How chromosomal inversions reorient the evolutionary process

Journal of Evolutionary Biology, Journal Year: 2023, Volume and Issue: 36(12), P. 1761 - 1782

Published: Nov. 9, 2023

Abstract Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce effective rate recombination in heterozygous state. They play major role adaptation, as well other evolutionary processes such speciation. Although inversions have been studied since 1920s, they remain difficult to investigate because reduced conferred by them strengthens effects drift hitchhiking, which turn can obscure signatures selection. Nonetheless, numerous found be under Given recent advances population genetic theory empirical study, here we review how different mechanisms selection affect evolution inversions. A key difference between mutations, single nucleotide variants, is fitness an inversion may affected larger number frequently interacting processes. This considerably complicates analysis causes underlying We discuss extent these disentangled, approach. often roles adaptation speciation, but direct their obscured characteristic makes so unique (reduced arrangements). In this review, examine impact evolution, weaving together both theoretical studies. emphasize most patterns overdetermined (i.e. caused multiple processes), highlight new technologies provide path forward towards disentangling mechanisms.

Language: Английский

---

Inversion invasions: when the genetic basis of local adaptation is concentrated within inversions in the face of gene flow

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 377(1856)

Published: June 13, 2022

Across many species where inversions have been implicated in local adaptation, genomes often evolve to contain multiple, large that arise early divergence. Why this occurs has yet be resolved. To address gap, we built forward-time simulations which flexible characteristics and can invade a metapopulation undergoing spatially divergent selection for highly polygenic trait. In our simulations, typically arose divergence, captured standing genetic variation upon mutation, then accumulated small-effect loci over time. Under special conditions, could also late adaptation capture locally adapted alleles. Polygenic behaved similarly single supergene of effect were detectable by genome scans. Our results show adaptive found empirical studies (e.g. multiple large, old are F ST outliers, sometimes overlapping with other inversions) consistent architecture, do not need any large-effect genes play an important role adaptation. By combining population quantitative framework, give deeper understanding the specific conditions needed involved when architecture is polygenic. This article part theme issue ‘Genomic supergenes: causes evolutionary consequences’.

Language: Английский

---

Advancing fish breeding in aquaculture through genome functional annotation

Aquaculture, Journal Year: 2024, Volume and Issue: 583, P. 740589 - 740589

Published: Jan. 17, 2024

Genomics is increasingly applied in breeding programmes for farmed fish and shellfish species around the world. However, current applications do not include information on genome functional activity, which can enhance opportunities to predict relationships between genotypes phenotypes hence increase accuracy of selection. Here, we review prospects improving aquaculture practises through uptake genomics data light EU Horizon 2020 project AQUA-FAANG: ‘Advancing European Aquaculture by Genome Functional Annotation’. This consortium targeted six major aquaculture, producing thousands genomic datasets from samples representing embryos mature adults both sexes, following immunological stimulation. was used catalogue activity across each species, revealing transcribed regions, distinct chromatin states regulatory elements impacting gene expression. These annotations were shared as open Ensembl browser using latest reference genomes species. AQUA-FAANG offers novel identify prioritize causative genetic variants responsible diverse traits including disease resistance, be exploited selective breeding. Such knowledge associated resources have potential improve sustainability boost production accelerating gain health robustness infection, whilst reducing requirement animal testing. We further outline directions advance leverage annotation beyond project. Given diversity sectors businesses, incorporation into decisions will depend technological readiness level scale operation, with cost-benefit analysis necessary determine most profitable approach system.

Language: Английский

---

The emergence of supergenes from inversions in Atlantic salmon

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 377(1856)

Published: June 13, 2022

Supergenes link allelic combinations into non-recombining units known to play an essential role in maintaining adaptive genetic variation. However, because supergenes can be maintained over millions of years by balancing selection and typically exhibit strong recombination suppression, both the underlying functional variants how are formed largely unknown. Particularly, questions remain importance inversion breakpoint sequences whether capture pre-existing variation or accumulate this following suppression. To investigate process supergene formation, we identified polymorphisms Atlantic salmon assembling eleven genomes with nanopore long-read sequencing technology. A genome assembly from sister species, brown trout, was used determine standard state inversions. We found evidence for through genotype–environment associations, but not accumulation deleterious mutations. One young 3 Mb segregating North American populations has captured that is still within arrangement inversion, while some accumulated after inversion. This two others had breakpoints disrupting genes. Three multigene inversions matched repeat structures at did show any signatures, suggesting shared repeats may obstruct formation. article part theme issue ‘Genomic architecture supergenes: causes evolutionary consequences’.

Language: Английский

---

Genomic architecture of supergenes: connecting form and function

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 377(1856)

Published: June 13, 2022

Supergenes are tightly linked sets of loci that inherited together and control complex phenotypes. While classical supergenes-governing traits such as wing patterns in Heliconius butterflies or heterostyly Primula-have been studied since the Modern Synthesis, we still understand very little about how they evolve persist nature. The genetic architecture supergenes is a critical factor affecting their evolutionary fate, it can change key parameters recombination rate effective population size, potentially redirecting molecular evolution supergene addition to surrounding genomic region. To evolution, must link with processes. This now becoming possible recent advances sequencing technology powerful forward computer simulations. present theme issue brings theoretical empirical papers, well opinion synthesis which showcase architectural diversity connect this processes polymorphism maintenance mutation accumulation. Here, summarize those insights highlight new ideas methods illuminate path for study article part 'Genomic supergenes: causes consequences'.

Language: Английский

---

Genomic architecture and functional effects of potential human inversion supergenes

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 377(1856)

Published: June 13, 2022

Supergenes are involved in adaptation multiple organisms, but they little known humans. Genomic inversions the most common mechanism of supergene generation and maintenance. Here, we review information about two large that best examples potential human supergenes. In addition, do an integrative analysis newest data to understand better their functional effects underlying genetic changes. We have found highly divergent haplotypes 17q21.31 inversion approximately 1.5 Mb phenotypic associations, with consistent brain-related traits, red white blood cells, lung function, male female characteristics disease risk. By combining gene expression nucleotide variation data, also analysed molecular differences between haplotypes, including duplications, amino acid substitutions regulatory changes, identify CRHR1, KANLS1 MAPT as good candidates be responsible for these phenotypes. The situation is more complex 8p23.1 inversion, where there no clear differentiation. However, associated several related phenotypes could linked specific one orientation. Our work, therefore, contributes characterization both exceptional variants illustrates important role inversions. This article part theme issue 'Genomic architecture supergenes: causes evolutionary consequences'.

Language: Английский

---

Predicting recombination suppression outside chromosomal inversions in Drosophila melanogaster using crossover interference theory

Heredity, Journal Year: 2023, Volume and Issue: 130(4), P. 196 - 208

Published: Feb. 1, 2023

Language: Английский

---

Cell atlas of the Atlantic salmon spleen reveals immune cell heterogeneity and cell-specific responses to bacterial infection

Fish & Shellfish Immunology, Journal Year: 2024, Volume and Issue: 145, P. 109358 - 109358

Published: Jan. 3, 2024

The spleen is a conserved secondary lymphoid organ that emerged in parallel to adaptive immunity early jawed vertebrates. Recent studies have applied single cell transcriptomics reveal the cellular composition of several species, cataloguing diverse immune types and subpopulations. In this study, 51,119 nuclei transcriptomes were comprehensively investigated commercially important teleost Atlantic salmon (Salmo salar L.), contrasting control animals with those challenged bacterial pathogen Aeromonas salmonicida. We identified clusters representing expected major types, namely T cells, B natural killer-like granulocytes, mononuclear phagocytes, endothelial mesenchymal erythrocytes thrombocytes. discovered heterogeneity within lineages, providing evidence for resident macrophages melanomacrophages, infiltrating monocytes, candidate dendritic subpopulations, cells at distinct stages differentiation, including plasma an igt + subset. provide twelve subsets, cd4+ helper regulatory one cd8+ subset, three γδT populations double negative cd4 cd8. number genes showing differential expression during infection was highly variable across largest changes observed followed by resting mature cells. Our analysis provides local inflammatory response alongside maturation spleen, upregulation ccr9 consistent recruitment gut deal infection. Overall, study new cell-resolved perspective actions highlighting extensive hidden bulk transcriptomics. further large catalogue cell-specific marker can be leveraged explore function structural organization salmonid system.

Language: Английский

---

The generation of the first chromosome-level de novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of North American Atlantic salmon

G3 Genes Genomes Genetics, Journal Year: 2023, Volume and Issue: 13(9)

Published: June 19, 2023

Atlantic salmon (Salmo salar) in Northeastern US and Eastern Canada has high economic value for the sport fishing aquaculture industries. Large differences exist between genomes of European origin North American (N.A.) origin. Given genetic genomic 2 lineages, it is crucial to develop unique resources N.A. salmon. Here, we describe that recently developed research aquaculture. Firstly, a new single nucleotide polymorphism (SNP) database consisting 3.1 million putative SNPs was generated using data from whole-genome resequencing 80 individuals. Secondly, high-density 50K SNP array enriched genic regions genome containing 3 sex determination 61 continent markers validated. Thirdly, map composed 27 linkage groups with 36K 2,512 individuals 141 full-sib families. Finally, chromosome-level de novo assembly male St. John River strain PacBio long reads. Information Hi-C proximity ligation sequences Bionano optical mapping used concatenate contigs into scaffolds. The contains 1,755 scaffolds only 1,253 gaps, total length 2.83 Gb N50 17.2 Mb. A BUSCO analysis detected 96.2% conserved Actinopterygii genes assembly, information guide formation chromosome sequences. Comparative reference confirmed karyotype lineages are caused by fission Ssa01 fusions including p arm Ssa23, Ssa08 Ssa29, Ssa26 Ssa28. have provide boost management farmed wild populations this highly valued species.

Language: Английский

---

Multifaceted framework for defining conservation units: An example from Atlantic salmon (Salmo salar) in Canada

Evolutionary Applications, Journal Year: 2023, Volume and Issue: 16(9), P. 1568 - 1585

Published: Sept. 1, 2023

Conservation units represent important components of intraspecific diversity that can aid in prioritizing and protecting at-risk populations, while also safeguarding unique contribute to species resilience. In Canada, identification assessments conservation is done by the Committee on Status Endangered Wildlife Canada (COSEWIC). COSEWIC recognize below level (termed "designatable units"; DUs) if unit has attributes make it both discrete evolutionarily significant. There are various ways which a DU meet criteria discreteness significance, increasing access "big data" providing unprecedented information directly inform criteria. Specifically, incorporation genomic data for an number non-model informing more assessments; thus, repeatable, robust framework needed integrating these into characterization. Here, we develop uses multifaceted, weight evidence approach incorporate multiple types, including genetic data, DUs. We apply this delineate DUs Atlantic salmon (

Language: Английский

---