A maternal-effect selfish genetic element in
            <i>Caenorhabditis elegans</i>

Ben-David, Eyal; Burga, Alejandro; Kruglyak, Leonid

doi:10.1126/science.aan0621

Cited by 97 publications

(131 citation statements)

References 58 publications

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“…pha-1 44 . However, these loci only account for four of the 366 distinct hyper-divergent regions we identified,…”

Section: Discussionmentioning

confidence: 99%

Balancing selection maintains hyper-divergent haplotypes inC. elegans

Lee¹,

Zdraljevic²,

Stevens³

et al. 2020

Preprint

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Summary paragraphThe mating system of a species profoundly influences its evolutionary trajectory1–3. Across diverse taxa, selfing species have evolved independently from outcrossing species thousands of times4. The transition from outcrossing to selfing significantly decreases the effective population size, effective recombination rate, and heterozygosity within a species5. These changes lead to a reduction in the genetic diversity, and therefore adaptive potential, by intensifying the effects of random genetic drift and linked selection6,7. Selfing has evolved at least three times independently in the nematode genus Caenorhabditis8, including in the model organism Caenorhabditis elegans, and all three selfing species show substantially reduced genetic diversity relative to outcrossing species8,9. Selfing and outcrossing Caenorhabditis species are often found in the same niches, but we still do not know how selfing species with limited genetic diversity can adapt to and inhabit these same diverse environments. Here, we discovered previously uncharacterized levels and patterns of genetic diversity by examining the whole-genome sequences from 609 wild C. elegans strains isolated worldwide. We found that genetic variation is concentrated in punctuated hyper-divergent regions that cover 20% of the C. elegans reference genome. These regions are enriched in environmental response genes that mediate sensory perception, pathogen response, and xenobiotic stress. Population genomic evidence suggests that these regions have been maintained by balancing selection. Using long-read genome assemblies for 15 wild isolates, we found that hyper-divergent haplotypes contain unique sets of genes and show levels of divergence comparable to that found between Caenorhabditis species that diverged millions of years ago. Taken together, these results suggest that ancient genetic diversity present in the outcrossing ancestor of C. elegans has been maintained by long-term balancing selection since the evolution of selfing. These results provide an example for how species can avoid the evolutionary “dead end” associated with selfing by maintaining ancestral genetic diversity.

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“…pha-1 44 . However, these loci only account for four of the 366 distinct hyper-divergent regions we identified,…”

Section: Discussionmentioning

confidence: 99%

Balancing selection maintains hyper-divergent haplotypes inC. elegans

Lee¹,

Zdraljevic²,

Stevens³

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Trait architectures underlying natural variation in C. elegans differ strongly over traits. For example, currently 25 quantitative trait nucleotides (QTNs) are known in C. elegans , capturing a majority of the heritable variation for particular traits (reviewed by (R ockman 2012) and (G aertner and P hillips 2010) and studies by (A ndersen et al 2014; N oble et al 2015; S chmid et al 2015; C ook et al 2016; G reene et al 2016a; G reene et al 2016b; L arge et al 2016; B en -D avid et al 2017; S terken et al 2017; Z draljevic et al 2017; H ahnel et al 2018; Z draljevic et al 2019). However, there are also examples of traits that are highly heritable but have only yielded complex or few QTL (let alone QTNs).…”

Section: Discussionmentioning

confidence: 99%

Dissecting the eQTL micro-architecture inCaenorhabditis elegans

Sterken

Bevers

Volkers

et al. 2019

Preprint

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The study of expression quantitative trait loci (eQTL) using natural variation in inbred populations has yielded detailed information about the transcriptional regulation of complex traits. Studies on eQTL using recombinant inbred lines (RILs) led to insights on local and distant regulatory loci of transcript abundance. However, determining the underlying causal polymorphic genes or variants is difficult, but ultimately essential for the understanding of regulatory networks of complex traits. This requires insight into whether associated loci are single eQTL or a combination of closely linked eQTL, and how this QTL micro-architecture depends on the environment. We addressed these questions by mapping eQTL in N2 x CB4856 C. elegans RIL populations across three different environments (control, heat-stress, and recovery). To test for independent replication of the RIL eQTL, we used introgression lines (ILs). Both populations indicate that the overall heritability, number, and position of eQTL differed among environments. Across environments we were able to replicate 70% of the local- and 40% of the distant-eQTL using the ILs. Simulation models revealed that additive effects explain up to 60-93% of RIL/IL heritability across environments. Closely linked eQTL explained up to 40% of RIL/IL heritability in the control environment whereas only 7% in the heat-stress and recovery environments. In conclusion, we show that reproducibility of eQTL was higher for local vs. distant eQTL and that the environment affects the eQTL micro-architecture.

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“…Caenorhabditis elegans (35). One current hypothesis is that speciation occurs on the gene cluster of the effector protein (toxin) and its immunity protein (anti-toxin), for example, through horizontal gene transfer, as these two-gene pairs are often in variable hotspots on the genome (2,3,7,15).…”

Section: And Inmentioning

confidence: 99%

A family of contact-dependent nuclease effectors contain an exchangeable, species-identifying domain

Sirias

Utter

Gibbs

2020

Preprint

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In mixed-species communities, bacteria can deploy contact-dependent effectors to compete with other organisms, often directly injecting these proteins into neighboring cells. One current hypothesis is that the entire protein contains information specific for a single 20 species; emergence of new effectors comes from acquiring genes. Here we have characterized a family of DNA-degrading effectors that are nucleases which cause death. Like other families of chimeric nucleases, these effectors contain two domains. One is a PD-(D/E)XK-containing domain necessary for DNA cleavage. The other domain, which does not contain known DNA-binding structures, encodes species-identifying information. 25 We capitalized on the species-identifying domain to differentiate among low-abundance species, as well as to reveal domain architectures within these proteins, in human gut and oral microbiomes. Emerging are questions about how low-abundance strains use effectors for survival and how strain-identifying effectors evolve.

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A maternal-effect selfish genetic element in Caenorhabditis elegans

Cited by 97 publications

References 58 publications

Balancing selection maintains hyper-divergent haplotypes inC. elegans

Balancing selection maintains hyper-divergent haplotypes inC. elegans

Dissecting the eQTL micro-architecture inCaenorhabditis elegans

A family of contact-dependent nuclease effectors contain an exchangeable, species-identifying domain

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