A Comprehensive Annotation of the Channel Catfish (Ictalurus punctatus) T Cell Receptor Alpha/Delta, Beta, and Gamma Loci

Temporal Dynamics of Immune Response Signalling in Largemouth Bass (Micropterus salmoides) Infected With Largemouth Bass Virus

The largemouth bass virus (LMBV) significantly impacts Chinese largemouth bass aquaculture. The molecular mechanisms regulating LMBV virulence and the gene responses stimulated in the host during infection remain unclear. This study investigates the transcriptional dynamics and signalling pathways activated during the immune response to LMBV by analysing the transcriptome of head kidney tissues at 1, 4, 7, and 28 days post-infection (dpi) using RNA sequencing. Histopathological and viral load analyses indicated early tissue disruption, followed by extensive recovery by 28 dpi. Analysis of differentially expressed genes (DEGs) and weighted gene co-expression network analysis (WGCNA), combined with Venn analysis of samples at 1, 4, and 7 dpi, identified significant and common genes. Early infection triggered robust innate immunity through activation of the RIG-I like receptor and cGAS-STING signalling pathways, which activated type I interferons (IFNs) and interferon-stimulated genes (ISGs). Later stages indicated activation of adaptive immune responses. Validation of randomly selected genes via RT-qPCR confirmed the RNA-seq results, showing consistent expression patterns. This comprehensive study offers new insights into the sustained innate and adaptive immune responses to LMBV.

Identification and annotation of the T cell receptor beta (TCRβ) locus in large yellow croaker (Larimichthys crocea)

The T cell receptor (TCR) plays a crucial role in antigen recognition and signal transduction during T cell immunity. While the TCR locus has been well characterized in mammals, its knowledge in teleosts remains limited. In this study, we identified the TCRβ locus in large yellow croaker (Larimichthys crocea), an important mariculture species in China, and found 31 V, 2 D, 13 J, and 2 C gene segments. The 2 C gene segments are highly similar in amino acid sequences, and share conserved residues with TCRβ from other species. A consensus recombination signal sequence (RSS) is found to flank the V, D, and J gene segments, with conserved spacer lengths as observed in mammals. The V gene segments are consisted of a leader exon, an intron, and a Vβ exon, and could be categorized into fourteen families based on the nucleotide identity. Furthermore, we found that the recombination of V, D, and J gene segments in the TCRβ locus occurred at the genomic DNA level, followed by fusion with the C gene segments at the mRNA level. Additionally, the usage of J gene segments is restricted to their adjacent downstream C gene segments. qRT-PCR analysis showed that the TCRβ was highly expressed in immune organs and was upregulated after PHA treatment. By exploring a previously published RNA-seq dataset, we found that the V gene segments were differentially expressed after P. plecoglossicida infection, suggesting their involvement in T cell immunity. In summary, we characterized the TCRβ locus in large yellow croaker, which would promote the understanding of T cell immunity in teleosts.

Evolution of T cell receptor beta loci in salmonids

T-cell mediated immunity relies on a vast array of antigen specific T cell receptors (TR). Characterizing the structure of TR loci is essential to study the diversity and composition of T cell responses in vertebrate species. The lack of good-quality genome assemblies, and the difficulty to perform a reliably mapping of multiple highly similar TR sequences, have hindered the study of these loci in non-model organisms. High-quality genome assemblies are now available for the two main genera of Salmonids, Salmo and Oncorhynchus. We present here a full description and annotation of the TRB loci located on chromosomes 19 and 25 of rainbow trout (Oncorhynchus mykiss). To get insight about variations of the structure and composition of TRB locus across salmonids, we compared rainbow trout TRB loci with other salmonid species and confirmed that the basic structure of salmonid TRB locus is a double set of two TRBV-D-J-C loci in opposite orientation on two different chromosomes. Our data shed light on the evolution of TRB loci in Salmonids after their whole genome duplication (WGD). We established a coherent nomenclature of salmonid TRB loci based on comprehensive annotation. Our work provides a fundamental basis for monitoring salmonid T cell responses by TRB repertoire sequencing.

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

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.