Progress 06/15/21 to 06/14/23
Outputs
Target Audience:Other scientists studying population genomics and evolution of fungal plant pathogens. Plant pathologists learning a more comprehensive understanding of evolutionary biology. Foresters designing management practices to slow the spread of sudden oak death in Curry County, Oregon Changes/Problems: Ongoing problems associated with the COVID pandemic prevented the PD from completing extensive wet lab work that was originally planned. Instead, the PD focused on the project goals that were accomplishable with computational analyses. What opportunities for training and professional development has the project provided? Mentorship of the PD by the Primary Mentor and other faculty at Oregon State University Productive scientific and professional discussions during lunches with scientists visiting Oregon State University to give seminars Regular conference calls with the Oregon Department of Forestry to understand what data and analyses are informative to stakeholders How have the results been disseminated to communities of interest? Scientific publications ready to submit to scientific journals for peer review National conference in the discipline of study where the PD was involved in work on three different presentations Calls with foresters working to manage the disease that was the primary focus of study of the project The dissertation defense seminar given by the PD was attended by about 50 faculty, staff, and other graduate students. Several posters were presented at the annual meeting for the American Phytopathological Society, Plant Health 2023, involving work completed by the PD Nicholas (Carleson) Cauldron. These were as follows: * Indicates presenting author CM Press, Z Foster, N Carleson, N Grunwald*. Development of the KRISP python tool and validation of a CRISPR Cas diagnostic assay for detection of Phytophthora ramorum. T Borland*, E Lopez, CM Ocamb, N Carleson, N Grunwald, D Gent. Understanding toxic relationships: Investigating mycotoxin production in pathogenic Fusarium sambucinum isolates. Nicholas C. Cauldron*, Caroline M. Press, Alexandra J. Weisberg, Marília Horta Jung, Tamara Corcobado, Joan F. Webber, Koji Kageyama, Ayaka Hieno, Hayato Masuya, Seiji Uematsu, Bruno Scanu, Clive M. Brasier, Thomas Jung, Jeff H. Chang and Niklaus J. Grünwald. Pangenome of global Phytophthora ramorum lineages reveals loss of crinkler effector genes and intra-specific plasticity. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Comparisons between multiple Phytophthora ramorum genomes from isolates collected in East Asia Improved understanding for how Phytophthora ramorum develops losses of heterozygosity in the landscape over time Insights into relationships between fitness and loss of heterozygosity mutations in P. ramorum PD Nicholas (Carleson) Cauldron earned his doctoral degree in Botany & Plant Pathology from Oregon State University Professional and scientific opportunities provided by the fellowship resulted in the PD obtaining a Postdoctoral Research position at Brown University, furthering his path to an academic career focusing on asexual evolution of pathogens Nicholas (Carleson) Cauldron earned a Doctorate of Philosophy in Botany & Plant Pathology. The title of his dissertation was: Inferring patterns and processes of emergence in clonal Phytophthora epidemics using population genomic approaches
Publications
- Type:
Book Chapters
Status:
Accepted
Year Published:
2023
Citation:
Nicholas C. Cauldron, Martha Sudermann, Camilo Parada Rojas, and Niklaus J. Gr�nwald. Annotation of RXLR effectors in oomycete genomes. Methods in Molecular Biology: Phytophthora
- Type:
Journal Articles
Status:
Other
Year Published:
2023
Citation:
Nicholas C. Cauldron, Caroline M. Press, Alexandra J. Weisberg, Mar�lia Horta Jung, Tamara Corcobado, Joan F. Webber, Koji Kageyama, Ayaka Hieno, Hayato Masuya, Seiji Uematsu, Bruno Scanu, Clive M. Brasier, Thomas Jung, Jeff H. Chang and Niklaus J. Gr�nwald. Intraspecific variation and recent loss of anciently conserved effector genes by the sudden oak death pathogen Phytophthora ramorum.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Citation: Martin S. Mullett, Kris Van Poucke, Annelies Haegeman, Fran Focquet, Nicholas C. Cauldron, Brian J. Knaus, Marilia Horta Jung, Koji Kageyama, Ayaka Hieno, Hayato Masuja, Seiji Uematsu, Joan F. Webber, Clive M. Brasier, J�zsef Bakonyi, Kurt Heungens, Niklaus J. Gr�nwald & Thomas Jung. Phylogeography and population structure of the global, wide host-range hybrid pathogen Phytophthora x cambivora. IMA Fungus.
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Progress 06/15/21 to 06/14/22
Outputs
Target Audience:I reached other scientists performing genome sequencing and assembly as well as other plant pathologists. I mentored other graduate students as well as young and developing scientists. Additionally, I reached economically and socially disadvantaged high school students, and economically disadvantaged people in Puerto Rico. Changes/Problems: Older P. ramorum isolates (from 2001-2005) we used did not behave as predictably in the lab as more recent collections Work on Curry County population genomics has taken longer than expected because of preliminary but interesting findings. This was not a major component of my thesis at the time I submitted this grant, but it has become one. I still anticipate graduating in June 2023. What opportunities for training and professional development has the project provided?Training: I am learning how to sequence genomes with Nanopore sequencing technology from a collaborating lab. Additionally, I learned how to measure radial growth and count sporangia from a graduate student mentored by Key Collaborator Jared LeBoldus. Professional development: I visited Puerto Rico in June 2022 and met several professionals and scientists who were interested in my research, and interested in training me after I complete my PhD. How have the results been disseminated to communities of interest?My research progress has been delivered in monthly calls to the Oregon Department of Forestry Sudden Oak Death task force. Additionally, I have published a paper with genome assemblies I completed for this grant, and I created a poster demonstrating my work in Puerto Rico. What do you plan to do during the next reporting period to accomplish the goals? Present poster of my work in Puerto Rico at college campus conference Identify software that can leverage whole-genome SNP data to perform Bayesian phylogeography Develop software to easily validate genome aberrations inferred with short sequence reads using long sequence reads Develop methods to infer selection with non-traditional population genomics on genome abberrations such as losses of heterozygosity (LOH) Select and sequence recently collected strains from the Oregon sudden oak death epidemic and compare aberrations to those observed in the beginning of the epidemic. Publish one paper on population genomics of the Oregon sudden oak death epidemic including data on LOH. Publish one paper comparing genomes I assembled from Asia and epidemic lineages Publish one paper on population genomics of Asian P. ramorum strains
Impacts
What was accomplished under these goals?
My USDA-NIFA Predoctoral Fellowship is to study an epidemic in coastal oak forests. This grant supports my thesis studying Phytophthora ramorum, the pathogen causing sudden oak death. I seek to understand how epidemic populations are evolving in space and time through traditional and novel approaches in genomics. Through this program, I am receiving training from a network of mentors on how best to conduct this research, and gaining a foothold in this field. In the next 10 years of my career, I aim to become a professor of plant pathology, and the first year of this grant has put me on track for that vision. Sub-objective 1.1.1: I have genotyped single nucleotide polymorphisms (SNPs) across the whole genome using two different softwares, and filtered them for quality. Further, I have recovered highly conserved genes in which SNPs will be suitable for this analysis. This will allow me to complete this objective and share with other scientists in my field best practices for the analysis. Sub-objective 1.1.2: I have tested software to use to assign alleles to haplotypes for these SNPs, and validated that genome-wide SNPs are accuratly assigned. I obtained additional data from collaborators in Canada that improved the global representation of my collection. Objective 1.2: I used genome-wide SNPs to identify loss of heterozygosity (LOH) aberrations. I selected samples whose aberrations I will validate with long-read sequencing technology, before spending too much time on 2.1 and 2.2 on results that the scientific community will not accept. Objective 2.1: I have learned substantially about the reproductive cycle and epidemiology of Phytophthora ramorum. Objective 2.2: I am on track to defend and obtain my PhD in eight months. Objective 2.3: In June 2022, went to Puerto Rico on a service trip with OSU's Minorities in Agriculture, Natural Resources, and Related Sciences. There, I met with scientists at the International Institute of Tropical Forestry and other Forest Service scientists at the University of Puerto Rico Mayaguez. I learned of potential postdoctoral research opportunities that would extend my training.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
High-Quality, Phased Genomes of Phytophthora ramorum Clonal Lineages NA1 and EU1. 10.1094/MPMI-11-21-0264-A
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