Tetraploid Ancestry Provided Atlantic Salmon With Two Paralogue Functional T Cell Receptor Beta Regions Whereof One Is Completely Novel

Abstract

Protective cellular immune responses have been difficult to study in fish, due to lack of basic understanding of their T cell populations, and tools to study them. Cellular immunity is thus mostly ignored in vaccination and infection studies compared to humoral responses. High throughput sequencing, as well as access to well assembled genomes, now advances studies of cellular responses. Here we have used such resources to describe organization of T cell receptor beta genes in Atlantic salmon. Salmonids experienced a unique whole genome duplication approximately 94 million years ago, which provided these species with many functional duplicate genes, where some duplicates have evolved new functions or sub-functions of the original gene copy. This is also the case for T cell receptor beta, where Atlantic salmon has retained two paralogue T cell receptor beta regions on chromosomes 01 and 09. Compared to catfish and zebrafish, the genomic organization in both regions is unique, each chromosomal region organized with dual variable- diversity- joining- constant genes in a head to head orientation. Sequence identity of the chromosomal constant sequences between TRB01 and TRB09 is suggestive of rapid diversification, with only 67 percent as opposed to the average 82-90 percent for other duplicated genes. Using virus challenged samples we find both regions expressing bona fide functional T cell receptor beta molecules. Adding the 292 variable T cell receptor alpha genes to the 100 variable TRB genes from 14 subgroups, Atlantic salmon has one of the most diverse T cell receptor alpha beta repertoire of any vertebrate studied so far. Perhaps salmonid cellular immunity is more advanced than we have imagined.

Evolution of T cell receptor beta loci in salmonids

“…The V-D-J-C TRB1 and TRB2 loci are in opposite transcriptional orientations (Figure 1; Supplementary File 2). The number of TRB loci present in the rainbow trout USDA_OmykA_1.1 genome assembly differs from what was recently described in Atlantic salmon (22), which has four TRB loci, two of them, TRB1 and TRB2, located on chromosome 9, and the other two, TRB3 and TRB4, on chromosome 1. The genome assembly from the Swanson clonal line of rainbow trout (Omyk_2.0 GenBank assembly [GCA_025558465.1]), as well as the Arlee rainbow trout genome assembly described in this paper, only contains three complete TRB V-D-J-C loci (two on chr.…”

“…A full annotation of the TRB locus has been reported in only a few fish species, including zebrafish, channel catfish, and recently the Atlantic salmon (22)(23)(24). In the latter species, TRB genes were reported to be organized in two sets of inverted duplicated TRB V-D-J-C loci, located on two different chromosomes.…”

“…Nineteen TRBV genes were located on chromosome 19, 17 of them in the same transcriptional orientation as the TRB3C gene, and 169 TRBV genes on chromosome 25, of which 39 and 130 were in the same transcriptional orientation as the TRB1C and TRB2C genes, respectively. As for the TRBV genes previously annotated in the Atlantic salmon genome (n=119), the 188 rainbow trout TRBV genes could be classified into the same 13 subgroups (22), as shown in a phylogenetic tree based on nucleotide sequences (Figure 5).…”

“…It has been previously reported for Atlantic salmon that TRBC1 ["type A" in (22)], was significantly more expressed than TRBC2 ["type B" in (22)]. Reads from available datasets of spleen transcriptomes were mapped to TRBC1 or TRBC2, of respectively rainbow trout, coho salmon, chinook salmon, and pink salmon.…”

The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for North American Atlantic salmon

“…For example, the T cell receptor beta 01 region which is found on Ssa01p in the European lineage reference genome has been shown to be translocated to Chr 23 (Ssa01p_Ssa23) in the assembly of the N.A. Atlantic salmon genome presented here (Grimholt et al 2022). In addition, the alignments of USDA_NASsal_1.1 (GCA_021399835.1) to the annotated Ssal_v3.1 (GCF_905237065.1) genome assembly are now available in the NCBI remap menu at: https://www.ncbi.nlm.nih.gov/genome/tools/remap.…”