Plasma proteomic profiling of bacterial cold water disease-resistant and -susceptible rainbow trout lines and biomarker discovery DOI Creative Commons
Gregory D. Wiens, David Marancik,

Christopher C. Chadwick

et al.

Frontiers in Immunology, Journal Year: 2023, Volume and Issue: 14

Published: Oct. 20, 2023

Genetic variation for disease resistance is present in salmonid fish; however, the molecular basis poorly understood, and biomarkers of susceptibility/resistance are unavailable. Previously, we selected a line rainbow trout high survival following standardized challenge with Flavobacterium psychrophilum (Fp), causative agent bacterial cold water disease. The resistant (ARS-Fp-R) exhibits over 60 percentage points higher compared to reference susceptible (ARS-Fp-S). To gain insight into differential host response between genetic lines, plasma proteomes from day 6 after intramuscular challenge. Pooled unhandled, PBS-injected, Fp-injected groups were simultaneously analyzed using TMT 6-plex label, relative abundance 513 proteins was determined. Data available via ProteomeXchange, identifier PXD041308, protein values mRNA measured prior, whole-body RNA-seq dataset. Our results identified subset differentially abundant intracellular identified, including troponin myosin, which not transcriptionally regulated, suggesting that these released pathogen-induced tissue damage. A separate high-abundance, secreted regulated infected fish. highest expressed C1q family member (designated complement C1q-like 3; C1q-LP3) upregulated 20-fold while only modestly upregulated, 1.8-fold, line. Validation performed immunoassays C1q-LP3, skeletal muscle C, cathelcidin 2, haptoglobin, leptin, growth differentiation factor 15 exhibited elevated concentration plasma. Complement H-like 1 both control challenged fish thus baseline differentiator lines. C1q-LP3 STNC Atlantic salmon experimental Fp. In summary, findings further understanding Fp identifies may have use evaluation on-farm health monitoring.

Language: Английский

Polyploid plants take cytonuclear perturbations in stride DOI Creative Commons
Daniel B. Sloan, Justin L. Conover, Corrinne E. Grover

et al.

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(4), P. 829 - 839

Published: Jan. 24, 2024

Hybridization in plants is often accompanied by nuclear genome doubling (allopolyploidy), which has been hypothesized to perturb interactions between and organellar (mitochondrial plastid) genomes creating imbalances the relative copy number of these producing genetic incompatibilities maternally derived half allopolyploid from paternal progenitor. Several evolutionary responses have predicted ameliorate effects, including selection for changes protein sequences that restore cytonuclear interactions; biased gene retention/expression/conversion favoring maternal copies; fine-tuning numbers expression levels. Numerous recent studies, however, found are inconsistent rarely scale genome-wide generalities. The apparent robustness plant allopolyploidy may reflect features general allopolyploids such as lack F2 hybrid breakdown under disomic inheritance, others more plant-specific, slow sequence divergence preexisting regulatory cell size endopolyploidy during development. Thus, only act main barrier establishment lineages, perhaps helping explain why so pervasive evolution.

Language: Английский

Citations

5
Gene Function is a Driver of Activin Signaling Pathway Evolution Following Whole-Genome Duplication in Rainbow Trout (Oncorhynchus mykiss) DOI Creative Commons
Jasmine A. Richman, L. Davis, Michael Phelps

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(5)

Published: May 1, 2024

The genomes of plant and animal species are influenced by ancestral whole-genome duplication (WGD) events, which have profound impacts on the regulation function gene networks. To gain insight into consequences WGD we characterized sequence conservation expression patterns ohnologs in highly duplicated activin receptor signaling pathway rainbow trout (RBT). RBT is defined tissue-specific inhibitors ligands broad receptors Co-Smad molecules. Signaling exhibited shared expression, while Smad molecules primarily express a single dominant ohnolog. Our findings suggest that influences ohnolog evolution following RBT.

Language: Английский

Citations

4
The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids DOI Creative Commons
Samuel A. May, Samuel W. Rosenbaum, Devon E. Pearse

et al.

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: April 18, 2025

ABSTRACT The increasing feasibility of whole‐genome sequencing has been highly anticipated, promising to transform our understanding the biology nonmodel species. Notably, dramatic cost reductions beginning around 2007 with advent high‐throughput inspired publications heralding ‘genomics revolution’, predictions about its future impacts. Although such served as useful guideposts, value is added when statements are evaluated benefit hindsight. Here, we review 10 key made early in genomics revolution, highlighting those realised while identifying challenges limiting others. We focus on concerning applied aspects and examples involving salmonid species which, due their socioeconomic ecological significance, have frontrunners applications Predicted outcomes included enhanced analytical power, deeper insights into genetic basis phenotype fitness variation, disease management breeding program advancements. many materialised, several expectations remain unmet technological, knowledge barriers. Additionally, largely unforeseen advancements, including identification applicability large‐effect loci, close‐kin mark–recapture, environmental DNA gene editing under‐anticipated value. Finally, emerging innovations artificial intelligence bioinformatics offer new directions. This retrospective evaluation impacts genomic revolution offers for

Language: Английский

Citations

0
A homology guide for Pacific salmon genus Oncorhynchus resolves patterns of ohnolog retention, resolution and local adaptation following the salmonid‐specific whole‐genome duplication event DOI Creative Commons
Bradford Dimos, Michael Phelps

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(4)

Published: April 1, 2023

Abstract Salmonid fishes have emerged as a tractable model to study whole‐genome duplications (WGDs) this group has undergone four rounds of WGDs. While most the salmonid genome returned diploid state, significant proportion genes are maintained duplicates and referred ohnologs. The fact that much modern gene repertoire is comprised ohnologs, while other their singleton state creates complications for genetic studies by obscuring homology relationships. difficulty particularly prominent in Pacific salmonids belonging genus Oncorhynchus who focus intense genetics‐based conservation management efforts owing important ecological cultural roles these fish play. To address gap, we generated guide six species with available genomes used describe patterns ohnolog retention resolution. Overall, find ohnologs comprise approximately half each repertoires, which functionally enriched involved DNA binding, less numerous heavily dosage‐sensitive processes such mitochondrial metabolism. Additionally, reanalyzing published expression data from locally adapted strains O. mykiss , show exhibit adaptive profiles; however, not more likely display signatures than either paralogs or singletons. Finally, demonstrate utility our investigating evolutionary relationship among highlighted playing role life‐history traits editing targets.

Language: Английский

Citations

9
Activin Signaling Pathway Specialization During Embryonic and Skeletal Muscle Development in Rainbow Trout (Oncorhynchus mykiss) DOI
Jasmine A. Richman, Michael Phelps

Marine Biotechnology, Journal Year: 2024, Volume and Issue: 26(4), P. 766 - 775

Published: July 25, 2024

Language: Английский

Citations

1
Activin signaling pathway specialization during embryonic and skeletal muscle development in rainbow trout (Oncorhynchus mykiss) DOI Creative Commons
Jasmine A. Richman, Michael Phelps

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: March 5, 2024

Abstract Activin signaling is essential for proper embryonic, skeletal muscle, and reproductive development. Duplication of the pathway in teleost fish has enabled diversification gene function across but how duplication influences activin non-mammalian species poorly understood. Full characterization receptor expression was performed embryonic development during early muscle growth rainbow trout (RBT, Oncorhynhus mykiss). Rainbow are a model salmonid that have undergone two additional rounds whole genome duplication. There limited Ab RBT embryos despite these genes exhibiting significantly elevated post-hatch muscle. Divergent patterns were also observed type IIB ohnologs. CRISPR targeting Aa2 Ab2 did not identify any developmental or phenotypes edited RBT, however, high percentage in-frame alleles identified targeted fish. The research identifies mechanisms specialization among duplicated ohnologs periods larval juvenile knowledge gained provides critical insights into viable gene-targeting approaches engineering to improve physiological performance species.

Language: Английский

Citations

0
Long-Read De Novo Genome Assembly of Gulf toadfish Opsanus beta. DOI Creative Commons
Nicholas S. Kron, Benjamin Young, Melissa K. Drown

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: April 5, 2024

Abstract The Gulf toadfish, Opsanus beta , within the family Batrachoididae, plays an important role ecologically and as a comparative research model. Only 4 genome assemblies are available for Batrachoids, with three being highly fragmentary not up to current assembly standards. Here we present new, de novo transcriptome toadfish using PacBio long read technology. final is among largest teleost genomes at 2.1 gigabases. This new improves significantly upon currently reference scaffold count of 62, which 23 chromosome scale, N50 98,402,768, BUSCO completeness score 97.3%. Annotation ab intio transcriptome-based methods generated 41,076 gene models. Modeling orthogroup change indicated expansion many immune associated orthogroups contraction olfactory receptor orthogroups. repetitive, ~ 70% composed simple repeats transposable elements. Satellite DNA analysis identified potential telomeric centromeric regions. improved represents valuable resource future this model organism genomics more broadly.

Language: Английский

Citations

0
Long-read de novo genome assembly of Gulf toadfish (Opsanus beta) DOI Creative Commons
Nicholas S. Kron, Benjamin D. Young, Melissa K. Drown

et al.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Sept. 18, 2024

The family Batrachoididae are a group of ecologically important teleost fishes with unique life histories, behavior, and physiology that has made them popular model organisms. remain understudied in the realm genomics, only four reference genome assemblies available for family, three being highly fragmented not up to current assembly standards. Among these is Gulf toadfish, Opsanus beta, organism serotonin which recently been bred captivity.

Language: Английский

Citations

0
Plasma proteomic profiling of bacterial cold water disease-resistant and -susceptible rainbow trout lines and biomarker discovery DOI Creative Commons
Gregory D. Wiens, David Marancik,

Christopher C. Chadwick

et al.

Frontiers in Immunology, Journal Year: 2023, Volume and Issue: 14

Published: Oct. 20, 2023

Genetic variation for disease resistance is present in salmonid fish; however, the molecular basis poorly understood, and biomarkers of susceptibility/resistance are unavailable. Previously, we selected a line rainbow trout high survival following standardized challenge with Flavobacterium psychrophilum (Fp), causative agent bacterial cold water disease. The resistant (ARS-Fp-R) exhibits over 60 percentage points higher compared to reference susceptible (ARS-Fp-S). To gain insight into differential host response between genetic lines, plasma proteomes from day 6 after intramuscular challenge. Pooled unhandled, PBS-injected, Fp-injected groups were simultaneously analyzed using TMT 6-plex label, relative abundance 513 proteins was determined. Data available via ProteomeXchange, identifier PXD041308, protein values mRNA measured prior, whole-body RNA-seq dataset. Our results identified subset differentially abundant intracellular identified, including troponin myosin, which not transcriptionally regulated, suggesting that these released pathogen-induced tissue damage. A separate high-abundance, secreted regulated infected fish. highest expressed C1q family member (designated complement C1q-like 3; C1q-LP3) upregulated 20-fold while only modestly upregulated, 1.8-fold, line. Validation performed immunoassays C1q-LP3, skeletal muscle C, cathelcidin 2, haptoglobin, leptin, growth differentiation factor 15 exhibited elevated concentration plasma. Complement H-like 1 both control challenged fish thus baseline differentiator lines. C1q-LP3 STNC Atlantic salmon experimental Fp. In summary, findings further understanding Fp identifies may have use evaluation on-farm health monitoring.

Language: Английский

Citations

0