Gephebase, a Database of Genotype-Phenotype Relationships for natural and domesticated variation in Eukaryotes

Courtier‐Orgogozo, Virginie; Arnoult, Laurent; Prigent, Stéphane; Wiltgen, Séverine; Martin, Arnaud

doi:10.1101/618371

Cited by 10 publications

(15 citation statements)

References 21 publications

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“…A central goal of biology is to understand the evolutionary forces and molecular processes by which new traits and functions emerge in living organisms. A major challenge toward this goal is that many cellular processes rely on interactions between molecular partners (protein-protein interactions or regulatory interactions between for example transcription factors and their binding sites; Boyle et al, 2017; Courtier-Orgogozo et al, 2019) rather than on the action of individual components in isolation. At present, the overall structure of protein-protein or regulatory interaction networks is just starting to be understood at the genome level in a handful of model organisms, and a general understanding of how the diversification of these networks led to the emergence of new biological functions in distinct lineages is crucially lacking (Nooren and Thornton, 2003; Andreani and Guerois, 2014).…”

Section: Introductionmentioning

confidence: 99%

Asymmetrical diversification of the receptor-ligand interaction controlling self-incompatibility in Arabidopsis

Chantreau

Poux

Lensink

et al. 2019

eLife

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How two-component genetic systems accumulate evolutionary novelty and diversify in the course of evolution is a fundamental problem in evolutionary systems biology. In the Brassicaceae, self-incompatibility (SI) is a spectacular example of a diversified allelic series in which numerous highly diverged receptor-ligand combinations are segregating in natural populations. However, the evolutionary mechanisms by which new SI specificities arise have remained elusive. Using in planta ancestral protein reconstruction, we demonstrate that two allelic variants segregating as distinct receptor-ligand combinations diverged through an asymmetrical process whereby one variant has retained the same recognition specificity as their (now extinct) putative ancestor, while the other has functionally diverged and now represents a novel specificity no longer recognized by the ancestor. Examination of the structural determinants of the shift in binding specificity suggests that qualitative rather than quantitative changes of the interaction are an important source of evolutionary novelty in this highly diversified receptor-ligand system.

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Section: Introductionmentioning

confidence: 99%

Asymmetrical diversification of the receptor-ligand interaction controlling self-incompatibility in Arabidopsis

Chantreau

Poux

Lensink

et al. 2019

eLife

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“…Mapping genotypic variation to phenotypic variation is one of the major goals of evolutionary biology. Hence, a multitude of candidate loci underlying adaptive trait variation have been identified in a wide range of organisms (Courtier-Orgogozo et al, 2020). Most of these studies are performed in species harbouring natural variation but that are typically considered non-model systems due to the lack of tractable genetic tools.…”

Section: Discussionmentioning

confidence: 99%

oca2targeting using CRISPR/Cas9 in the Malawi cichlidAstatotilapia calliptera

Clark

Elkin

Marconi

et al. 2022

Preprint

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Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterising the role of genetic loci requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing in Astatotilapia calliptera, a generalist cichlid of the remarkably diverse Lake Malawi radiation. By targeting the gene oca2 required for melanin synthesis in other vertebrate species, we show efficient editing and germline transmission. Gene edits include indels in the coding region, likely a result of non-homologous end joining, and a large deletion in the 3′ UTR due to homology-directed repair. We find that oca2 knock-out A. calliptera lack melanin, which may be useful for developmental imaging in embryos and studying colour pattern formation in adults. As A. calliptera resembles the presumed generalist ancestor of the Lake Malawi cichlids radiation, establishing genome editing in this species will facilitate investigating speciation, adaptation and trait diversification in this textbook radiation.

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“…Large deletions have repeatedly been observed in cases of both natural variation and domestication, with 29 deletions affecting regulatory regions which are larger than 1 kb listed on GepheBase (72). Recurrent deletions of a pitx1 enhancer in sticklebacks, up to 8 kb in length, have caused convergent pelvic reduction (73), and the deletion of a 60.7 kb regulatory region at the AR gene in humans, which removes enhancers present in chimpanzee and conserved in other mammals, leads to loss of penile spines (74).…”

Section: Discussionmentioning

confidence: 99%

“…Those recessive effects make the mutant allele unfit for breeding in the homozygous state, resulting in a form of heterozygote advantage where mutant heterozygotes are selectively bred in spite of inviable or undesirable effects in homozygotes (83,84). We compiled similar situations from the literature using a database of gene-to-phenotype relationships (72), and found 38 analogous gene-to-trait relationships spanning domesticated mammals and birds (Table 2). Large structural variations (SVs) such as the ivory deletion accounted for 9 out of 46 derived alleles in this dataset, suggesting that the recessive deleterious effects of macromutations occasionally provide heterozygous states of interest to artificial selection.…”

Section: Heterozygote Advantage Of Deleterious Mutations In Captivitymentioning

confidence: 99%

A macromutation eliminates colour patterning in captive butterflies

Hanly

Livraghi

Heryanto

et al. 2021

Preprint

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Captive populations often harbor variation that is not present in the wild due to artificial selection. Recent efforts to map this variation have provided insights into the genetic and molecular basis of variation. Heliconius butterflies display a large array of pattern variants in the wild and the genetic basis of these patterns has been well-described. Here we sought to identify the genetic basis of an unusual pattern variant that is instead found in captivity, the ivory mutant, in which all scales on both the wings and body become white or yellow. Using a combination of autozygosity mapping and coverage analysis from 37 captive individuals, we identify a 78kb deletion at the cortex wing patterning locus as the ivory mutation. This deletion is undetected among 458 wild Heliconius genomes samples, and its dosage explains both homozygous and heterozygous ivory phenotypes found in captivity. The deletion spans a large 5’ region of the cortex gene that includes a facultative 5’UTR exon detected in larval wing disk transcriptomes. CRISPR mutagenesis of this exon replicates the wing phenotypes from coding knock-outs of cortex, consistent with a functional role of ivory-deleted elements in establishing scale color fate. Population demographics reveal that the stock giving rise to the ivory mutant has a mixed origin from across the wild range of H. melpomene, and supports a scenario where the ivory mutation occurred after the introduction of cortex haplotypes from Ecuador. Homozygotes for the ivory deletion are inviable, joining 40 other examples of allelic variants that provide heterozygous advantage in animal populations under artificial selection by fanciers and breeders. Finally, our results highlight the promise of autozygosity and association mapping for identifying the genetic basis of aberrant mutations in captive insect populations.

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Gephebase, a Database of Genotype-Phenotype Relationships for natural and domesticated variation in Eukaryotes

Cited by 10 publications

References 21 publications

Asymmetrical diversification of the receptor-ligand interaction controlling self-incompatibility in Arabidopsis

Asymmetrical diversification of the receptor-ligand interaction controlling self-incompatibility in Arabidopsis

oca2targeting using CRISPR/Cas9 in the Malawi cichlidAstatotilapia calliptera

A macromutation eliminates colour patterning in captive butterflies

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