Oncorhynchus mykiss as a Salmonid Functional Genomics Model: A Structured Narrative Review of Genomic Resources, Mucosal Immunity, Disease Resistance, Environmental Stress, and Causal Validation

Integrated Genomic, Transcriptomic and Metabolomic Analyses Identify Key Genetic Determinants and Regulatory Networks for Salinity Tolerance in Macrobrachium rosenbergii

Genome-Wide Selection Signatures in Nili-Ravi Buffalo (Bubalus bubalis) Reveal a T-Cell Costimulatory and Cytokine-Signaling Gene Network Distinct from Classical Bovine Tuberculosis Candidate Genes

Genomic signatures of selection can reveal loci underlying adaptation and disease resistance in livestock populations, but such analyses in water buffalo (Bubalus bubalis) have historically been constrained by the absence of a chromosome-level, species-native reference genome for SNP array data. We re-analyzed genotype data from 85 Nili-Ravi buffalo (Axiom Buffalo Genotyping 90K array, originally positioned using bovine (Bos taurus, UMD3.1) proxy coordinates, by performing a full coordinate liftover to the buffalo-native UOA_WB_1 assembly using an independently published SNP remapping resource. Following quality control (51,209 markers retained), haplotype phasing, and genome-wide integrated haplotype score (iHS) and Wright’s Fst (case/control) selection scans, we evaluated 14 classical bovine-tuberculosis (bTB) candidate genes and identified six additional genes with putative immune function through an unbiased genome-wide screen. None of the 14 classical candidates (including SLC11A1, the Toll-like receptors, and IFNG) reached genome-wide significance in either scan. In contrast, six novel loci TNFSF18, IL2RB, TNFRSF19, IRF2, IL15, and CD28 showed significant iHS or Fst signals, four of which (TNFSF18, IL2RB, IL15, CD28) converge functionally on T-cell costimulation and cytokine receptor signaling (KEGG pathways map04660 and map04060, Bos taurus proxy annotation). Using extended haplotype homozygosity (EHH) decay, haplotype furcation structure, and per-marker haplotype counts as three independent lines of corroborating evidence, we classified these six genes into confidence tiers: TNFSF18 and IL2RB showed the strongest, most balanced support, while CD28 and IL15 signals were driven by very few haplotypes (3 and 5 of 30, respectively) and should be interpreted cautiously pending replication. These findings suggest that adaptive, cell-mediated immune signaling rather than the innate/macrophage-centred mechanisms emphasized by existing bTB candidate gene panels may be a more productive avenue for future selection studies in Nili-Ravi buffalo, while underscoring the value of buffalo-native coordinate systems for accurate genomic inference in this species.

Pangenomic sequencing and gene-unit genome-wide association study insights into genome plasticity and gene functions in Magnaporthe oryzae.

INTRODUCTION Magnaporthe oryzaeis a model pathogenic fungus that causes serious disease in the two most important staple crops, rice and wheat. Elucidating the genetic variation within natural populations ofM. oryzaeand identifying genes involved in pathogenicity and environmental adaptation are essential for sustainable disease control. OBJECTIVES This study aimed to elucidate the mechanisms underlying genomic variation within the M. oryzae population and to develop a novel GWAS method specifically tailored to this species. METHODS The genomes ofM. oryzaediversity population 1 (MDP1), comprising 118 strains, were sequenced andde novoassembled. In addition, a novel gene-unit GWAS (GU-GWAS) method was developed to identify associated loci. RESULTS Phylogenetic analyses revealed three subgroups among the sequenced strains, which were associated with indica and japonica rice differentiation. We also characterized core and accessory genes in theM. oryzaepopulation through pan-genome analysis. Using GU-GWAS followed by functional validation, we cloned three new genes associated with pathogenesis (SPP1), fungicide tolerance (MoFCS1), and heavy metal tolerance (MoHMT1). CONCLUSION This study provides new insights into the pangenome ofM. oryzaeand introduces a method for the identification of functionally important genes in fungal species.

Nuclear genome population genomics of the potato wart pathogen (Synchytrium endobioticum) reveals high-resolution relationships of global strains

ABSTRACT The chytrid Synchytrium endobioticum causes potato wart disease and is a regulated quarantine pathogen. Due to its obligate association with the potato host, obtaining pure genome sequences has been technically challenging. Previous population studies were limited to microsatellites or mitochondrial genomes, which capture only a small portion of the pathogen’s genetic diversity. To enable the first population genomic analyses of the nuclear genome of S. endobioticum, we designed and applied a robust single-nucleotide polymorphism (SNP) discovery strategy to existing and novel sequence data sets that represent the global diversity in potato production systems. We demonstrate that reliable nuclear genome data can be recovered from contaminated environmental samples, where S. endobioticum constitutes only ~5% of total reads. After stringent filtering, 74 high‑quality data sets for isolates from 10 countries and 12 pathotypes were retained. Phylogenetic analyses of genome-wide SNP alignments, some with up to 188 817 SNPs, identified three well-supported nuclear phylogroups that largely corresponded to mitochondrial haplogroups: (i) a basal Peruvian clade; (ii) a European/Canadian clade containing mostly pathotypes 1(D1), 2(G1), 6(O1), and 8(F1); and (iii) a clade with pathotypes 18(T1) and 38(Nevşehir). Using a subset of 13 327 homozygous SNPs, population structure analysis and phylogenetic networks confirmed three genetic clusters with limited admixture. Our analyses indicate that potato wart was introduced into Canada from a European source. Pathotype designations do not correspond to exclusive monophyletic lineages. Analysis of the AvrSen1 effector revealed that distinct loss-of-function variants can occur in multiple nuclear phylogroups, suggesting independent emergence of some virulence phenotypes. Isolates contain a reservoir of genetic variation, which may allow adaptation to changing host resistance pressures. This nuclear genome approach provides significantly greater resolution than previous molecular markers used for strain tracking. Furthermore, the solid phylogenetic framework developed here will support future effector-based pathotype inference and will aid regulators in surveillance and quarantine decisions for this high-risk pathogen.

Genomic signatures of selection and putative adaptive introgression during the African expansion of the house mouse

How species adapt to novel environments following biological invasion remains a central question in evolutionary biology. The recent human-mediated expansion of the western house mouse (Mus musculus domesticus) across Africa provides an opportunity to investigate the genomic basis of these rapid evolutionary responses. Using whole-genome data from 218 wild mice sampled across Europe and Africa, we combined complementary genome-wide differentiation, genotype–environment association, haplotype-based selection, and localized introgression analyses to investigate genomic signatures of selection and assess the contribution of interspecific gene flow from the native congener Mus spretus to these patterns. Genome-wide differentiation analyses identified candidate regions enriched for immune and epithelial-barrier functions, chemosensory perception, and neural or developmental pathways. Genotype–environment association analyses recovered fewer candidates linked mainly to precipitation, whereas haplotype-based scans highlighted recent selective signals involving sensory, immune, and neural functions. Across analyses, candidate regions were dominated by non-coding variation, supporting a predominantly regulatory and likely polygenic genomic architecture. Although excess allele sharing with M. spretus varied among populations, overlap between introgression and selection candidates was limited but greater than expected by chance. Several overlapping regions were also present in European populations, indicating that introgressed variants likely predated African colonization. Overall, our results suggest that the genomic signatures accompanying the African expansion of house mice were driven mainly by selection on M. m. domesticus variation, whereas introgressed M. spretus alleles contributed to a smaller subset of candidate loci and may have played a role in adaptation in African populations.

From Genogroups to Control Strategies: A Comprehensive Review of Piscirickettsia salmonis and Piscirickettsiosis to Optimize Health Management in Salmonid Aquaculture

Piscirickettsiosis, caused by the facultative intracellular bacterium Piscirickettsia salmonis , remains the primary infectious disease economically limiting salmonid aquaculture in Chile, while its incidence has also increased in farmed salmonids in Ireland, Scotland, Australia, and Canada in recent years. This comprehensive review synthesizes 181 peer‐reviewed publications (2014–2026) to integrate transformative advances in P. salmonis genomics, pathogenesis, epidemiology, host immunity, and control strategies, updating the foundational 2014 review by Rozas and Enríquez. Comparative genomic studies have consistently resolved LF‐89‐like and EM‐90‐like isolates as two distinct phylogenomic clusters, with marked differences in pan‐genome composition, lineage‐specific proteins, ribosomal operon organization, and Dot/Icm‐associated genomic architecture, supporting genogroup‐level divergence that should not be inferred from any single threshold‐based metric such as Average Nucleotide Identity (ANI) alone. Genogroup‐specific disease phenotypes are also well established. LF‐89 produces chronic granulomatous infections, whereas EM‐90 causes acute hemorrhagic septicemia. Mechanistically, P. salmonis evades cell‐mediated immunity by inhibiting phagosome–lysosome fusion and suppressing MHC‐I–mediated antigen presentation, impairing CD8 + cytotoxic T‐lymphocyte priming and likely explaining the consistently low vaccine efficacy and genogroup‐restricted cross‐protection observed under field conditions. Treatment failures persist despite absent widespread acquired resistance, attributable to intracellular persistence, biofilm formation, and pharmacokinetic–pharmacodynamic mismatches. Despite exponential growth in mechanistic knowledge, a substantial translational gap persists between research findings and operational implementation. This review identifies critical priorities requiring urgent investment: genogroup‐specific bivalent vaccine development, climate‐adaptive biosecurity frameworks, molecular diagnostic standardization for real‐time genogroup surveillance, and integrated control strategies tailored to P. salmonis genomic heterogeneity.