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ARS Home » Southeast Area » Auburn, Alabama » Aquatic Animal Health Research » Research » Publications at this Location » Publication #414953
Research Project: Integrated Research to Improve Aquatic Animal Health in Warmwater Aquaculture

Location: Aquatic Animal Health Research

Title: Single-nuclei transcriptome analysis of channel catfish IgM-positive splenic fractions provides insight into the fish immunome from an aquaculture-relevant species

Author
item ALDERSEY, JOHANNA - Orise Fellow
item Lange, Miles
item Beck, Benjamin
item Abernathy, Jason

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 6/23/2024
Publication Date: 6/23/2024
Citation: Aldersey, J.E., Lange, M.D., Beck, B.H., Abernathy, J.W. 2024. Single-nuclei transcriptome analysis of channel catfish IgM-positive splenic fractions provides insight into the fish immunome from an aquaculture-relevant species. 14th North American Comparative Immunology Workshop[ABSTRACT].

Interpretive Summary:

Technical Abstract: The catfish industry is the largest sector of U.S. aquaculture production. Channel catfish, Ictalurus punctatus, is an important model for studying teleost fish immunity. Given its role in food production, the catfish immune response to industry-relevant pathogens has been extensively studied. To further examine the channel catfish immune system, we performed single-nuclei RNA sequencing on IgM-positive splenic B-cells (n=3). Spleen cell suspensions were passed through a cell sieve. To isolate IgM-positive B-cells, spleen lymphocytes were labeled with a recombinant monoclonal antibody that is reactive to catfish IgM and sorted using flow cytometry. Single-nuclei RNAseq libraries were then prepared using the 10X Genomics platform and sequenced on an Illumina NovaSeq X Plus. The demultiplexed samples was aligned to the CoCo_2.0 channel catfish reference assembly and filtered using Cell Ranger (v.5.0.0). Integrated data were analysed in Seurat (v.5.0.1) and trajectory analysis was carried out using with velocyto (v.17.17) and scVelo (0.2.5). The fractionated B Cell samples generated a total of 753,493,178 reads from an estimated 21,776 cells with approximately 34,602 reads/cell. 67% of reads mapped confidently to approximately 22,822 genes which equated to approximately 1,048 genes/cell. Preliminary analysis has identified 14 clusters in the aggregated data and 12 clusters expressed B cell markers. These data will create a profile of B cell subsets to a high-resolution in channel catfish and will provide crucial information on innate and adaptive immune function during disease progression.