Holosteans contextualize the role of the teleost genome duplication in promoting the rise of evolutionary novelties in the ray-finned fish innate immune system

NITR12+ NK Cells Release Perforin to Mediate IgMhi B Cell Killing in Turbot (Scophthalmus maximus)

B lymphocytes engaged in humoral immunity play a critical role in combating pathogenic infections; however, the mechanisms of NK cells in regulating the responses of B cells remain largely unknown. In the present study, we established an Edwardsiella piscicida infection model in turbot (Scophthalmus maximus) and found that the production of IgM was decreased. Meanwhile, through establishing the head kidney-derived lymphocyte infection model, we revealed that the impairment of IgMhi B cells was associated with bacterial infection-induced perforin production. Interestingly, we reveal that perforin production in NK cells is tightly regulated by an inhibitory novel immune-type receptor, NITR12. Moreover, we confirm that inhibiting NITR12 can result in elevated perforin production, engaging the impairment of IgMhi B cells. Taken together, these findings demonstrate an innovative strategy of NK cells in mediating B lymphocyte killing in turbot and suggest that relieving NK cells through NITR12 might be the target for the development of efficacious vaccines.

Ancient fish lineages illuminate toll-like receptor diversification in early vertebrate evolution

Since its initial discovery over 50 years ago, understanding the evolution of the vertebrate RAG- mediated adaptive immune response has been a major area of research focus for comparative geneticists. However, how the evolutionary novelty of an adaptive immune response impacted the diversity of receptors associated with the innate immune response has received considerably less attention until recently. Here, we investigate the diversification of vertebrate toll-like receptors (TLRs), one of the most ancient and well conserved innate immune receptor families found across the Tree of Life, integrating genomic data that represent all major vertebrate lineages with new transcriptomic data from Polypteriformes, the earliest diverging ray-finned fish lineage. Our analyses reveal TLR sequences that reflect the 6 major TLR subfamilies, TLR1, TLR3, TLR4, TLR5, TLR7, and TLR11, and also currently unnamed, yet phylogenetically distinct TLR clades. We additionally recover evidence for a pulse of gene gain coincident with the rise of the RAG-mediated adaptive immune response in jawed vertebrates, followed by a period of rapid gene loss during the Cretaceous. These gene losses are primarily concentrated in marine teleost fish and synchronous with the mid Cretaceous anoxic event, a period of rapid extinction for marine species. Finally, we reveal a mismatch between phylogenetic placement and gene nomenclature for up to 50% of TLRs found in clades such as ray-finned fishes, cyclostomes, amphibians, and elasmobranchs. Collectively, these results provide an unparalleled perspective of TLR diversity and offer a ready framework for testing gene annotations in non-model species.

A chromosome-level genome assembly of longnose gar, Lepisosteus osseus

Holosteans (gars and bowfins) represent the sister lineage to teleost fishes, the latter being a clade that comprises over half of all living vertebrates and includes important models for comparative genomics and human health. A major distinction between the evolutionary history of teleosts and holosteans is that all teleosts experienced a genome duplication event in their early evolutionary history. As the teleost genome duplication occurred after teleosts diverged from holosteans, holosteans have been heralded as a means to bridge teleost models to other vertebrate genomes. However, only three species of holosteans have been genome-sequenced to date, and sequencing of more species is needed to fill sequence sampling gaps and provide a broader comparative basis for understanding holostean genome evolution. Here we report the first high quality reference genome assembly and annotation of the longnose gar (Lepisosteus osseus). Our final assembly consists of 22,709 scaffolds with a total length of 945 bp with contig N50 of 116.61 kb. Using BRAKER2, we annotated a total of 30,068 genes. Analysis of the repetitive regions of the genome reveals the genome to contain 29.12% transposable elements, and the longnose gar to be the only other known vertebrate outside of the spotted gar and bowfin to contain CR1, L2, Rex1, and Babar. These results highlight the potential utility of holostean genomes for understanding the evolution of vertebrate repetitive elements, and provide a critical reference for comparative genomic studies utilizing ray-finned fish models.

A highly diverse set of novel immunoglobulin-like transcript (NILT) genes in zebrafish indicates a wide range of functions with complex relationships to mammalian receptors

Multiple novel immunoglobulin-like transcripts (NILTs) have been identified from salmon, trout, and carp. NILTs typically encode activating or inhibitory transmembrane receptors with extracellular immunoglobulin (Ig) domains. Although predicted to provide immune recognition in ray-finned fish, we currently lack a definitive framework of NILT diversity, thereby limiting our predictions for their evolutionary origin and function. In order to better understand the diversity of NILTs and their possible roles in immune function, we identified five NILT loci in the Atlantic salmon (Salmo salar) genome, defined 86 NILT Ig domains within a 3-Mbp region of zebrafish (Danio rerio) chromosome 1, and described 41 NILT Ig domains as part of an alternative haplotype for this same genomic region. We then identified transcripts encoded by 43 different NILT genes which reflect an unprecedented diversity of Ig domain sequences and combinations for a family of non-recombining receptors within a single species. Zebrafish NILTs include a sole putative activating receptor but extensive inhibitory and secreted forms as well as membrane-bound forms with no known signaling motifs. These results reveal a higher level of genetic complexity, interindividual variation, and sequence diversity for NILTs than previously described, suggesting that this gene family likely plays multiple roles in host immunity.

A subset of leukocyte immune-type receptors (LITRs) regulates phagocytosis in channel catfish (Ictalurus punctatus) leukocytes

Channel catfish, Ictalurus punctatus, leukocyte immune-type receptors (LITRs) constitute a large family of paired, immunoregulatory receptors unique to teleosts. A role for LITRs in phagocytosis has been proposed based on studies in mammalian cell lines; however, LITR-mediated phagocytosis has not been examined in the catfish model. In this study, we use two anti-LITR monoclonal antibodies, CC41 and 125.2, to contrast the effects of crosslinking subsets of inhibitory and activating LITRs. Briefly, LITRs expressed by catfish γδ T cells, αβ T cells, and macrophage cell lines were crosslinked using mAb-conjugated fluorescent microbeads, and bead uptake was evaluated by flow cytometry and confirmed by confocal microscopy. A clear difference in the uptake of 125.2- and CC41-conjugated beads was observed. Crosslinking LITRs with mAb 125.2 resulted in efficient bead internalization, while mAb CC41 crosslinking of inhibitory LITRs resulted predominantly in a capturing phenotype. Pretreating catfish macrophages with mAb CC41 resulted in a marked decrease in LITR-mediated phagocytosis of 125.2-conjugated beads. Overall, these findings provide insight into fish immunobiology and validate LITRs as regulators of phagocytosis in catfish macrophages and γδ T cells.

Phylogenomic analysis of the bowfin (Amia calva) reveals unrecognized species diversity in a living fossil lineage

The Bowfin (Amia calva), as currently recognized, represents the sole living member of the family Amiidae, which dates back to approximately 150 Ma. Prior to 1896, 13 species of extant Bowfins had been described, but these were all placed into a single species with no rationale or analysis given. This situation has persisted until the present day, with little attention given to re-evaluation of those previously described nominal forms. Here, we present a phylogenomic analysis based on over 21,000 single nucleotide polymorphisms (SNPs) from 94 individuals that unambiguously demonstrates the presence of at least two independent evolutionary lineages within extant Amia populations that merit species-level standing, as well as the possibility of two more. These findings not only expand the recognizable species diversity in an iconic, ancient lineage, but also demonstrate the utility of such methods in addressing previously intractable questions of molecular systematics and phylogeography in slowly evolving groups of ancient fishes.

On the relationship between extant innate immune receptors and the evolutionary origins of jawed vertebrate adaptive immunity

For over half a century, deciphering the origins of the genomic loci that form the jawed vertebrate adaptive immune response has been a major topic in comparative immunogenetics. Vertebrate adaptive immunity relies on an extensive and highly diverse repertoire of tandem arrays of variable (V), diversity (D), and joining (J) gene segments that recombine to produce different immunoglobulin (Ig) and T cell receptor (TCR) genes. The current consensus is that a recombination-activating gene (RAG)-like transposon invaded an exon of an ancient innate immune VJ-bearing receptor, giving rise to the extant diversity of Ig and TCR loci across jawed vertebrates. However, a model for the evolutionary relationships between extant non-recombining innate immune receptors and the V(D)J receptors of the jawed vertebrate adaptive immune system has only recently begun to come into focus. In this review, we provide an overview of non-recombining VJ genes, including CD8β, CD79b, natural cytotoxicity receptor 3 (NCR3/NKp30), putative remnants of an antigen receptor precursor (PRARPs), and the multigene family of signal-regulatory proteins (SIRPs), that play a wide range of roles in immune function. We then focus in detail on the VJ-containing novel immune-type receptors (NITRs) from ray-finned fishes, as recent work has indicated that these genes are at least 50 million years older than originally thought. We conclude by providing a conceptual model of the evolutionary origins and phylogenetic distribution of known VJ-containing innate immune receptors, highlighting opportunities for future comparative research that are empowered by this emerging evolutionary perspective.