- Author: Kathy Keatley Garvey
The research, “Root-Knot Nematodes Produce Functional Mimics of Tyrosine-Sulfated Plant Peptides,” is published in the current edition of the Proceedings of the National Academy of Sciences (PNAS).
It's like hijacking plant development to facilitate parasitism, according to nematologist Shahid Siddique, an associate professor in the Davis Department of Entomology and Nematology and one of the corresponding authors of this study. “This finding showcases an amazing case of convergent evolution across three different types of organisms, revealing how diverse life forms can develop similar strategies for survival.”
The root-knot nematode, which threatens global food security, is a small worm-like organism that is a highly evolved obligate parasite, or an organism that cannot survive without its host. It is known to infest some 2000 crops worldwide. “These parasites have a remarkable ability to establish elaborate feeding sites in roots, which are their only source of nutrients throughout their life cycle,” the authors wrote.
“Root-knot nematodes are a major threat to various crops, including fruit trees and vegetables,” Siddique said. “In California, tomatoes, almonds, and walnuts are among the major hosts susceptible to root-knot nematode infection.”
Siddique and UC Davis distinguished professor Pamela Ronald, a plant pathologist and geneticist in the Department of Plant Pathology and the Genome Center, are the joint corresponding authors. Joint first-authors are Henok Zemene Yemer, formerly of the Siddique lab and now with Gingko Bioworks, Emeryville, and Dee Dee Lu of the Ronald lab.
The team also included emerita professor Valerie Williamson of the former Department of Nematology; Maria Florencia Ercoli, postdoctoral fellow in the Ronald lab; Alison Coomer Blundell, a doctoral candidate in the Siddique lab; and Paulo Vieira of the USDA's Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, Md.
“Plant peptides containing sulfated tyrosine (PSY)-family peptides are peptide hormones that promote root growth via cell expansion and proliferation,” the authors explained. “A PSY-like peptide produced by a bacterial pathogen has been shown to contribute to bacterial virulence. Here, we discovered that PSY-like peptides are encoded by a group of plant-parasitic nematodes known as root-knot nematodes. These nematode-encoded PSY mimics facilitate the establishment of parasitism in the host plant. Our findings are an example of a functional plant peptide mimic encoded by a phytopathogenic bacterium (prokaryote) and a plant-parasitic nematode (an animal).”
The research involved gene expression analysis and parasitism of tomato and rice plants.
The project drew financial support from a collaborative grant awarded to Siddique and Ronald from the National Science Foundation's Division of Integrative Organismal Systems.
Siddique, a member of the UC Davis faculty since 2019, focuses his research on basic as well as applied aspects of interaction between parasitic nematodes and their host plants. “The long-term object of our research is not only to enhance our understanding of molecular aspects of plant–nematode interaction but also to use this knowledge to provide new resources for reducing the impact of nematodes on crop plants in California.”
Ronald, noted for her innovative work in crop genetics, especially rice, is recognized for her research in infectious disease biology and environmental stress tolerance. Thomson Reuters named her one of the world's most influential scientific minds and Scientfic American recognized her as among the world's 100 most influential people in biotechnology. In 2022 Ronald received the Wolf Prize in Agriculture.
The next steps? “Currently, we are working to understand the mechanism by which these peptides contribute to the nematode infection,” Siddique said. “This entails the characterization of receptors involved and gaining insights into transcriptional changes.”
- Author: Kathy Keatley Garvey
Doctoral student Ching-Jung Lin of the laboratory of nematologist Shahid Siddique, associate professor, UC Davis Department of Entomology and Nematology, is the recipient of a two-year, $32,000 Ministry of Education Taiwan Government Scholarship to Study Abroad (GSSA).
The scholarships are awarded to young Taiwanese doctoral students in various fields to support their research.
Lin enrolled in the UC Davis plant pathology doctoral program, with a designated emphasis in biotechnology, in 2020. In the Siddique lab, she is working on nematode transformation and nematode-induced plant immunity.
Lin received her bachelor's degree in agronomy in 2015 from the National Chung Hsing University, Taichung, Taiwan, and her master's degree in plant biology in 2018 from National Taiwan University, Taipei, Taiwan. Her master's research, in the lab of Chiu-Ping Cheng, involved the study of tomato innate immunity mediated by bacterial-wilt-associated QTL (quantitative trait locus) genes. Before joining the Siddique lab, she was a research assistant in the lab of Erh-Min Lai of Academic Sinica, where she studied Agrobacterium-triggered immunity in Arabidopsis.
“I am fascinated by plant-microbe interaction,” Lin says. ‘Currently I am interested in the development of functional genetic tools in plant-parasitic nematodes and the characterization of nematode-induced plant immunity.
A frequent presenter at conferences, Lin presented her research at the 2023 Bay Area Worm meeting at UC Davis; the 2019 International Society for Molecular Plant-Microbe Interactions (IS-MPMI) Congress in Glasgow, and at several Taiwanese conferences. She will compete in a 12-minute presentation competition at the 62nd annual Society of Nematologists' meeting, to be held July 9-14 at The Ohio State University, Columbus. She received a $600 Bayer Crop Science Student Travel Award to attend the conference.
Lin also presented at the 2019 at International Society for Molecular Plant-Microbe Interactions (IS-MPMI) Congress in Glasgow, and at several Taiwanese conferences.
Plant-parasitic nematodes are destructive pests causing losses of billions of dollars annually. Siddique says the research in his lab “focuses on elucidating interactions between plant parasitic nematodes and their hosts using molecular and applied methodologies.”
- Author: Kathy Keatley Garvey
Alison Coomer, Pallavi Shakya and Ching-Jung Lin are among the record 18 students given travel awards by SON, thanks to industry sponsors. All travel award recipients will deliver a presentation or provide a poster at the international meeting.
Bayer Crop Science will sponsor 10 travel awards, and Microbes, Inc., Certis Biologicals and Corteva, will each sponsor two awards. In addition, the United Soybean Board will provide two travel awards to students presenting nematode research in soybean production.
Alison Coomer
Alison, a third-year graduate student in the Department of Plant Pathology, is focusing her research on plant parasitic nematodes, specifically root-knot nematodes, and their molecular mechanisms to defend against plant immune systems. "I am also working to gain more understanding in the defense mechanism in plants towards plant parasitic nematodes."
Alison, originally from the St. Louis, Mo., region, received two undergraduate degrees from Concordia University, Neb.: a bachelor's degree in biology and a bachelor's degree in chemistry.
"I am very thankful to Cobb Foundation and Mai-Ferries-Bird for receiving one of the most prestigious student awards: Cobb Foundation/Mai-Ferris-Bird Student Travel Award," she said.
In her leisure time, Alison enjoys "the outdoors, animals of all varieties, and serving my community."
Pallavi Shakya
Pallavi is a second-year doctoral student in Siddique lab. "I come from Nepal, the land of Himalayas and I am interested in exploring plant parasitic nematodes from a combination of plant pathology and bioinformatics viewpointism," she related. Pallavi received her master's degree in plant biotechnology from Wageningen University in the Netherlands where she was introduced to transcriptomics of potato cyst nematodes.
"Working with these nematodes showed me the importance of understanding plants along with the parasites they have co-evolved with," she said. "In the Siddique lab, I plan to learn about the genomics and transcriptomics aspects of plant-nematode interaction."
"I am very thankful to Bayer Crop Science for my student travel award, and I am looking forward to meeting all the amazing nematologists in the meeting."
Ching-Jung Lin
Ching-Jung is a doctoral student in the Department of Plant Pathology with a designated emphasis in biotechnology. "I am fascinated by plant-microbe interaction," she said. "Currently I am interested in the development of functional genetic tools in plant-parasitic nematodes and the characterization of nematode-induced plant immunity. Originally from Taiwan, she holds a bachelor of science degree in agronomy from National Chung-Hsing University, and a master's degree in plant biology from National Taiwan University.
"I am very thankful to Bayer Crop Science for funding my student award and I look forward to delivering my presentation at the SON conference," she said. Outside of the lab, Ching-Jung enjoys "reading, jogging, playing badminton, and going to the gym." And, she added, "I am a coffee and dog person."
Research in Shahid Siddique Lab
Research in the Siddique lab focuses on basic as well as applied aspects of interaction between parasitic nematodes and their host plants. "The long-term object of our research," he says, "is not only to enhance our understanding of molecular aspects of plant–nematode interaction but also to use this knowledge to provide new resources for reducing the impact of nematodes on crop plants in California."
SON is an international organization formed to advance the science of nematology in both its fundamental and economic aspects.
"Nematodes are the most abundant multicellular animals on the face of the earth," SON relates on its website. "They occur literally everywhere--in soil and decaying matter from the poles to the tropics, in all forms of plant life, in the bodies of almost all animals, including humans, and in insects. Living in such diverse environments as the sand and mud of the ocean bottom, stony mountain soils, and arid polar deserts are thousands to millions of nematodes per square meter."
SON defintes nematodes as "nonsegmented roundworms with complete sensory, digestive, excretory, and reproductive systems. Most, but not all, are microscopic. The variety of nematode forms and habitats is almost unbelievable: they range from the minute inhabitant of your favorite mushroom to the 27-foot-long parasite in the placenta of a sperm whale."
"Nematodes are essential elements of ecosystems, but most have no direct effect on humans," the SON website points out. "Those that do, however, can be devastating. In many places, people still suffer from diseases such as elephantiasis, river blindness, and hookworm, caused by nematodes. In most places, the effect on humans is indirect. For example, in the United States, plant-parasitic nematodes cause more than $3 billion worth of crop losses each year, and cause similar losses in cattle, sheep, and swine." (See more information about nematodes on its website.)
- Author: Kathy Keatley Garvey
The Shahid Siddique laboratory was out in force on Saturday, Feb. 18 during the 12th annual UC Davis Biodiversity Museum Day.
The nematologists set up their display in the Katherine Esau Science Hall, formerly the Sciences Lab Building, and drew nearly 1000 visitors, the most ever.
“BioDiv Day went really well,” said Siddique, an assistant professor of nematology, UC Davis Department of Entomology and Nematology. “A lot of people took interest in getting information about dog heartworms and root-knot nematodes infecting tomatoes. Some people said that nematodes were their favorite stop for BioDiv Day. We had 906 visitors in total and a vast majority of them were kids with family.”
Participating with Siddique were his graduate students Alison Coomer, Veronica Casey, Pallavi Shakya, and Ching-Jung Lin, and professor emeritus Valerie Williamson of Plant Pathology.
The Siddique lab focuses on basic as well as applied aspects of interaction between parasitic nematodes and their host plants. "The long-term object of our research is not only to enhance our understanding of molecular aspects of plant–nematode interaction," Siddique says, "but also to use this knowledge to provide new resources for reducing the impact of nematodes on crop plants in California."
- Celery infected with root-knot nematodes
- Anisakis nematodes from a Minke whale stomach
- Heart of a dog infected with heartworms (Dirofilaria immitis)
- Parasitic nematodes (Baylisascaris transfuga) isolated from the stomach of a bear
- White-tailed deer eye infected with parasitic nematodes (Thelazia spp.)
- Sugar beet infected with root-knot nematodes
- Dog ascaris (Toxocara canis) cause of visceral larva migrans
- Common parasitic worms of human (Ascaris lumbricoides) cause of Ascaris isolated from human intestine
- Dog intestine infected with whipworms
- Horse stomach parasite community including 1) Parascaris 2) Tapeworms 3) Botfly larvae
- Yam infected with root-knot nematode
- Tomato root infected with root-knot nematode
- Adult raccoon roundworms
- Filarial nematodes (Onchocerca volvulus) cause of Onchocerciasis river blindness
- Zoonotic hookworms (Ancylostoma caninum)
- Ascaris lumbricoides (common parasitic worms of human)
- Tree swallow infected with Diplotriaena nematode
- Sugar beet infected with cyst nematode (Heterodera schachtii)
- Grape roots infected with Root-knot nematodes
- Mormon crickets infected with horsehair worms (Gordius robustus)
- Peach roots infected with root-knot nematodes
- Anisakis nematodes from fish intestine
- Hysterotahylaciun nematodes isolated from fish
- Pinworms isolated from human intestine
- Whipworms isolated from human Intestine
- Anisakis nematodes isolated from seals
- Adult dog heartworms
BioDiv Day, founded by the Bohart Museum, is traditionally held on Presidents' Day weekend. Some 3000 attended this year's event, estimated chair Tabatha Yang, education and outreach coordinator of the Bohart Museum. The "Super Science Day" is free and family friendly. Yang is encouraging donations to help pay expenses; access the UC Davis crowdfunding page.
The Esau Science Hall is newly named for UC Davis professor emeritus Katherine Esau, 1898-1997. Internationally known as one of the most influential plant biologists and professors in history, Esau is lauded for her pioneering work on plant anatomy and structure that laid the foundation for much of today's research in the field. She won the National Medal of Science awarded by then president George Bush.
Esau was born in Ukraine. Her family fled to Berlin after World War I and then emigrated to the United States. She joined the UC Davis faculty after receiving her doctorate in 1931. She was elected to the National Academy of Sciences in 1957, only the sixth woman to receive that honor. Following her retirement, she relocated to UC Santa Barbara in 1965. According to Wikipedia, she continued research well into her 90s, publishing a total of 162 articles and five books.
Esau died June 4, 1997 at age 99 in Santa Barbara. A New York Times article quoted Peter Raven, director of the Missouri Botanical Garden: "She absolutely dominated the field of plant anatomy and morphology for several decades. She set the stage for all kinds of modern advances in plant physiology and molecular biology."
In 1982, at age 84, Esau delivered her final UC Davis lecture, covering plasmodesmata. In 1988, she donated $648,000 to UC Davis to establish an endowment to fund plant research fellowships in perpetuity. As of 2020, the endowment's market value has increased by almost six times its original amount, standing at $3.7 million, according to a UC Davis news story.
/span>- Author: Kathy Keatley Garvey
The open-access journal Nature Communications, published the peer-reviewed research Oct. 19.
“Plant-parasitic nematodes are a threat to crop production,” said Siddique, an assistant professor in the UC Davis Department of Entomology and Nematology. “We used a combination of genomic, genetic, and biochemical approaches to show that the plant pathogen cyst nematode possesses an incomplete vitamin B5 synthesis pathway, of potential prokaryotic origin, which is complemented by its plant host. This approach has identified new targets for future development of nematode-resistant crops.”
The 33-member research team included scientists from universities in Germany, France, The Netherlands, Poland, and the United Kingdom, as well as scientists from three universities in the United States: Iowa State University, Ames; and the University of Tennessee, Knoxville; and UC Davis.
The article is titled “The Genome and Lifestage-Specific Transcriptomes of a Plant-Parasitic Nematode and its Host Reveal Susceptibility Genes Involved in Trans-Kingdom Synthesis of Vitamin B5.”
“The scarcity of classical resistance genes highlights a pressing need to find new ways to develop nematode-resistant germplasm,” the scientists wrote in their abstract. “Here, we sequence and assemble a high-quality phased genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major parasitism stages. Analysis of the hologenome of the plant nematode infection site identified metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that a highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is required for full pathogenicity. Knockout of either plant encoded or now nematode-encoded steps in the pathway significantly reduces parasitic success. Our experiments establish a reference for cyst nematodes, further our understanding of the evolution of plant parasitism by nematodes, and show that congruent differential expression of metabolic pathways in the infection hologenome represents a new way to find nematode susceptibility genes. The approach identifies genome-editing-amenable targets for future development of nematode-resistant crops.”
Corresponding authors are Florian Grundler of the Rheinische Friedrich-Wilhelms-University of Bonn, Germany, and Sebastian Eves-van den Akker of the Crop Science Centre, Department of Plant Sciences, University of Cambridge, UK.
Research in the Siddique lab focuses on basic as well as applied aspects of interaction between parasitic nematodes and their host plants. “Plant-parasitic nematodes are destructive pests causing losses of billions of dollars annually,” Siddique said. “The long-term object of our research is not only to enhance our understanding of molecular aspects of plant–nematode interaction but also to use this knowledge to provide new resources for reducing the impact of nematodes on crop plants in California.”