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

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Siddique, Shahid
Maier, Tom R.
Masonbrink, Rick E.
et al.
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Baum, Thomas
Distinguished Professor
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Plant Pathology and Microbiology
The Department of Plant Pathology and Microbiology and the Department of Entomology officially merged as of September 1, 2022. The new department is known as the Department of Plant Pathology, Entomology, and Microbiology (PPEM). The overall mission of the Department is to benefit society through research, teaching, and extension activities that improve pest management and prevent disease. Collectively, the Department consists of about 100 faculty, staff, and students who are engaged in research, teaching, and extension activities that are central to the mission of the College of Agriculture and Life Sciences. The Department possesses state-of-the-art research and teaching facilities in the Advanced Research and Teaching Building and in Science II. In addition, research and extension activities are performed off-campus at the Field Extension Education Laboratory, the Horticulture Station, the Agriculture Engineering/Agronomy Farm, and several Research and Demonstration Farms located around the state. Furthermore, the Department houses the Plant and Insect Diagnostic Clinic, the Iowa Soybean Research Center, the Insect Zoo, and BugGuide. Several USDA-ARS scientists are also affiliated with the Department.
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Genome Informatics Facility
The Genome Informatics Facility serves as a centralized resource of expertise on the application of emerging sequencing technologies and open source software as applied to biological systems. Its mission is to integrate this knowledge into pipelines that are easy to understand and use by faculty, staff and students to enable the transformation of ‘big data’ into data that dramatically accelerates our understanding of biology and evolutionary processes.
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Plant-parasitic nematodes are a major, and in some cases a dominant, threat to crop production in all agricultural systems. The relative scarcity of classical resistance genes highlights a pressing need to identify new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality 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 stages of the interaction. This novel approach enabled the analysis of the hologenome of the infection site, to identify 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 the highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is critically important for parasitism. Knockout of either the plant-encoded or the now nematode-encoded steps in the pathway blocks parasitism. Our experiments establish a reference for cyst nematodes, use this platform to further our fundamental understanding of the evolution of plant-parasitism by nematodes, and show that understanding congruent differential expression of metabolic pathways represents a new way to find nematode susceptibility genes, and thereby, targets for future genome editing-mediated generation of nematode-resistant crops.
This article is published as Siddique, Shahid, Zoran S. Radakovic, Clarissa Hiltl, Clement Pellegrin, Thomas J. Baum, Helen Beasley, Oliver Chitambo et al. "The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B." bioRxiv (2021). DOI: 10.1101/2021.10.01.462558. Copyright 2021 The Authors. Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). Posted with permission.