About

Judith Brown is a Regents Professor in the School of Plant Sciences at the University of Arizona. Her research focuses on the dynamics of distribution, prevalence, and co-diversification driving emergent hemipteran-transmitted plant pathogens in cultivated and natural scapes, including the phytobiome. She investigates functional genomics to identify arthropod vector-pathogen effectors and determinants that confer vector specificity, as well as cross-kingdom interactions. Her interests include emerging plant DNA virus-vector complexes, phylogeography, gene flow, and evolution of the Bemisia tabaci cryptic species group, and the biology and functional genomics of begomovirus-whitefly transmission specificity. She also studies determinants and effectors of psyllid vector-Ca. Liberibacter invasion, biopesticides using dsRNA, pathogenicity determinants of Vampirovibrio chlorellavorus, plant viral partners in the phyomicrobiome, and applications of high-throughput sequencing for discovery and molecular diagnostics. Dr. Brown holds a Ph.D. in Plant Pathology from the University of Arizona, an M.S. in Plant Pathology from Washington State University, and a B.S. in Horticulture from Texas A&M University. She teaches courses in Virology and specializes in biodiversity, evolutionary biology, controlled environment agriculture, genomics, bioinformatics, microbiology, and plant protection and pathology.

Research topics

• Biology
• Genetics
• Virology
• Ecology
• Law
• Computational biology
• Cell biology
• Zoology
• Botany

Selected publications

• Spatial and temporal detection of ‘Candidatus Liberibacter asiaticus’ in Diaphorina citri through optimized scouting, sampling, DNA isolation, and qPCR amplification in California citrus groves

  PLoS ONE · 2025-05-12 · 1 citations

  articleOpen accessSenior author

  Huanglongbing (citrus greening disease) is caused by the bacterium 'Candidatus Liberibacter asiaticus' (CLas) (Alphaproteobacteria) and is one of the most destructive bacterial-vector diseases affecting the citrus industry. The bacterium is transmitted by the Asian citrus psyllid (ACP; Diaphorina citri). Early detection in citrus trees is challenging due to uneven distribution of CLas throughout the tree and a long pre-symptomatic phase of the disease. Due to these limitations, ACP sampling has been suggested as a more reliable early detection strategy. The objective of this study was to develop and optimize approaches for detecting CLas in ACP adults and nymphs collected in citrus groves in California using real-time quantitative PCR (qPCR) and droplet digital PCR (ddPCR). The goal was to establish the optimal number of ACP adults and nymphal instar life stages (stages 1-2, 3, or 4-5) that yielded the most reliable detection of CLas (Cq values ≤ 38). Results indicated that CLas detection correlated with psyllid developmental stage, with the 4th-5th instar nymphs (sample size of five to ten per tube) or adult ACP (sample size of three to ten per tube) providing the most consistent qPCR detection. While CLas detection rates increased with adult ACP age, nymphs were preferred for field sampling as adult ACP might have dispersed from non-infected trees, potentially misrepresenting the grove's CLas status. Detection by droplet digital PCR confirmed the presence and genome copies of CLas in a subset of ACP across life stages. In field populations, detection rates in nymphs were consistent or stable throughout the year, whereas CLas detection in adults exhibited seasonal variation, with CLas detection and genome load peaking in January. These targeted ACP sampling strategies and optimized laboratory processing methods will facilitate CLas detection in psyllids for streamlining citrus greening disease management.

  PublisherDOI

• First Complete Genome Sequence of Palo Verde Broom Emaravirus, Virus-Derived siRNA Signatures, and Phytohormone-Metabolite Profiling of Witches’ Broom-Affected Palo Verde Trees

  Viruses · 2025-08-15 · 1 citations

  articleOpen accessSenior authorCorresponding

  Witches’ broom disease of blue palo verde (Parkinsonia florida) was reported more than sixty years ago. Characteristic symptoms consist of dense clusters of shortened, brittle branches and stunted leaves. The suspect causal agent has been identified as palo verde broom virus (PVBV), genus, Emaravirus, family, Fimoviridae. Here, the first complete PVBV genome sequence was determined, and virus small interfering RNAs (vsiRNAs), primary metabolites, and phytohormone profiles were characterized from infected palo verde leaves, adventitious shoots, flowers, and seeds. Based on pairwise distances, PVBV RNAs 1–4 shared 54–65% nucleotide identity and 19–51% amino acid similarity, respectively, with other emaraviruses, while PVBV RNA 5 shared no sequence homology with any emaravirus. The 21–24-nt virus-derived vsiRNAs, indicative of post-transcriptional gene silencing (PTGS), represented nearly the entire PVBV genome in flowers, leaves, seeds, and adventitious shoots; however, PVBV RNA 3 and RNA 4 were most heavily targeted in all plant parts. Evidence that six major phytohormones were altered in PVBV-infected compared to virus-free trees indicated that emaravirus-infected trees mount classical defense responses to virus infection and/or eriophyid mite infestations. Detection of PVBV RNA genome segments 1–5, accumulation of predominantly 21-nt vsiRNAs, homologous to the PVBV genome and transcripts, and altered levels of phytohormones and metabolites in PVBV-infected trees strongly implicate PVBV as the causal agent of witches’ broom disease.

  PublisherOA PDFDOI

• Prevalence, host range, and characterization of multiple Palo verde broom emaravirus genomes and eriophyid mites from Parkinsonia spp. in Arizona

  Virus Research · 2025-10-16

  articleOpen accessSenior authorCorresponding

  • Witches’ broom disease symptoms prevalence, palo verde broom emaravirus incidence and palo verde eriophyid mite ( Aculus cercidi ; Keifer, 1965) colonization of four Parkinsonia spp. and two hybrids. • First evidence that PVBV infects four Parkinsonia spp. and two Parkinsonia x hybrids, and not exclusively, the blue palo verde Parkinsonia florida . • Characterization of additional PVBV genomes and evidence for genomic variability manifest either as divergent RNA segments or full-length genome copies. • Improved understanding of the dynamics of a recently discovered host-emaravirus-vector pathosystem and ecological insights in the context of the Sonoran Desert ecosystem The palo verde tree is native to the Sonoran Desert and consists of multiple species classified in the genus Parkinsonia , family, Fabaceae. Palo verde broom virus (PVBV), Fimoviridae, Emaravirus, is the suspect causal agent of witches’ broom disease of blue palo verde, P. florida . Here, PVBV was detected in four palo verde species and two hybrids by reverse transcription polymerase chain reaction (RT-PCR) amplification of a 679-base pair (bp) fragment of RNA3, which encodes the nucleocapsid gene (NP). The prevalence of witches’ broom symptoms among the different Parkinsonia species (n=70), collected from naturally-occurring, nursery- or urban landscape trees was 54%. Within-species PVBV infection spanned 50-100% and 81% across four species and two hybrids combined. The PVBV genome segments RNAs 1-5 were de novo and reference based-assembled from Illumina® RNAseq reads obtained from total RNA isolated from PVBV-positive trees. Pairwise nucleotide identity and amino acid identity for 29 field isolates and GenBank reference PVBV RNA1-5 segfments/predicted proteins was 73-100% and 68-100%, respectively. Phylogenetic analysis of concatenated RNA1-5 segments resolved four sister clades with no basis in host range among the four palo verde species or hybrids. Five predicted recombinants were identified with breakpoints in either tfhe RNA1 or RNA5 genomic segment. Consistent recovery of PVBV full-length genomes from four Parkinsonia spp. and two hybrids indicated that additional Parkinsonia species and hybrids besides blue palo verde, the only previously reported host, harbored PVBV. Previous studies have linked emaravirus transmission with Eriophyidae mite vectors. Here, the palo verde mite Aculus cercidii Keifer ( Eriophyidae ) (1965) counts ranged from eight to >1,000 per tree. Prolific or minimally-detectable colonization of PVBV-infected trees by A. cercidii , together with consistent detection of PVBV in symptomatic and asymptomatic trees implicate the palo verde mite as the vector of and PVBV as the causal agent of witches’ broom disease.

  PublisherDOI

• First Report of Beet Western Yellows Virus Infecting Wheat in Uzbekistan

  Plant Disease · 2025-10-28

  articleSenior author

  Uzbekistan produces more than one million hectares of wheat (Triticum aestivum L.) annually, which is an important staple crop (Poaceae) consumed throughout the world. During April 2024 wheat plants in spring-planted fields in the Yukori Chirchiq and Qibray districts of Tashkent region of Uzbekistan, exhibited chlorotic spots at leaf tips and stunted growth, reminiscent of a virus-like disease. The incidence ranged from 25-30% and aphids were observed colonizing wheat plants in symptomatic fields in both districts. Aphids (alate and apterous) were collected and submitted for identification to the Entomology Laboratory Institute of Zoology, Academy of Sciences, Republic of Uzbekistan. Leaves of symptomatic (n = 5) and apparently symptom-free (n = 5) were collected from aphid-infested plants at the boot stage using a random sampling approach from a 50 × 50 m2 quadrant plot in three wheat fields. Total RNA was isolated and purified from wheat leaves, followed by cDNA synthesis. PCR was carried out on cDNA using the universal polerovirus primers, PococpR-3’-CGTCTACCTATTTSGGRTTN-5’ and PoconF- 3’-TGYTCYGGTTTTGACTGG-5’ (Xiang et al., 2008) to amplify a suspect polerovirus fragment encoding the partial RNA-dependent RNA polymerase, coat protein, and putative movement protein genes of ~1400 base pairs (bp) in size. A PCR amplicon of ~1400 bp in size was molecularly cloned and subjected to whole plasmid sequencing. To exclude mixed infection all samples tested negative for BYDV and BWYV in RT-PCR. A BLASTn analysis was carried out to identify the best matches yielding the highest sequence coverage among sequences available in the GenBank database. The sequence shared the highest similarity at 97.80% with beet western yellows virus (BWYV) isolate R3a (LC428357) from Raphanus sativus plants in Japan. The sequence was deposited in GenBank and assigned accession no. PV298533. The aphids collected from wheat plants were identified as Myzus persicae (Sulzer) based on established morphological characters (Blackman and Eastop 2000), a known vector of BWYV (Seddas et al. 2004). The results confirm that a BWYV-like polerovirus is associated with symptomatic, aphid-infested wheat plants, and represents the first report of BWYV in wheat plants in Central Asia (Uzbekistan), and only the second report of BWYV infecting wheat following that from China (Jin et al. 2023). Thus, BWYV and potentially other poleroviruses are emerging in grain crops because of increasing early-season infestations of the cereal aphid in Central Asia wheat crops, aggravated by extended periods of mild winter temperatures. These results suggest the impending emergence of poleroviruses as new threats to wheat production.

  PublisherDOI

• Time-Course Gene Expression of ‘Candidatus Liberibacter solanacearum’, Prophage, and Wolbachia Genes in Bactericera cockerelli from Ingestion to in Planta Transmission

  Microorganisms · 2025-09-11

  articleOpen accessSenior authorCorresponding

  Psyllids are vectors of fastidious plant pathogenic ‘Candidatus Liberibacter’ species that infect both the psyllid vector and plant host. Understanding the molecular and cellular basis of ‘Ca. Liberibacter’ interactions with the psyllid host will aid in identification of effectors involved in invasion and multiplication and facilitate transmission to the host plant. The differential expression of previously identified genes/loci with predicted involvement in tomato host–plant– ‘Ca. L. solanacearum’–prophage–Wolbachia endosymbiont dynamics was quantified by RT-qPCR amplification. Fifteen ‘Ca. Liberibacter solanacearum genes and/or prophage loci and four predicted Wolbachia spp. loci were analyzed in potato psyllids in a 14-day time-course study, post-48-h acquisition-access period by potato psyllids on ‘Ca. L. solanacearum’-infected tomato plants. The ‘Ca. L. solanacearum’-infected tomato host plants were used as an infected host ‘calibrator’ species lacking involvement of psyllid effectors. ‘Ca. L. solanacearum’ genes with predicted functions in adhesion, motility, transport, and virulence that are associated with the prophage lysogenic lifestyle were differentially expressed. In contrast, the prophage-loci expression was synchronous with early or late phase of psyllid-‘Ca. L. solanacearum’ infection, respectively. The observations are consistent with the previously in silico-predicted ‘Ca. L. solanacearum’ gene and prophage/Wolbachia loci functions and time-course global expression patterns. Knockdown of ‘Ca. L. solanacearum’ genes involved in invasion, biofilm formation, and colonization would be expected to impair the vertical and horizontal transmission of ‘Ca. L. solanacearum’ to psyllid offspring and host plants, respectively.

  PublisherOA PDFDOI

• Quantitative analysis of pathogenesis-related protein expression in Gossypium hirsutum L. to elicitor-induced resistance against cotton leaf curl disease and predicted in-silico protein-protein interactions

  Physiological and Molecular Plant Pathology · 2025-02-14 · 4 citations

  article
  PublisherDOI

• Disease Tolerance in ‘Anaheim’ Pepper to PepGMV-D Strain Involves Complex Interactions Between the Movement Protein Putative Promoter Region and Unknown Host Factors

  Viruses · 2025-02-15

  articleOpen accessSenior authorCorresponding

  Pepper golden mosaic virus (PepGMV) is a bipartite begomovirus of pepper and tomato from North America. In 'Anaheim' pepper plants PepGMV-Mo strain (Mo) causes systemic yellow foliar mosaic symptoms, while PepGMV-D strain (D) causes distortion of 1st-6th expanding leaves, and asymptomatic infection of subsequently developing leaves, like other known 'recovery' phenotypes. Infections established with DNA-A Mo and D components expressing red-shifted green fluorescent protein in place of coat protein and in situ hybridization, showed PepGMV-Mo localized to phloem and mesophyll cells, while -D was mesophyll restricted. Alignment of PepGMV-Mo and -D DNA-B components revealed three indels upstream of the BC1 gene that encodes the movement protein (MP). To determine if this non-coding region (*BC1) D-strain MP putative promoter contributed to 'recovery', plants were inoculated with chimeric DNA-B Mo/D components harboring reciprocally exchanged *BC1, and wild-type DNA-A Mo and D components. Symptoms were reminiscent but not identical to wild-type -Mo or -D infection, respectively, suggesting 'recovery' cannot be attributed solely to the *BC1. Both BC1 and D*BC1 were targeted by post-transcriptional gene silencing; however, 'recovered' leaves accumulated fewer transcripts and 21-24 nt vsiRNAs. Thus, inefficient in planta movement of PepGMV-D is associated with a non-pepper-adapted 'defective' BC1 that facilitates hyper-efficient PTGS, leading to BC1 transcript degradation that in turn limits virus spread, thereby recapitulating disease 'tolerance'.

  PublisherOA PDFDOI

• Efficacy of Multiplex Grna in Down-Regulating Tomato Leaf Curl New Delhi Virus

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access
  PublisherDOI

• Potential for Duplexed, In-Tandem gRNA-Mediated Suppression of Two Essential Genes of Tomato Leaf Curl New Delhi Virus in Crop Plants

  Pathogens · 2025-07-10 · 1 citations

  articleOpen access

  Tomato leaf curl New Delhi virus (ToLCNDV) is among the most prevalent and widely distributed begomovirus infecting chili pepper (Capsicum annuum) and tomato in the Indian subcontinent. In this study, a guide RNA (gRNA) sequence-CRISPR-Cas9 approach was used to target and cleave two essential coding regions in the begomovirus genome. The gRNAs were designed to target conserved regions of the ToLCNDV replication-associated protein (rep) gene or ORF AC1, and/or the coat protein (cp) gene or AV1 ORF, respectively. Based on an alignment of 346 representative ToLCNDV genome sequences, all predicted single nucleotide polymorphisms off-target sites were identified and eliminated as potential gRNA targets. Based on the remaining genome regions, four candidate gRNAs were designed and used to build gRNA-Cas9 duplexed constructs, e.g., containing two gRNAs cloned in tandem, in different combinations (1–4). Two contained two gRNAs that targeted the coat protein gene (cp; AV1 ORF), while the other two constructs targeted both the cp and replication-associated protein gene (rep; AC1 ORF). These constructs were evaluated for the potential to suppress ToLCNDV infection in Nicotiana benthamiana plants in a transient expression-transfection assay. Among the plants inoculated with the duplexed gRNA construct designed to cleave ToLCNDV-AV1 or AC1-specific nucleotides, the construct designed to target both the cp (293–993 nt) and rep (1561–2324) showed the greatest reduction in virus accumulation, based on real-time quantitative PCR amplification, and attenuated disease symptoms, compared to plants inoculated with the DNA-A component alone or mock-inoculated, e.g., with buffer. The results demonstrate the potential for gRNA-mediated suppression of ToLCNDV infection in plants by targeting at least two viral coding regions, underscoring the great potential of CRISPR-Cas-mediated abatement of begomovirus infection in numerous crop species.

  PublisherDOI

• Cacao Mild Mosaic Virus Infection of Cacao (Theobroma cacao) Plants in Puerto Rico Does Not Affect Yield

  HortScience · 2025-07-15 · 1 citations

  articleOpen access

  Cacao mild mosaic virus (CaMMV), a member of the Badnavirus genus, has emerged as a prevalent virus in cacao ( Theobroma cacao L.) trees in the Caribbean region, Central America, some cacao-producing locations in South America, and Indonesia. Eight cacao genotypes were grown on an Ultisol soil in Corozal, PR, and evaluated for 2 years of production under intensive management to determine their response to CaMMV infection. The results showed significant varietal effects ( P < 0.01) on key parameters, including number of pods, dry bean yield, and pod index. The year and the genotype × year interaction did not show a significant effect except for pod index. Virus infection among experimental trees averaged 80%, ranging from 73.3% to 100% across genotypes. ‘TARS-9’ was the highest producer with 5544 kg·ha −1 per year dry beans, followed by ‘SHRS-7’ (5002 kg·ha −1 ). Despite high CaMMV infection, yield levels were remarkably high, indicating no adverse impact on production. This study marks the first formal report of extraordinary cacao yields reaching 5500 kg·ha −1 per year.

  PublisherDOI

Frequent coauthors

• A. M. Idris

  65 shared

• Celine M. Vachon

  Mayo Clinic in Florida

  50 shared

• Christopher G. Scott

  Mayo Clinic in Florida

  50 shared

• Fergus J. Couch

  WinnMed

  48 shared

• V. Shane Pankratz

  48 shared

• Per Hall

  Stockholm South General Hospital

  44 shared

• Kamila Czene

  Karolinska Institutet

  44 shared

• Louise Eriksson

  Umeå University

  44 shared