About

Abhaya M. Dandekar is a Distinguished Professor and the Director of the Plant Transformation Facility at the Department of Plant Sciences, UC Davis. His educational background includes a Ph.D. and M.S. in Microbiology from the University of Baroda, India, and a postdoctoral fellowship at the National Institutes of Health in Bethesda, Maryland. His research interests focus on dissecting plant phenotypes to understand the physiological and genetic basis of agriculturally significant problems, with particular emphasis on trees and phenotypic traits that influence productivity and quality of fruit and nuts. His laboratory aims to define plant responses by analyzing the underlying molecular genetics, physiological, and biochemical mechanisms that regulate these responses. Key areas of his research include developing disease and pest-resistant walnut rootstocks, understanding the genetic and metabolic pathways responsible for traits such as pellicle coloration in walnuts, and studying host and pathogen responses in grapevines to Xylella fastidiosa, the causative agent of Pierce’s disease. He is also involved in developing resistant rootstocks, genome-editing tools for walnut genomics, and enhancing plant-produced human therapeutic glycoproteins. Dandekar has contributed to the development of sustainable disease management strategies and transgraft protection methods. In addition to his research, he teaches Principles of Plant Biotechnology and Introduction to Biotechnology. He holds several leadership roles, including Chair of the Designated Emphasis in Biotechnology, Director of the Ralph M. Parsons Plant Transformation Facility, and advisor to various graduate groups. His scholarly contributions are recognized through numerous awards and honors, including the title of Distinguished Professor at UC Davis, the Award for Excellence in Research from the Citrus Research Board, and international fellowships. His work has significantly advanced understanding in plant molecular biology, functional genomics, pathogen-plant interactions, and biotechnology, with a focus on improving crop resilience and productivity.

Research topics

• Biology
• Botany
• Agronomy
• Genetics
• Microbiology
• Biochemistry
• Biotechnology
• Horticulture
• Chemistry
• Computational biology

Selected publications

• Unlocking the genetic arsenal of Xanthomonas arboricola: new insights into taxonomic classification, pathogenicity and adaptation beyond the effectorome

  BMC Genomics · 2026-05-06

  articleOpen access

  BACKGROUND: Xanthomonas arboricola (Xar) is a phytopathogenic bacterial species responsible for economically significant diseases in a wide range of plants, including agricultural, ornamental, and forest species. This study aimed to investigate the genomic basis of host specificity, adaptation, and virulence in Xar through comprehensive comparative genomics. RESULTS: A total of 177 genomes from nine Xar pathovars were analyzed for evolutionary relationships and effector repertoires. From these, 30 genetically diverse genomes were selected for in-depth comparison. Core, unique, and shared genes were identified and functionally annotated, focusing on their potential roles in adaptation and pathogenicity. Nineteen of the genomes were originally misclassified and did not belong to the Xar species. The remaining 158 genomes clustered into three major clades: I (Xar. pv. juglandis), II (Xar. pv. pruni + Xar. pv. corylina), and III (miscellaneous Xar). Clades I and II exhibited high effector diversity, ranging from 38 to 54 genes, with Xar. pv. corylina harboring the most. In contrast, Clade III genomes had significantly fewer effectors, with subclade IIIa containing only 5 and IIIb up to 15. Only one TAL effector was found in nine Xar. pv. corylina strains (with no conserved RVD patterns) and in both Xar. pv. guizotiae strains (up to 31 RVDs identified). Phylogenomic and effectorome analyses revealed potential genomic islands acquired via horizontal gene transfer, encoding metal metabolism genes, type II/IV secretion systems, and DNA modification enzymes. Additionally, several gene losses were observed: 19 genomes lacked flagellar assembly genes, 15 lacked nitrate metabolism genes, and 9 lacked cellulose biosynthesis and secretion genes. In contrast, all genomes possessed a lasso peptide biosynthetic cluster, highlighting recurrent genomic rearrangements through insertions and deletions. CONCLUSIONS: This study provides a refined understanding of the genetic diversity and adaptive mechanisms in X. arboricola, emphasizing gene gain/loss events as central to pathovar-specific metabolic and virulence traits. These findings identify novel molecular markers with potential applications in diagnostics and targeted disease control strategies. In particular, the characterization of conserved and lineage-specific effector repertoires provides a framework to inform strategies for breeding resistance through the identification of candidate targets for durable host immunity.

  PublisherDOI

• The Walnut’s Dark Secret: Polyphenol Oxidase and the Enigmatic Pathway to Melanin

  International Journal of Molecular Sciences · 2026-02-09

  articleOpen access1st authorCorresponding

  The biosynthesis of melanin in plants remains an enduring biochemical enigma. Unlike the well-characterized pathways of animals and fungi that produce the canonical “true melanins”, the enzymatic origins and physiological functions of melanin-like pigments in plants are poorly described. Recent advances in Juglans regia (walnut) have begun to illuminate this “dark metabolism,” revealing a dual polyphenol oxidase (PPO) system, constitutive JrPPO1 and stress-inducible JrPPO2, that orchestrates the oxidation of phenolics into amorphous, heterogeneous polymeric pigments. Functional studies demonstrate that JrPPO1 maintains tyrosine and redox homeostasis, while silencing triggers a lesion-mimic phenotype, highlighting the enzyme’s role in detoxifying reactive intermediates. In contrast, JrPPO2 responds to redox and pathogen stress, driving pigment formation as part of the defense response. The integration of biological evidence, encompassing genomics, genetics, and phenotyping, reveals that walnut pigmentation represents a genetically encoded, developmentally regulated adaptation balancing metabolic cost and oxidative protection. Decoding this system reframes melanin biosynthesis in plants as a strategic redox resilience mechanism, one that transforms potentially toxic phenolic oxidation into protective polymerization, bridging primary metabolism, defense, and evolution.

  PublisherOA PDFDOI

• Presence of Diverse Resistance Mechanisms in Grapevine Accessions Derived from Pierce's Disease U0505 Line

  Phytopathology · 2026-02-25

  articleSenior author

  Xylella fastidiosa ( Xf) is the etiological agent of Pierce's disease (PD), a major threat to viticulture worldwide. The Xf prtA − mutant, characterized by its planktonic phenotype and absence of biofilm formation, has been previously labeled as hypervirulent due to its aggressive symptomatology in the PD-susceptible Vitis vinifera ‘Thompson Seedless’. This study challenges the hypervirulent concept by demonstrating that a diverse range of grapevine accessions, especially the PD line U0505, exhibited resistance to Xf prtA − . Our findings suggest that different resistance mechanisms are present against the planktonic and biofilm phenotypes of Xf, as represented by the prtA − Xf mutant and the wild-type Temecula1 Xf strain, respectively. This study underscores the complexity of host–pathogen interactions and highlights the importance of multiple host defense mechanisms in countering specific virulence strategies of Xf. The resistance assessed in the U0505 line against Xf prtA − infection provides valuable insights into potential genetic and molecular targets for breeding PD-resistant grapevine cultivars and developing effective disease management strategies.

  PublisherDOI

• Rapid Design and Production of Alpha-1 Antitrypsin Fusion Proteins in a Plant-Based Cell-Free Expression System

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access
  PublisherDOI

• Microbial biotherapeutic metabolite alleviates liver injury by restoring hepatic lipid metabolism through PPARα across the gut-liver axis

  mBio · 2025-08-12 · 7 citations

  articleOpen access

  ABSTRACT Infectious and non-infectious liver diseases are marked by disrupted liver metabolism and are frequently accompanied by gut epithelial barrier dysfunction and microbial dysbiosis, reflecting the compromised gut-liver axis. Despite the pivotal role of the gut-liver axis in health, transformative therapeutic interventions that simultaneously target both the liver and gut remain underexplored. Peroxisome proliferator-activated receptor alpha (PPARα) suppression drives both gut and liver metabolic diseases. In this study, we report on the therapeutic impact of microbial metabolite, 10-hydroxystearic acid (10-HSA), on restoring lipid metabolism and liver regeneration through PPARα activation, leading to a functional gut-liver axis in an in vivo liver injury model. We previously identified 10-HSA, a known PPARα agonist, in Lactiplantibacillus plantarum- treated intestine. Here, we report that oral administration of 10-HSA prevented AFB1-induced gut epithelial barrier disruption and preserved mucosal T cell populations. Prominent downstream effects of 10-HSA-activated PPARα signaling included significant upregulation of known PPARα-regulated gene expression in the gut and liver; prevention of fibrotic changes and reduction of TGF-β signaling-related gene expression in the gut and liver; and activation of toxicant clearance metabolic pathways in the liver through the PPARα-NRF2 pathway. Restoration of the functional gut microenvironment during 10-HSA treatment was evident by increased gut microbial diversity and circulating citrulline levels. Our findings unveil a novel therapeutic trajectory that harnesses a single microbial metabolite to activate PPARα-mediated tissue repair/renewal pathways across the gut-liver axis, offering a promising biologic therapeutic for treatment of metabolic and inflammatory liver diseases. IMPORTANCE Chronic liver diseases, including liver steatosis and fibrosis, are driven in part by dysregulation of PPARα and lipid metabolism. These diseases also generate gut barrier disruption and microbiome dysbiosis, leading to dysfunction of the gut-liver axis. Therapeutic strategies that concurrently support liver regeneration and gut mucosal repair can be highly effective in resolving liver metabolic diseases but remain underexplored. Microbial biotherapeutic metabolite 10-HSA induced repair and regeneration of both liver and gut through the activation of PPARα and restored lipid metabolism. Our findings reveal the therapeutic potential of a single microbial bioactive lipid molecule to repair both hepatic and gut mucosal sites simultaneously with important ramifications for treatment of diseases that disrupt the gut-liver axis.

  PublisherDOI

• Expression and Characterization of Sars-Cov-2 Spike Protein in Thermothelomyces Heterothallica C1

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access
  PublisherDOI

• Reduced Sorbitol Genotype Alters Postharvest Microbiomes of ‘Greensleeves’ Apples

  Journal of the American Society for Horticultural Science · 2025-09-01 · 2 citations

  articleOpen access

  Fruit microbiomes are capable of protecting their hosts from harmful pathogens and aiding in biocontrol; therefore, it is important to understand how differences in host genotype shape fruit microbial communities. The fruit species and even cultivars within a species can harbor different fruit microbiomes, but it has been difficult to establish how a single host gene can shape the microbiome structure. We investigated two genotypes of ‘Greensleeves’ apples with reduced sorbitol biosynthesis through antisense suppression of aldose 6-phosphate reductase with the wild type (WT) to assess how sugar composition of the fruit surface impacts microbial communities. We hypothesized that reduced sorbitol genotypes A4 and A10 would show an epiphytic microbiome different from that of the WT that corresponds to a difference in sugar composition on the fruit surface at harvest and during storage with and without postharvest treatment of fruit with 1-methycyclopropene (1-MCP), which is an inhibitor of ethylene perception. Throughout the sampling window (at harvest, 7 weeks storage, 13 weeks storage) across the 2 years of the study, the genotype, but not 1-MCP, was a significant predictor of microbiome composition. The A10 and A4 lines had an increased abundance of the pathogenic fungal genus Acremonium compared with that of the WT in one year. However, while A4 and A10 had different sugar compositions than that of WT in fruit flesh, no differences on the fruit surface were found. In addition, A4 and A10 showed microbiomes that were different from each other as well as different from that of the WT despite having the same reduced sorbitol phenotype, thus making it difficult to link microbiome differences to a specific physiological mechanism. This work represents an important step in showing the first example, to our knowledge, of how the cascading effects resulting from silencing a single gene can impact the assembly of postharvest fruit microbiomes.

  PublisherDOI

• Exploring multitasking proteins in Xanthomonas secretomes: Insights into mechanisms of plant-pathogen interactions

  Heliyon · 2025-02-27

  articleOpen access

  Recent advances in large-scale functional genomic analysis have significantly increased interest in multitask proteins. The role of these proteins in Xanthomonas phytopathogens, a model for plant-pathogen interaction studies, remains largely underexplored. In this study, we introduce an innovative systematic comparative analysis of secretomes from 18 different Xanthomonas species, integrating data from multiple proteomic studies to identify potential multitasking proteins. This approach led to the identification of 93 proteins primarily involved in central metabolism that are secreted under various physiological conditions, including 16 previously characterized moonlighting proteins. Promiscuity analysis of five selected enzymes revealed that three (asparaginase, chorismate mutase, and phosphoenolpyruvate synthase) exhibit high potential for catalyzing reactions with non-canonical substrates, suggesting additional functional roles beyond their primary enzymatic activities. Additionally, we re-annotated previously hypothetical secreted proteins, assigning functions related to central metabolism and indicating a high potential for promiscuous activity. This comprehensive compilation of potential moonlighting and promiscuous proteins in Xanthomonas provides new insights into the molecular mechanisms driving plant-pathogen interactions and establishes a foundation for future experimental validations of these multifunctional proteins.

  PublisherDOI

• Expression and characterization of SARS-CoV-2 spike protein in Thermothelomyces heterothallica C1

  Vaccine · 2025-09-30

  articleOpen access

  The COVID-19 pandemic demonstrated a pressing need for rapid, adaptive, and scalable manufacturing of vaccines and reagents. With the transition into an endemic disease and rising threats of other emerging pandemics, production of these biologicals requires a stable and sustainable supply chain and accessible distribution methods. In this study, we demonstrate the strength of an engineered filamentous fungal platform, Thermothelomyces heterothallica C1, for high volumetric productivity of the full-length spike glycoprotein. Spike protein produced in this system is highly thermostable and immunization of mice with spike made in C1 or mammalian platforms resulted in a similar humoral response. Additionally, it was shown that the native N-glycan profile can be redecorated with complex sialylated structures, if necessary, resulting in a more human-like glycan profile, without impacting binding characteristics as shown experimentally and in simulations. Through extensive physicochemical analysis, the C1-produced spike performs similarly to spike proteins produced in other commercially available systems. The data presented is evidence that C1 can be a strong platform for production of complex glycosylated recombinant proteins such as subunit antigen vaccines. • Engineered filamentous fungal platform, Thermothelomyces heterothallica C1 is suitable for high volumetric productivity of the full-length spike glycoprotein. • Spike protein produced in this system is highly thermostable and immunization of mice with spike made in C1 or mammalian platforms resulted in a similar humoral response. • The native N-glycan profile can be redecorated with complex sialylated structures, if necessary, resulting in a more human-like glycan profile. • C1 produced spike performs similarly to spike proteins produced in other commercially available systems. • This can be a useful platform for production of complex glycosylated recombinant proteins such as subunit antigen vaccines.

  PublisherDOI

• Nanopore RNA direct sequencing identifies that m6A modification is essential for sorbitol-controlled resistance to Alternaria alternata in apple

  Developmental Cell · 2025-01-13 · 9 citations

  article
  PublisherDOI

Frequent coauthors

• Charles A. Leslie

  University of California, Davis

  107 shared

• Sandeep Chakraborty

  70 shared

• Kourosh Vahdati

  University of Tehran

  48 shared

• Timothy Butterfield

  United States Department of Agriculture

  44 shared

• Sandra L. Uratsu

  University of California, Davis

  44 shared

• Daniel A. Kluepfel

  Agricultural Research Service

  44 shared

• Fatemeh Khodadadi

  37 shared

• Masoud Tohidfar

  Shahid Beheshti University

  37 shared

Education

• Postdoctoral Research, Pathophysiology Laboratory

  National Institutes of Health

  1982

• Ph.D, Microbiology

  M. S. University of Baroda

  1979

• M.Sc, Microbiology

  M.S. University of Baroda

  1974

• B.Sc

  SMDR Sanathan Dharm College

  1971

Awards & honors

• CAPES Visiting Professor, Ministry of Education, Brazil (201…
• Distinguished Professor, University of California, Davis (20…
• Award for Excellence in Research, Citrus Research Board, Cal…
• American Society for Horticultural Science, Cross Commodity…
• John E. Fogarty International Fellowship (1979-1982)