Channel catfish, Ictalurus punctatus, are the primary cultured species of the catfish industry. Significant losses in production are attributed to bacterial diseases which are challenging to control and new interventions need to be developed. To gain insight into the in situ catfish immune system, we used single-nuclei RNA sequencing.
We produced a single-nuclei atlas from three individual catfish. Libraries were prepared using the 10X Genomics Chromium X system and sequenced on an Illumina sequencer. After aligning to the channel catfish reference genome (Ip Coco_2.0) and filtering for valid nuclei, the cell types were characterized, and trajectory was predicted for B cells.
The spleen atlas included 19,613 cells sequenced to ~34.5 thousand reads/cell, and a median of 665 genes/cell. Both innate and adaptive immune cells were identified including B cells, T/NK cells and myeloid cells (Figure 1). Looking closer at the expressed genes, we characterized immature and mature B cells, plasma cells, γδ T cells, dendritic cells, and macrophages. Several sub-clusters that were not characterized may represent rare cell types.
The splenic cell atlas is a rich resource for examining the immunome of I. punctatus. The data will be used to inform future research directions into disease control and interventions