Description

Model organisms have been fruitful tools for elucidating core biological principles. The power of model organism study, in part, is due to the ability to grow large populations with known genetic makeup. One of the most widely adopted genetic models is the hermaphroditic nematode Caenorhabditis elegans. The reproductive style of C. elegans makes it particularly easy to generate and maintain large populations of genetically identical individuals. In fact, the control over genetic variability helped make C. elegans the first multi-cellular organism to have its entire genome sequenced (C. elegans Sequencing Consortium 1998). Despite the success garnered using genetically homogeneous populations, it has become increasingly apparent that many of the phenotypes of interest for study are dependent on genetic background (see Evans et al. 2021 for review). Examples of these background-influenced phenotypes range from α-synuclein toxicity (Wang et al. 2019), to behavioral responses to temperature (Stegeman et al. 2013), dietary influence on lifespan and reproduction (Stastna et al. 2015), and pharmacological efficacy (Lucanic et al. 2017). The dependence on genetic background suggests that attempts to identify core biological systems and functionality could benefit from assaying across genetic diversity to identify genetic background-independent phenotypes. One way to achieve this is to use a panel of populations with intra-population homogeneity and inter-population diversity.

With the importance of genetic background effects in mind, the Caenorhabditis Intervention Testing Program (CITP) was designed to identify anti-aging and longevity-promoting compound interventions effective in a genetically diverse set of Caenorhabditis nematode populations (Lucanic et al. 2017). To date, 55 chemical compounds have been tested for reproducible, genetic background-independent effects on longevity (Lucanic et al. 2017; Banse et al. 2019; Coleman-Hulbert et al. 2019; Coleman-Hulbert et al. 2020; Morshead et al. 2020; Osman et al. 2021; Banse et al. 2021; Onken et al. 2021). The genetic diversity panel used by the CITP is composed of 22 strains from three hermaphroditic species, which facilitates maintenance of intra-population homogeneity. While the full panel is composed of 22 stains, a smaller core sub-panel of nine strains (three from each of three species, C. elegans (N2-PD1073, JU775, MY16), C. briggsae (AF16, HK104, ED3092), and C. tropicalis (JU1373, JU1630, QG843) is used in initial compound effect characterization (Banse et al. 2021). Here, we present estimates of the genetic diversity encapsulated by the constituent strains of the CITP panel, and core sub-panel, based on their most recently published and publicly available whole-genome sequences.

When establishing the genetic diversity panel for compound screening, the CITP sought strains that represented both broad geographic and genetic diversity. The three species represented in the panel are themselves globally distributed, but with ecological restrictions. For example, C. elegans is typically isolated from cooler ecological niches than C. tropicalis (Kiontke et al. 2011; Frézal and Félix 2015; Noble et al. 2021), while C. briggsae is found in niches that range from cool to warm (Frézal and Félix 2015). The wide species distributions enabled the CITP to assemble a panel of strains isolated worldwide, with representatives from most continents (Figure 1A). We next sought to determine the genetic diversity encapsulated by the panel by collecting genomic data for the strains (see Reagents) and analyzing the genomes for variation within each species (see Software). To visualize the population structure within the panel for each species we used a variational autoencoder approach, popVAE (Battey et al. 2021), to project genotypes of the strains on two latent dimensions (Figure 1B). We then determined the nucleotide diversity in the panel. The observed average genome-wide nucleotide diversity (π) among the C. elegans, C. briggsae, and C. tropicalis strains were, respectively, 1.2e-3, 7.5e-3, and 2.6e-3 (3.8e-4, 6.2e-3, and 2.4e-3 for the nine core CITP strains), which is consistent with previous estimates for those species (Graustein et al. 2002; Jovelin et al. 2009; Andersen et al. 2012; Crombie et al. 2019; Noble et al. 2021). Figure 1C shows nucleotide diversity estimated on 100 kb windows along the genomes for both the 20 strains in the full panel with available sequencing data, and for the nine strains in the core sub-panel. The estimated level of genetic diversity within these Caenorhabditis species is higher than that within human populations (Yu et al. 2004; Perry et al. 2013; Prado-Martinez et al. 2013; Arbiza et al. 2014; 1000 Genomes Project Consortium et al. 2015) and comparable to that found in mouse populations (Halligan et al. 2010; Booker and Keightley 2018). Our analysis supports the assumption that the CITP screening panel encompasses broad genetic diversity, suggesting that lifespan-extending chemicals with efficacy across the panel should be enriched for interventions that function on conserved processes that are shared across genetic backgrounds. While the diversity panel was established by the CITP for studying longevity interventions, the panel may prove useful for the broader research community when seeking broadly efficacious interventions for any phenotype with potential genetic background effects.