs distribution. Morphology and polymerase chain reaction (PCR) markers confirmed that all isolates were Fusarium oxysporum f. sp. lycopersici (FOL) and most of them were race 3. Virulence analysis on four different tomato cultivars revealed that virulence among isolates, resistance in tomato cultivars, and the interaction between the isolates and cultivars differed significantly (P < 0.001). Cultivar ‘Happy Root’ (I-1, I-2, and I-3 genes for resistance) was highly resistant to FOL isolates tested. We sequenced and examined for the presence of 15 pathogenicity genes from different classes (Fmk1, Fow1, Ftf1, Orx1, Pda1, PelA, PelD, Pep1, Pep2, eIF-3, Rho1, Scd1, Snf1, Ste12, and Sge1), and 14 Secreted In Xylem (SIX) genes to use as genetic markers to identify and differentiate pathogenic isolates of FOL. Sequence data analysis showed that five pathogenicity genes, Fmk1, PelA, Rho1, Sge1, and Ste12 were present in all isolates while Fow1, Ftf1, Orx1, Peda1, Pep1, eIF-3, Scd1, and Snf1 genes were dispersed among isolates. Two genes, Pep2 and PelD, were absent in all isolates. Of the 14 SIX genes assessed, SIX1, SIX3, SIX5, SIX6, SIX7, SIX8, SIX12, and SIX14 were identified in most isolates while the remaining SIX genes varied among isolates. All isolates harbored one of the two mating-type (MAT-1 or MAT-2) idiomorphs, but not both. The SIX4 gene was present only in race 1 isolates. Diversity assessments based on sequences of the effector SIX3- and the translation elongation factor 1-α encoding genes SIX3 and tef1-α, respectively were the most informative to differentiate pathogenic races of FOL and resulted in race 1, forming a monophyletic clade while race 3 comprised multiple clades. Furthermore, phylogeny-based on SIX3- and tef1-α gene sequences showed that the predominant race 3 from greenhouse production systems significantly overlapped with previously designated race 3 isolates from various regions of the globe.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Adhikari, Tika B. and Gao, Anne and Ingram, Thomas and Louws, Frank J.}, year={2020}, month={Aug} }