Collaborative Research: IntBIO: Investigating the drivers of interspecific variation in antibody immunity using comparative genomic and phylogenetic approaches

The immune system is the primary defense animals have against infectious diseases. A key component of this defense, the adaptive immune system, generates antibodies that recognize and neutralize bacteria, viruses, and other pathogens. The repertoire of antibodies an animal can produce is determined by a set of genes that vary considerably across mammalian species, yet this variation is almost poorly describe outside of humans, mice, and cattle. This project will conduct the first systematic comparison of immune genes and antibodies across 60 species of mammals, using state-of-the-art DNA and RNA sequencing technologies. The research team will generate high-quality genome assemblies focused on immune-related genes and expressed antibody repertoires, develop new computational tools to analyze them, and identify patterns that explain why species differ in their capacity to respond to infection. All data, genome assemblies, and software produced by this project will be made freely and publicly available, providing a foundational resource for immunology and disease research for years to come with the potential to facilitate biotechnological advances. The project will also provide meaningful research training for graduate and undergraduate students in computational biology, genetics, and immunology. Graduate students will gain hands-on experience with both laboratory sequencing methods and advanced computational analysis, while undergraduate students will participate in paid summer research positions. The team will also host a working group to establish community standards for comparing immune gene data across species, laying the groundwork for a broader research consortium that will expand this work well beyond the lifetime of this grant and further facilitate biotechnology advances. This project will generate paired datasets of antibody repertoires and germline immunoglobulin (IG) loci across approximately 60 mammalian species. For each species, expressed antibody repertoires will be profiled using long-read bulk RNA sequencing (PacBio Iso-Seq, a technology enabling full-length transcript recovery) of whole blood samples, enabling unbiased identification of V(D)J recombinations, the combinatorial gene rearrangements that generate antibody diversity, across all antibody chains. In parallel, high-quality genome assemblies will be generated using long-read whole-genome sequencing (PacBio HiFi), and IG loci will be assembled using state-of-the-art assemblers followed by targeted quality evaluation. New computational methods will be developed to integrate repertoire and genomic data to: (i) improve detection and annotation of germline IG genes, including highly divergent and previously unrecognized gene families; (ii) identify non-canonical antibody features such as ultralong or structurally atypical antigen-binding sites; and (iii) characterize structural variation and gene organization within IG loci. Using these data, the project will quantify species-level variation in germline gene content, gene usage frequencies, and V(D)J recombination features. Phylogenetic comparative models will then be applied to test hypotheses linking variation within antibody repertoires to ecological and life-history variables (including lifespan, diet, and population dynamics) and to reconstruct the evolutionary history of IG gene families. Finally, the project will analyze relationships between germline IG gene copy number, genomic organization, and expression bias to assess how the molecular evolution of IG loci shapes antibody repertoires. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria. NSF Award ID: 2536096 | Program: 01002627DB NSF RESEARCH & RELATED ACTIVIT | Principal Investigator: Corey Watson | Institution: University of Louisville Research Foundation Inc, LOUISVILLE, KY | Award Amount: $542,324 View on NSF Award Search: https://www.nsf.gov/awardsearch/show-award/?AWD_ID=2536096 View on Research.gov: https://www.research.gov/awardapi-service/v1/awards/2536096.html