About

Tika Adhikari is a Principal Research Scholar and Adjunct Assistant Professor in the Department of Entomology and Plant Pathology at North Carolina State University. Her research interests encompass applied and molecular plant pathology, genomics, bacterial and fungal population biology of tomato and strawberry pathogens, integrated disease management, plant microbiome, plant-pathogen interactions, and the discovery of disease resistance genes and QTLs through linkage mapping, genome-wide association studies, and next-generation sequencing techniques such as RNA-sequencing and genotyping-by-sequencing. She has contributed to developing resistant tomato cultivars, understanding soil health impacts, and managing key diseases in organic and conventional crop systems. Her work includes significant projects aimed at improving the resilience and sustainability of tomato and strawberry production, with a focus on disease resistance, soil health, and integrated pest management strategies.

Research topics

• Biology
• Biotechnology
• Microbiology
• Ecology
• Agronomy
• Horticulture
• Genetics
• Botany
• Engineering

Selected publications

• Genomic insights and comparative analysis of Colletotrichum species associated with anthracnose fruit rot and crown rot of strawberry in North Carolina

  Frontiers in Microbiology · 2025-02-10 · 4 citations

  articleOpen access1st authorCorresponding

  Colletotrichum is a large genus of fungal phytopathogens responsible for significant economic losses in numerous crops globally. These pathogens exhibit varying host specificities; some have a broad host range, while others are more limited. To explore the genetic composition and underlying factors of fungal virulence and pathogenicity, we sequenced the genomes of seven isolates of Colletotrichum spp.: three from the C. acutatum and four from the C. gloeosporioides . These isolates were sourced from anthracnose fruit rot and crown rot of strawberry in North Carolina. Phylogenetic and phylogenomic analyses classified the isolates within the C. acutatum as C. nymphaeae , while those in the C. gloeosporioides were identified as C. siamense . The genome sizes of the C. nymphaeae isolates ranged from 50.3 Mb to 50.7 Mb, with 14,235 to 14,260 predicted protein-coding gene models. In contrast, the genome sizes of the C. siamense isolates ranged from 55.7 Mb to 58.6 Mb, with predicted protein-coding gene models ranging from 17,420 to 17,729. The GC content across all genomes spanned from 51.9 to 53.7%. The predicted gene models included effectors (339 to 480), secondary metabolic gene clusters (67 to 90), and carbohydrate-active enzymes (800 to 1,060), with C. siamense isolates exhibiting the highest numbers in these categories. The genomic resources from this study will aid in resolving taxonomic challenges associated with Colletotrichum spp., elucidate their evolutionary history, and enhance the understanding of fungal biology and ecology, which is crucial for developing effective disease management strategies.

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• Real-Time Quantitative PCR Method for Assessing Wheat Cultivars for Resistance to <i>Zymoseptoria tritici</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-06

  preprintOpen access1st author

  Septoria tritici blotch, caused by Zymoseptoria tritici (formerly Mycosphaerella graminicola ), is an economically significant disease of wheat ( Triticum aestivum ) worldwide. However, there is little understanding of the fungus’ growth dynamics during the 14- to 18-day latent period between penetration and symptom expression, making it challenging to develop wheat cultivars resistant to Z. tritici Furthermore, environmental factors and variations in disease-scoring systems among evaluators add to the complexity. To address these issues and quantify the fungus’ growth during the initial stages of infection, we developed a real-time quantitative polymerase chain reaction (real-time PCR) method to monitor the T. aestivum - Z. tritici pathosystem. The assay used specific primers designed from ß-tubulin gene sequences of Z. tritici to quantify fungal DNA in susceptible and resistant wheat cultivars and segregating recombinant-inbred lines (RILs) that were inoculated at seedling and adult-plant stages with low or high concentrations of inoculum. The real-time PCR method was compared with visual disease assessment for 0 to 27 days after inoculation (DAI). The results showed that fungal DNA increased more quickly in two susceptible cultivars than in resistant cultivars with the Stb4 or Stb8 genes for resistance. In the susceptible cultivars, the amount of fungal DNA remained low until symptoms became visible at around 18 DAI. Disease severity and fungal DNA in the two resistant cultivars were less than in either susceptible cultivar, starting at 12 DAI. The differences in fungal DNA between resistant and susceptible cultivars were more significant in adult plant tests that used a higher concentration of inoculum. The data analyses showed that the fungus was not eliminated during resistant interactions but could persist throughout the 27 days. Our results suggest that the real-time PCR method can distinguish between resistant and susceptible cultivars starting at 12 DAI and can be used to evaluate early-stage breeding materials for both quantitative and qualitative resistance to Z. tritici .

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• Real-time quantitative PCR method for assessing wheat cultivars for resistance to Zymoseptoria tritici

  Frontiers in Plant Science · 2025-06-24 · 1 citations

  articleOpen access1st authorCorresponding

  Introduction Septoria tritici blotch, caused by Zymoseptoria tritici (formerly Mycosphaerella graminicola), is an economically significant disease of wheat ( Triticum aestivum ) worldwide. However, there is little understanding of the growth dynamics of the causal fungus during the 14- to 18-day latent period between penetration and symptom expression, making it challenging to develop wheat cultivars resistant to Z. tritici . Furthermore, environmental factors and variations in disease-scoring systems among evaluators add to the complexity. To address these issues and quantify fungal growth during the initial stages of infection, we developed a real-time quantitative polymerase chain reaction (qPCR) method to monitor the T. aestivum - Z. tritici pathosystem. Methods The assay used specific primers designed from ß-tubulin gene sequences of Z. tritici to quantify fungal DNA in susceptible and resistant wheat cultivars and segregating recombinant-inbred lines (RILs) that were inoculated at seedling and adult-plant stages with low or high concentrations of inoculum. The real-time PCR method was compared with visual disease assessment for 0 to 27 days after inoculation (DAI). Results The results showed that fungal DNA increased more quickly in two susceptible cultivars than in resistant cultivars with the Stb4 or Stb8 genes for resistance. In the susceptible cultivars, the amount of fungal DNA remained low until symptoms became visible at around 18 DAI. Disease severity and fungal DNA in the two resistant cultivars were less than in either susceptible cultivar, starting at 12 DAI. The differences in fungal DNA between resistant and susceptible cultivars were more significant in adult plant tests that used a higher concentration of inoculum. Discussion The data analyses showed that the fungus was not eliminated during resistant interactions but could persist throughout the 27 days. Our results suggest that the real-time PCR method can distinguish between resistant and susceptible cultivars starting at 12 DAI and can be used to evaluate early-stage breeding materials for both quantitative and qualitative resistance to Z. tritici .

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• Elucidating the impact of organic amendments on soil bacterial communities and strawberry yield in North Carolina

  Frontiers in Sustainable Food Systems · 2025-03-19 · 3 citations

  articleOpen access1st authorCorresponding

  Strawberry ( Fragaria × ananassa Duchesne ex Rozier) is an important small fruit grown worldwide. Organic amendments can alter microbial communities and increase crop productivity. While research on organic amendments in strawberry cultivation has primarily focused on various regions in the U.S., especially the West Coast, there has been little to no investigation into their potential benefits in North Carolina (NC). A three-year trial was conducted from 2019 to 2022 at the Horticultural Crops Research Station in Castle Hayne, NC, U. S. A. The main objective of the study was to examine the effects of reduced rates of dried molasses (5.60 t/ha) and mustard meal (2.24 t/ha), a half-rate combination of both, a positive control (Pic Clor 60), and a negative control (no fumigated and no amended) on soil bacterial communities and strawberry yield. Our results from 16S microbiome amplicon sequencing showed significant variations in the composition of the soil bacterial community over time between the organic amendment treatments and the controls. The alpha diversity indices (Shannon index) of the soil bacterial microbiome were generally higher in plots with organic amendments than those treated with Pic Clor 60. Taxonomic classification revealed that the two phyla, Proteobacteria and Actinobacteriota , were prominent in the organic amendment treatments. The total marketable yield rankings for the three organic amendment treatments (dried molasses, mustard meal, and the half-rate combination of both) were comparable to those achieved through fumigation. The results indicated that bacterial structure and yield improved in the organic amendment plots, while microbial diversity decreased in the fumigation plots, and yields were lower in the untreated plots. This study will inform the selection of organic amendments to enhance microbial diversity and promote sustainability in strawberry farming in NC.

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• Genome Sequence Resource of Four <i>Botrytis cinerea</i> Isolates from North Carolina

  PhytoFrontiers™ · 2025-01-03 · 2 citations

  articleOpen access1st authorCorresponding

  Botrytis cinerea is a fungal pathogen that affects over 1,400 plant species and causes significant damage to crops. It is also responsible for causing gray mold in small fruits, such as blueberries and strawberries. In this study, four isolates of B. cinerea were collected (two from blueberry and two from strawberry) in North Carolina. Their genomes were sequenced using Illumina paired-end sequencing. The core genome of the isolates was analyzed for carbohydrate-active enzymes, secretomes, effectors, and secondary metabolite repertoires. The genome assembly of the four isolates ranged from 41.9 Mb for NC5 to 44.9 Mb for KC33. Based on Benchmarking Universal Single-Copy Orthologs analysis, all of the genomes had high levels of completeness, ranging from 98.2 to 99.1%. The annotation revealed the presence of 500 to 565 carbohydrate-active enzymes, 649 to 688 secreted proteins, and 162 to 181 potential fungal effectors. This study not only provides valuable genomic resources for B. cinerea but also significantly contributes to the existing resources available for understanding host–pathogen interactions and the factors that affect disease development in the host. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

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• First Report of <i>Ralstonia pseudosolanacearum</i> Phylotype I Sequevar 14 Causing Bacterial Wilt on Tomato (<i>Solanum lycopersicum</i>) and Eggplant (<i>Solanum melongena</i>) in North Carolina, U.S.A.

  Plant Disease · 2025-03-04 · 5 citations

  articleOpen accessSenior author

  Ralstonia solanacearum species complex (RSSC) consists of three species, including R. solanacearum, R. pseudosolanacearum, and R. syzygii. The K60-type strain of R. solanacearum was isolated from a wilted 'Marglobe' tomato in Raleigh, North Carolina (NC) in 1953 (Kelman 1954). It is classified as phylotype IIA, sequevar 7 (Prior and Fegan 2005). In July 2023, during a field visit in Eastern NC, patches of >50 eggplant (Solanum melongena cv. Pingtung Oriental) and tomato (Solanum lycopersicum cv. Saybrook) plants showing wilt symptoms were observed in a 1 ha field. Two plants from each host were collected from this site and tested positive for bacterial streaming in sterile deionized water for 2 min. One plant from each host was used for bacterial isolation by plating a 10 μl aliquot of the resulting bacterial streaming suspension on triphenyl tetrazolium chloride (TZC) medium (Kelman 1954) and incubated at 28°C for 48 hr. Multiple fluidal white colonies with a pink center and irregularly round morphology reminiscent of strains in the RSSC were observed on all plates. Only one colony from each plant host, NG-RL and EP-RL from tomato and eggplant, respectively, was selected for molecular characterization. Neither strain amplified the 357 bp band and was not R. solanacearum Select Agent (Opina et al. 1997). Genomic DNA from both NG-RL and EP-RL generated the 280 bp and 144 bp bands and confirmed as R. pseudosolanacearum phylotype I using the RSSC multiplex PCR (Fegan and Prior 2005). To determine sequevar, the primers Endo-F/Endo-R (Poussier et al. 2000; Fegan and Prior 2005) were used to sequence the partial endoglucanase (egl) gene from EP-RL and NG-RL (GenBank accessions: PQ554799 and PQ554800). These sequences were compared to publicly available egl sequences from GenBank and Cellier et al. (2023). A maximum likelihood phylogenetic tree showed that both NG-RL and EP-RL clustered with reference strains PSS81, MLI71-15, and Zo4 with 100% identity, confirming NG-RL and EP-RL are R. pseudosolanacearum phylotype I sequevar 14. To fulfill Koch's postulates, NG-RL and EP-RL inoculant was prepared from 48 h cultures grown on TZC plates at 28°C. Plates were flooded with sterile deionized water and then transferred to a falcon tube, adjusting O.D. 600 to 0.2 (~1×108 CFU/ml). The roots of six-week-old eggplants (cv. Black Beauty) and tomatoes (cv. Bonny Best) were wounded by running a scalpel through the soil 2 cm from the stem. This was repeated on six plants for both NG-RL and EP-RL. Mock-inoculated plants treated with sterile deionized water (SDW) served as controls. Plants incubated at 28°C in the greenhouse showed bacterial wilt symptoms nine days post-inoculation. R. pseudosolanacearum phylotype I sequevar 14 was confirmed from all bacteria-inoculated plants using the multiplex PCR and egl sequencing methods described above. No symptoms or bacteria were isolated from SDW mock-inoculated plants. There have been no prior reports of R. pseudosolanacearum phylotype I in North Carolina. To our knowledge, this is the first report on R. pseudosolanacearum phylotype I and the sequevar 14 in both tomato and eggplant in NC. This phylotype I is endemic to Asia and was first reported in the US in 2003 on pepper in Florida (Ji et al. 2006) and in 2015 on tomatoes in Louisiana (Jimenez Madrid et al. 2019). This finding highlights the need for a nationwide RSSC survey program, which can undoubtedly inform pathogen spread and management for crops in NC and beyond.

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• Genome assembly and comparative analysis of Alternaria linariae reveal novel genes associated with host colonization and virulence

  BMC Genomics · 2025-07-07 · 1 citations

  articleOpen accessSenior author

  Early blight (EB) is one of the most economically devastating diseases affecting tomato production, leading to significant yield losses. Traditionally, EB has been associated with the fungus Alternaria solani. However, recent evidence indicates that A. linariae (previously known as A. tomatophila) is the main causative agent. This revised understanding improves diagnostic accuracy and underscores A. linariae as a valuable resource for studying host-pathogen interactions, host adaptation, and evolutionary mechanisms within the Alternaria genus due to its distinct pathogenic profile and host specificity. The A. linariae strain 25, isolated from EB-infected tomatoes in Swain County, North Carolina, United States, was confirmed through analyses of its asexual morphs, cultural characteristics, and PCR-based identification. Nonetheless, the genomic structure and genetic factors influencing host specificity in A. linariae on tomatoes remain poorly understood. To address this knowledge gap, we sequenced the complete genome of A. linariae. This study will help elucidate its structure, compare its genomic features with those of other Alternaria spp., and identify the genetic basis for its host specificity. These insights are crucial for understanding its pathogenicity and host adaptation and for developing effective disease management strategies. The genome of A. linariae strain 25 has been fully assembled and spans 33.1 Mb. It comprises 18 rRNA genes and 117 tRNA genes, and approximately 272,542 base pairs (0.8%) of repetitive elements. The genome features 11,768 predicted gene models, with 221 genes identified as potential candidate effector proteins that may play a role in host colonization and specificity. Additionally, the genome encodes 573 carbohydrate-active enzymes (CAZymes) and 37 secondary metabolite gene clusters, which are likely involved in pathogenicity and interactions with the host. A comparative genomic analysis of effector genes across different Alternaria spp. revealed that the A. linariae strain 25 possesses unique effectors, which may enhance its ability to colonize and adapt precisely to tomato plants. These findings lay the groundwork for further investigation into the molecular mechanisms that drive host specificity and pathogenicity in A. linariae and provide a foundation for developing targeted strategies to control early blight in tomato crops.

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• High-Quality Complete Genomes of Three Phylotype IIA <i>Ralstonia solanacearum</i> Strains Isolated from Tomatoes in North Carolina

  PhytoFrontiers™ · 2025-05-28 · 1 citations

  articleOpen access

  Ralstonia solanacearum ( R. sol) is a destructive bacterial plant pathogen and the causal agent of bacterial wilt in various crops, including tomatoes, blueberries, and eucalyptus. The type strain for this pathogen species is K60, isolated in North Carolina in 1953, and is one of two high-quality closed genomes for R. sol phylotype IIA strains in public databases. To enhance resources that support investigations into the genotypic diversity of R. sol in the United States, three complete, high-quality phylotype IIA R. sol genomes for strains isolated from tomatoes in North Carolina were generated using hybrid long- and short-read sequencing technologies. These new genomes have high and low CheckM scores for completeness and contamination, respectively, and provide valuable resources for studying R. sol evolution, epidemiology, and virulence, particularly in the context of U.S. pathogen populations. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

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• Genome‐wide association study identifies quantitative trait loci associated with resistance to <i>Verticillium dahliae</i> race 3 in tomato

  The Plant Genome · 2025-10-14 · 1 citations

  articleOpen access1st authorCorresponding

  Verticillium wilt (VW) disease, caused by Verticillium dahliae Kleb., is a major threat to tomato (Solanum lycopersicum L.) production. Identifying loci associated with VW resistance can accelerate breeding efforts and support sustainable disease management. Although the Ve1 and Ve2 genes confer resistance to V. dahliae races 1 and 2, the emergence of race 3 in the United States poses a new challenge. To investigate the genetic basis of quantitative resistance to the race 3 strain KJ14a, we evaluated 250 diverse tomato accessions. Disease severity and incidence were assessed weekly over 5 weeks, using chlorosis/necrosis percentage (CN_perc) and the number of symptomatic leaves (LC) as phenotypes. OmeSeq quantitative reduced-representation sequencing yielded 42,941 high-quality single nucleotide polymorphism and insertion-deletion markers. Genome-wide association study (GWAS) and local linkage disequilibrium analyses identified four candidate genes associated with VW resistance on chromosomes 3, 5, and 7, including two loci mapping to previously reported quantitative trait loci and two novel resistance loci on chromosome 5. The candidate genes are involved in plant defense and the modification of cell walls. To validate and assess the breeding potential of marker-trait associations, we applied GWAS-assisted best linear unbiased prediction (GWABLUP). Using an additive + dominance model and GWABLUP with top 100 associated markers, predictive ability for LC improved by 16.4% and 4.8%, and for CN_perc by 11.7% and 7.9%, compared to standard genomic best linear unbiased prediction using 100 and 18,000 genome-wide markers, respectively. These results offer valuable insights into the genetic architecture of VW resistance to race 3 and demonstrate the potential of combining GWAS and genomic prediction to accelerate tomato breeding for durable disease resistance.

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• Septoria Leaf Spot of Tomatoes: Historical Insights, Present Challenges, and Future Prospects

  Horticulturae · 2024-12-05 · 2 citations

  articleOpen accessCorresponding

  Septoria leaf spot (SLS), caused by the hemibiotrophic fungus Septoria lycopersici, poses a significant threat to tomato production systems. While fungicides can effectively reduce disease epidemics, planting resistant cultivars remains the most efficient and economical control method. Conventional screening and breeding have identified new sources of resistance to S. lycopersici among wild relatives. However, gaps exist in the literature concerning tomato—S. lycopersici interactions, such as plant defense mechanisms, fungal pathogenicity mechanisms, and interaction dynamics that can inform the development of durable resistance through additional research. To further enhance host resistance to S. lycopersici, molecular methods such as marker-assisted breeding, gene editing, genomic selection, and transgenic approaches can be employed. Moreover, the durability of resistance and efficacy of disease management can be optimized within an integrated pest management (IPM) framework that advances diverse tactics to suppress diseases and improve plant productivity. This review highlights the current understanding of pathogen biology, host genetic solutions, and novel strategies to combat the SLS problem and suggests directions for future research.

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Frequent coauthors

• Suraj Gurung

  22 shared

• P. K. Singh

  22 shared

• Mohamed Mergoum

  University of Georgia

  21 shared

• Stephen B. Goodwin

  Agricultural Research Service

  19 shared

• Frank J. Louws

  18 shared

• Shaukat Ali

  South Dakota State University

  16 shared

• J. M. Bonman

  15 shared

• E. M. Elias

  North Dakota State University

  10 shared

Awards & honors

• NSERC Industrial Research Fellowship, Canada
• Rockefeller Foundation Rice Biotechnology Career Fellowship,…
• Rockefeller Foundation Post-Doctoral Fellowship, USA
• Asian Development Bank Fellowship, Philippines
• USAID/MUCIA Fellowship, Philippines