Assistant Project Scientist/Siddique Lab

University of California; Davis (CA); On-site; USD 90,000 - 115,000; Full time

Job summary

University of California Davis invites applications for an Assistant Project Scientist to lead a research project on genomic understanding of plant-parasitic nematodes, with emphasis on root-knot nematodes and resistance-breaking mechanisms. The role includes generating genome assemblies, performing transcriptomic studies, and validating gene functions in host infection.

The successful candidate will culture nematodes, conduct virulence assays, analyze data with statistical and computational

Qualifications

• Ph.D. in Entomology, Biology, or related field required by start date.
• Experience culturing and maintaining plant-parasitic nematodes and performing virulence assays.
• Ability to design and execute genomic and transcriptomic analyses and publish results.

Responsibilities

• Characterize genomes of root-knot nematode populations using chromosome-level assemblies.
• Conduct comparative and population genomics analyses to identify resistance-breaking features.
• Perform RNA-seq studies and functional characterization of virulence-related genes.
• Maintain nematode cultures in greenhouse and conduct virulence phenotyping on host genotypes.
• Collaborate with team members and assist in grant reporting and manuscript preparation.

Skills

Genomics

Bioinformatics

Nematology

Statistical analysis

Team collaboration

Education

Ph.D. in Entomology/Biology/related field

Tools

RNA-seq analysis

Genome assembly pipelines

Variant calling

Nucleic acid extraction

Job description

NATURE AND PURPOSE

The Project Scientist makes significant and creative contributions to a research or creative project in his/her academic discipline. The appointee possesses the subject matter expertise and the creative energy necessary to function at a high level of competence. The appointee will participate in activities to increase, improve, or upgrade competency. Appointees with Project (e.g., Scientist) titles may engage in University and public service. They do not have teaching responsibilities. Although the Project Scientist is expected to work independently under the general guidance of an academic member with an independent research program (i.e., Professor, Professional Researcher, Specialist in Cooperative Extension, etc.), he/she is not required to develop an independent research program or reputation. He/she will conduct research or creative programs with supervision by an individual in an academic title that carries with it automatic Principal Investigator status. The Project Scientist does not usually serve as a Principal Investigator but may do so by exception.

The Assistant Project Scientist will lead a research project that aims to improve the genomic understanding of plant-parasitic nematodes, with an emphasis on root-knot nematodes (Meloidogyne spp.) and the mechanisms underlying resistance-breaking (Rk-breaking) populations that overcome host resistance in vegetable cropping systems. Specifically, the candidate will generate and analyze high-quality whole-genome assemblies of polyploid root-knot nematode isolates, perform comparative and population genomic analyses to characterize the genetic basis of resistance-breaking phenotypes, and conduct transcriptomic (RNA-seq) studies to identify genes and effectors associated with virulence and host adaptation. The candidate must have experience culturing and maintaining plant-parasitic nematode populations on host plants, performing nematode phenotyping and virulence assays, extracting high-quality nucleic acids from nematodes, and conducting bioinformatic analyses of chromosome-level genome assembly, variant calling, and differential gene expression. The Assistant Project Scientist will be employed by UC Davis in the laboratory of Dr. Shahid Siddique in the Department of Entomology and Nematology and will work full-time under his supervision.

The candidate is expected to develop and execute protocols to conduct the research, analyze the data using appropriate statistical and computational methods, and report on the outcomes of the work in the form of project meetings, grant reports, and peer reviewed scientific manuscripts. In addition, the candidate is expected to work in a highly collaborative environment with university researchers, undergraduate students and lab technicians, as well as stakeholders from the leafy greens and vegetable industry.

MAJOR RESPONSIBILITIES AND DESIGNATED AREAS OF EXPERTISE

Research in Specialized areas (95%)

The candidate will characterize the genomes of root-knot nematode populations, including resistance-breaking isolates, by generating chromosomal level whole-genome sequence assemblies and implementing bioinformatic pipelines for assembly, annotation, and variant analysis. The candidate will conduct comparative and population genomic analyses to identify genomic features associated with resistance-breaking, and will perform transcriptomic (RNA-seq) studies and wet-lab functional characterization to resolve the expression of virulence-associated genes and effectors during host infection. The candidate will be responsible for establishing and maintaining nematode populations on host plants in a greenhouse, and for conducting virulence and phenotyping assays on a panel of resistant and susceptible vegetable and leafy green genotypes. As such, the candidate will be expected to independently design research projects, implement research protocols, analyze the data using the appropriate statistical and computational methods, and to publish research results in scientific peer reviewed journals. In addition, the candidate must be able to work collaboratively with the director and other members of the research team and assist in preparing required grant reports. Responsibilities are broken down as follows: Demonstrate significant, original, and creative contributions to the outlined research (75%), publish research results in scientific peer reviewed journals (15%), and assist in the preparation of grant reports (5%).

Professional Competence and Activity (5%)

The candidate will participate in grower and extension meetings, workshops, and present abstracts at scientific conferences specific to the field of nematology, plant pathology, and genomics. The candidate will engage with and advise students to enhance the overall mission of the research program and to promote teamwork, cooperation, and a trustworthy and secure work environment.

This position requires possession of a Ph.D. degree in Entomology, Biology, or related field is required. Degree must be awarded by start of position