Amanda M. Larracuente

Recognizing the broad importance of selfish elements, the GSA journals have established a series to highlight the genetic mechanisms and evolutionary consequences of selfish non-Mendelian inheritance. GENETICS and G3 invited high-quality submissions with a focus on selfish non-Mendelian transmission, including both theoretical and empirical studies of natural and synthetic systems. This first issue of the series features natural selfish genetic elements—including genes, chromosomes, endosymbiotic bacteria, and autonomous plasmids—and synthetic selfish genetic elements. Together, these studies investigate the dynamics, mechanisms, genomic features, and consequences of selfish elements.

Meiotic drivers achieve biased transmission to the next generation, often at the expense of their host. Drive is widespread and can shape the evolution of proteins, chromosome structure, and karyotypes. The sperm killer Segregation Distorter ( SD ) in Drosophila melanogaster is a well-studied driver but like most complex drivers, its mechanism remains elusive. SD is a multigene complex frequently associated with chromosomal inversions where the main driver locus, a truncated duplication of the gene RanGAP, kills wild-type sperm containing a satellite DNA called Responder ( Rsp ). Small RNAs are frequently implicated in the mechanisms of sperm killers, and we recently showed that Rsp is a source of small RNAs. Here we study the transcriptomes of two SD haplotypes and our results link Rsp expression and/or RNAs to drive. We found that Rsp -derived small RNAs are underrepresented in driving testes of only one of the SD haplotypes. We show that over-expressing Rsp is sufficient to reduce drive strength in the haplotype with downregulated Rsp but not the other. We therefore shed light on the mechanism of SD by making a connection between the target and the drive phenotype. Additionally, our data imply that different haplotypes of complex drivers, like SD , can vary in their mechanism.

Highly repetitive sequences pose problems for genome assembly and analysis. While advances in long-read sequencing technologies have helped reveal the organization of repetitive genomic sequences at unprecedented resolution, their functional characterization remains difficult because molecular assays that probe protein-DNA interactions and characterize expression often rely on short read sequencing. The repetitive nature of these regions poses major challenges for methods relying on sequence mapping, which is exacerbated for short reads. Repetitive genome regions often have low mappability, leading to substantial information loss during downstream filtering. To address this challenge, we developed a bioinformatic tool—kmerRRR—that leverages k-mer frequency analyses to enhance the mappability of repetitive regions. KmerRRR compares k-mer frequencies within user-defined loci to their frequencies across the genome to identify repetitive sequences that are overrepresented locally relative to the global background. This approach quantifies locus uniqueness, allowing users to distinguish sequences that are globally repetitive from those that are repetitive, but restricted to specific genomic loci. We demonstrated the utility of this method by reanalyzing chromatin profiling data from human, Drosophila , and Arabidopsis centromeres and small RNA sequencing data. Our results show that incorporating local k-mer ratio information enhances read retention and signal interpretation within repetitive regions, thereby recovering biologically meaningful information that is typically lost in conventional analyses. The tool is freely available under MIT license in github: ( https://github.com/LarracuenteLab/kmerRRR ).

Satellite DNAs (satDNAs) are tandemly repeated sequences that can comprise large fractions of eukaryotic genomes. For decades, we have known that satellite DNAs are among the most rapidly evolving genomic components, yet few studies have examined their dynamics across broad evolutionary frameworks—likely in part because their rapid evolution complicates or precludes homology identification. We investigated satDNA dynamics across 50 ground beetle (Carabidae) species, sampling above and below the species level in the subgenus Plataphus of Bembidion . We used RepeatExplorer2 and a novel homology detection pipeline, which we validated using species of Drosophila for which satDNAs are well-documented, to study satDNA dynamics in a comparative framework. We show that satDNAs comprise large genomic fractions (mean = 25.7%, range = 3.2%–53%), with individual satDNA motifs accounting for >30% of total DNA within some species. We quantify major satDNA turnover among closely related species which drives extensive repatterning of repeat content over short evolutionary scales. To place our findings in a broader context, we also surveyed satDNA diversity across the beetle suborder (Adephaga), the beetle order (Coleoptera), and the next six largest insect orders (Lepidoptera, Diptera, Hymenoptera, Hemiptera, Orthoptera, Trichoptera), representing 400 additional species. While satDNA abundance was significantly elevated in the focal subgenus ( Plataphus ), high genomic proportions were also found in species across Adephaga, Coleoptera, Hymenoptera, and Diptera. Conversely, satDNA proportions were notably reduced in Lepidoptera and Trichoptera. Our investigation of satDNA dynamics at narrow and broad taxonomic scales provides a quantitative illustration of satDNA turnover across a well-sampled clade. It also identifies new high-potential systems for gaining mechanistic insights into the drivers and impacts of satDNA evolution, and raises questions regarding potential links between satDNA turnover, speciation, and core strategies of chromosome and genome architecture in diverse clades.

Meiotic drivers are selfish genetic elements that subvert Mendelian inheritance to increase their own transmission, yet they are typically found at low frequencies across natural populations. The factors that limit their spread remain unclear. The Segregation Distorter (SD) system, a selfish coadapted gene complex in Drosophila melanogaster, is an excellent model to study this paradox. SD biases its transmission by killing sperm carrying a homologous chromosome bearing a target locus, Responder (Rsp), which corresponds to satellite repeats. Such selfish killing impairs male fertility and imposes selective pressure on the host genome to evolve resistance, either by deleting Rsp copies or acquiring unlinked suppressors. The interplay of these factors in natural populations is poorly understood. We studied the genetic factors contributing to drive strength in strains derived from a natural population of D. melanogaster from Raleigh, North Carolina, known as Drosophila Genome Reference Panel (DGRP). Here, we characterized the spectrum of Rsp alleles and the frequency of segregating suppressors in 90 DGRP strains. Our approach disentangles drive resistance at Rsp from suppression. Rather than loss of Rsp, we found that over half of the strains harbor suppressors located on the X chromosome or autosomes, but not the Y chromosome. The widespread presence of strong suppressors limited the resolution of our genome-wide association mapping; however, recombination analysis using a DGRP strain identified a strong X-linked suppressor to a ∼300 kb interval on the chromosome. Together, our findings suggest that pervasive, multilocus suppression constrains the spread of SD in natural populations.

Meiotic drivers are selfish genetic elements that gain transmission advantages by distorting equal, Mendelian segregation. For decades, biologists have considered meiotic drivers as interesting, albeit esoteric, case studies. It is now clear, however, that meiotic drive is more common and phylogenetically widespread than previously supposed. Indeed, intensive study of a few well-known cases has begun to reveal the evolutionary genomic consequences of meiotic drive. We argue here that many features of genome evolution, content, and organization that are seemingly inexplicable by organismal adaptation or nearly neutral processes are instead best accounted for by recurrent histories of meiotic drive. We review how meiotic drive can affect the evolution of sequences, gene copy numbers, genes with functions in meiosis and gametogenesis, signatures of “selection,” chromosome rearrangements, and karyotype evolution. We also explore the interactions of meiotic drive elements with other classes of selfish genetic elements, including satellite DNAs, transposable elements, and with the endogenous host genes involved in drive suppression. Finally, we argue that some aspects of drive-mediated genome evolution are now sufficiently well established that we might reverse the direction of discovery—rather than ask how drive affects genome evolution, we can use genome data to discover new putative drive elements.

Eukaryotic genomes are abundant in satellite DNA (satDNA): large blocks of tandemly-repeated sequences that accumulate in heterochromatic genome regions. SatDNAs are dynamic in their genomic location and abundance across species. Some satDNAs overlap essential genome regions such as centromeres and telomeres, but even pericentromeric satDNA can have effects on phenotypes, raising questions about their functional significance. However, it remains unclear whether these effects depend on satDNA sequence, copy number, higher-order structural organization, or genomic context. The highly repetitive nature of satDNA arrays has long hindered detailed genomic and genetic analyses. Recent advances in long-read sequencing now facilitate both the detailed characterization of satDNA structure and the development of more targeted approaches to genetic analysis. Here we present a sequential CRISPR/Cas9-based strategy to make mutations in satDNA arrays and demonstrate its utility using an autosomal pericentromeric satDNA in Drosophila melanogaster called Responder (Rsp). Rsp is the target of a sperm-killing male meiotic driver, Segregation Distorter ( SD ), where sensitivity to sperm killing positively correlates with Rsp copy number. Using our CRISPR/Cas9 approach, we generated an allelic series of Rsp deletion and expansion variants in two genetic backgrounds and examined their effects on spermatogenesis. Our approach produced precise satDNA variants efficiently, with minimal detectable off-target effects. The resulting mutations affect sensitivity to SD that scale with Rsp copy number. This work establishes a new framework for experimentally dissecting satDNA function and provides insights into the evolutionary and functional roles of satDNA in genome organization.

Meiotic drivers achieve biased transmission to the next generation, often at the expense of their host. Drive is widespread and can shape the evolution of proteins, chromosome structure, and karyotype. The sperm killer Segregation Distorter ( SD ) in Drosophila melanogaster is a well-studied driver but like most complex drivers its mechanism remains elusive. SD is a multigene complex, frequently associated with chromosomal inversions, where the main driver locus, a truncated duplication of the gene RanGAP kills wild-type sperm containing a satellite DNA called Responder ( Rsp ). Functional small RNAs are frequently implicated in the mechanisms of sperm killers, and we recently showed that Rsp is a source of these RNAs. Here we use transcriptomics in two SD haplotypes to link Rsp expression and/or RNAs to drive. We found that Rsp -derived small RNAs are underrepresented in driving testes of only one of the SD haplotypes. We show that over-expressing Rsp is sufficient to reduce drive strength in the haplotype with downregulated Rsp but not the other. We therefore shed light on the mechanism of SD by making a connection between the target and the drive phenotype. Additionally, our data imply that different haplotypes of complex drivers, like SD , can vary in their mechanism.

Meiotic drivers are selfish genetic elements that subvert Mendelian inheritance to increase their own transmission, yet they are typically found at low frequencies across natural populations. The factors that limit their spread remain unclear. To investigate this paradox, we studied the Segregation Distorter (SD) system, a selfish coadapted gene complex in Drosophila melanogaster. SD biases its transmission by killing sperm carrying a homologous chromosome bearing a target locus, Responder ( Rsp ), which appear as satellite repeats. Such selfish killing impairs male fertility and imposes selective pressure on the host genome to evolve resistance, either by deleting Rsp copies or acquiring unlinked suppressors. To characterize the spectrum of Rsp alleles and the frequency of segregating suppressors, we surveyed 90 strains from the Drosophila Genome Reference Panel. Rather than loss of Rsp , we found that over half of the strains (52/90) harbor suppressors located on the X chromosome or autosomes, but not the Y chromosome. The widespread presence of strong suppressors limited the resolution of our genome-wide association mapping; however, recombination analysis identified a strong X-linked suppressor to a ∼300 kb interval on the chromosome. Together, our findings suggest that pervasive, multilocus suppression constrains the spread of SD in natural populations.