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ARS Home » Southeast Area » Stoneville, Mississippi » Warmwater Aquaculture Research Unit » Research » Publications at this Location » Publication #388528

Research Project: Improving the Productivity and Quality of Catfish Aquaculture

Location: Warmwater Aquaculture Research Unit

Title: A comprehensive annotation of the channel catfish (Ictalurus punctatus) T cell receptor alpha/delta, beta and gamma loci

item CRIDER, JONATHAN - University Of Mississippi Medical Center
item Quiniou, Sylvie
item FELCH, KRISTIANNA - University Of Mississippi Medical Center
item SHOWMAKER, KURTIS - University Of Mississippi Medical Center
item BENGTEN, EVA - University Of Mississippi Medical Center
item WILSON, MELANIE - University Of Mississippi Medical Center

Submitted to: Frontiers in Immunology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/5/2021
Publication Date: 11/25/2021
Citation: Crider, J.D., Quiniou, S., Felch, K.L., Showmaker, K., Bengten, E., Wilson, M. 2021. A comprehensive annotation of the channel catfish (Ictalurus punctatus) T cell receptor alpha/delta, beta and gamma loci. Frontiers in Immunology.

Interpretive Summary: Infectious diseases represent a major economical hindrance to Channel catfish production. Two different subsets of immune cells that respond to pathogens are alpha (A)/beta (B) and gamma (G)/delta (D) T cells. These cells express T cell receptors (TR) which are critical for their functions. As such, the goal of this project was to determine the complete repertoire of the TR genes in channel catfish. In this report, a scientist at the USDA, ARS, Warmwater Aquaculture Research Unit in Stoneville, Mississippi worked together with scientists at UMMC in Jackson, Mississippi to create a comprehensive annotation of the TRB, TRAD, and TRG loci. This TR gene annotation was then used to create a database of the catfish TR genes. Channel catfish is an important U.S. agricultural food crop, and this comprehensive TR database will create a resource that can be used by researchers who are studying immune responses in catfish after any pathogenic challenge or immunization. In the future, this information will be useful for selective breeding of disease-resistant catfish or vaccine development.

Technical Abstract: The complete germline repertoires of the channel catfish, Ictalurus punctatus, T cell receptor (TR) loci, TRAD, TRB, and TRG were obtained by analyzing genomic data from PacBio sequencing. The catfish TRB locus spans 214 kb, and contains 112 TRBV genes, a single TRBD gene, 31 TRBJ genes and two TRBC genes. In contrast, the TRAD locus is very large, at 1,285 kb. It consists of four TRDD genes, one TRDJ gene followed by the exons for TRDC, 125 TRAJ genes and the exons encoding the TRAC. Downstream of the TRAC, are 140 TRADV genes, and all of them are in the opposite transcriptional orientation. The catfish TRGC locus spans 151 kb and consists of four diverse V-J-C cassettes. Altogether, this locus contains 15 TRGV genes and 10 TRGJ genes. To place our data into context, we also analyzed the zebrafish TR germline gene repertoires. Overall, our findings demonstrated that catfish possesses a more restricted repertoire compared to the zebrafish. For example, the 140 number of TRADV genes in catfish form eight subgroups based on members sharing 75% nucleotide identity. However, the 149 TRAD genes in zebrafish form 53 subgroups. This difference in subgroup numbers between catfish and zebrafish is best explained by expansions of catfish TRADV subgroups, which likely occurred through multiple, relatively recent gene duplications. Similarly, 112 catfish TRBV genes form 30 subgroups, while the 51 zebrafish TRBV genes are placed into 36 subgroups. Notably, several catfish and zebrafish TRB subgroups share ancestor nodes. In addition, the complete catfish TR gene annotation was used to compile a TR gene segment database, which was applied in clonotype analysis of an available gynogenetic channel catfish transcriptome. Combined the TR annotation and clonotype analysis suggested that the expressed TRA, TRB, and TRD repertoires were generated by different mechanisms. The diversity of the TRB repertoire depends on the number of TRBV subgroups, while TRA diversity relies on the many different TRAJ genes, which appear to be only minimally trimmed. In contrast, TRD diversity relies on nucleotide additions and the utilization of up to four TRDD segments.