Evolution and Expression of the Immune System of a Facultatively Anadromous Salmonid

Genetic architecture and correlations between the gut microbiome and gut gene transcription in Chinook salmon (Oncorhynchus tshawytscha)

Population divergence through selection can drive local adaptation in natural populations which has implications for the effective restoration of declining and extirpated populations. However, adaptation to local environmental conditions is complicated when both the host and its associated microbiomes must respond via co-evolutionary change. Nevertheless, for adaptation to occur through selection, variation in both host and microbiome traits should include additive genetic effects. Here we focus on host immune function and quantify factors affecting variation in gut immune gene transcription and gut bacterial community composition in early life-stage Chinook salmon (Oncorhynchus tshawytscha). Specifically, we utilized a replicated factorial breeding design to determine the genetic architecture (sire, dam and sire-by-dam interaction) of gut immune gene transcription and microbiome composition. Furthermore, we explored correlations between host gut gene transcription and microbiota composition. Gene transcription was quantified using nanofluidic qPCR arrays (22 target genes) and microbiota composition using 16 S rRNA gene (V5-V6) amplicon sequencing. We discovered limited but significant genetic architecture in gut microbiota composition and transcriptional profiles. We also identified significant correlations between gut gene transcription and microbiota composition, highlighting potential mechanisms for functional interactions between the two. Overall, this study provides support for the co-evolution of host immune function and their gut microbiota in Chinook salmon, a species recognized as locally adapted. Thus, the inclusion of immune gene transcription profile and gut microbiome composition as factors in the development of conservation and commercial rearing practices may provide new and more effective approaches to captive rearing.

Development of the Thymus and Kidney and Effects of Resveratrol on Their Aging in a Short-Lived Fish

Annual fishes of the genus Nothobranchius have been widely used in cognitive, behavioral, and genetic studies, and have become an excellent animal model for studying aging. However, the development and degeneration of immune organs in annual fishes and the antagonistic effects of resveratrol remain unclear. In the present study, the development of thymus and kidney was investigated systematically using Nothobranchius guentheri from larvae, juveniles, and young and old fish with hematoxylin and eosin staining. We found that thymus primordium was observed first in the larvae at 2 days after hatching (dah). After the lymphoid cells became evident at 5 dah, the thymus acquired an irregular shape at 7 dah. Then it formed a wedge shape at 15 dah. Thymus looked as homogeneous distribution of lymphocytes at 1 month old, and it differentiated into cortex and medulla approximately in 2-month-old fish. Combined with TUNEL and senescence-associated β-galactosidase (SA-β-gal) staining, it showed the degeneration of the thymus appeared in 4-month-old fish. Kidney primordium appeared on 1 dah, and the glomerulus was visible at 7 dah. The nephrogenic activity was most apparent in 1-month-old fish. A large hematopoietic tissue was arranged in the renal interstitium in 2- and 3-month-old fish. In 6-month-old fish, the kidney structure became less dense. By 12 months, the kidney exhibited the most pronounced histological characteristics of aging. Feeding resveratrol ameliorated renal fibrosis and SA-β-gal staining with age, increased SIRT1 and SIRT3 expression, and decreased the levels of NF-κB and inflammatory factors in thymus and kidney of the fish. We provided basic data for the development and degeneration of immune organs and resveratrol's anti-aging effects in short-lived fish.

Understanding the evolution of immune genes in jawed vertebrates

Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics

The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.

CNS and CNS diseases in relation to their immune system

The central nervous system is the most important nervous system in vertebrates, which is responsible for transmitting information to the peripheral nervous system and controlling the body's activities. It mainly consists of the brain and spinal cord, which contains rich of neurons, the precision of the neural structures susceptible to damage from the outside world and from the internal factors of inflammation infection, leading to a series of central nervous system diseases, such as traumatic brain injury, nerve inflammation, etc., these diseases may cause irreversible damage on the central nervous or lead to subsequent chronic lesions. After disease or injury, the immune system of the central nervous system will play a role, releasing cytokines to recruit immune cells to enter, and the immune cells will differentiate according to the location and degree of the lesion, and become specific immune cells with different functions, recognize and phagocytose inflammatory factors, and repair the damaged neural structure. However, if the response of these immune cells is not suppressed, the overexpression of some genes can cause further damage to the central nervous system. There is a need to understand the molecular mechanisms by which these immune cells work, and this information may lead to immunotherapies that target certain diseases and avoid over-activation of immune cells. In this review, we summarized several immune cells that mainly play a role in the central nervous system and their roles, and also explained the response process of the immune system in the process of some common neurological diseases, which may provide new insights into the central nervous system.

Polygenic discrimination of migratory phenotypes in an estuarine forage fish

Migration is a complex phenotypic trait with some species containing migratory and nonmigratory individuals. Such life history variation may be attributed in part to plasticity, epigenetics, or genetics. Although considered semianadromous, recent studies using otolith geochemistry have revealed life history variation within the critically endangered Delta Smelt. Broadly categorizable as migratory or freshwater residents, we examined Restriction site Associated DNA sequencing data to test for a relationship between genetic variation and migratory behaviors. As previously shown, we found no evidence for neutral population genetic structure within Delta Smelt; however, we found significant evidence for associations between genetic variants and life history phenotypes. Furthermore, discriminant analysis of principal components, hierarchical clustering, and machine learning resulted in accurate assignment of fish into the freshwater resident or migratory classes based on their genotypes. These results suggest the presence of adaptive genetic variants relating to life history variation within a panmictic population. Mechanisms that may lead to this observation are genotype dependent habitat choice and spatially variable selection, both of which could operate each generation and are not exclusive. Given that the population of cultured Delta Smelt are being used as a refugial population for conservation, as a supply for wild population supplementation, and currently represent the majority of all living individuals of this species, we recommend that the hatchery management strategy consider the frequencies of life history-associated alleles and how to maintain this important aspect of Delta Smelt biological variation while under captive propagation.

Alternative migratory tactics in brown trout (Salmo trutta) are underpinned by divergent regulation of metabolic but not neurological genes

The occurrence of alternative morphs within populations is common, but the underlying molecular mechanisms remain poorly understood. Many animals, for example, exhibit facultative migration, where two or more alternative migratory tactics (AMTs) coexist within populations. In certain salmonid species, some individuals remain in natal rivers all their lives, while others (in particular, females) migrate to sea for a period of marine growth. Here, we performed transcriptional profiling ("RNA-seq") of the brain and liver of male and female brown trout to understand the genes and processes that differentiate between migratory and residency morphs (AMT-associated genes) and how they may differ in expression between the sexes. We found tissue-specific differences with a greater number of genes expressed differentially in the liver (n = 867 genes) compared with the brain (n = 10) between the morphs. Genes with increased expression in resident livers were enriched for Gene Ontology terms associated with metabolic processes, highlighting key molecular-genetic pathways underlying the energetic requirements associated with divergent migratory tactics. In contrast, smolt-biased genes were enriched for biological processes such as response to cytokines, suggestive of possible immune function differences between smolts and residents. Finally, we identified evidence of sex-biased gene expression for AMT-associated genes in the liver (n = 12) but not the brain. Collectively, our results provide insights into tissue-specific gene expression underlying the production of alternative life histories within and between the sexes, and point toward a key role for metabolic processes in the liver in mediating divergent physiological trajectories of migrants versus residents.