Parental-effect gene-drive elements under partial selfing, or why do Caenorhabditis genomes have hyperdivergent regions? DOI Creative Commons
Matthew V. Rockman

Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 30, 2024

Abstract Self-fertile Caenorhabditis nematodes carry a surprising number of Medea elements, alleles that act in heterozygous mothers and cause death or developmental delay offspring do not inherit them. At some loci, both cross operate as independent Medeas, affecting all the homozygous progeny selfing heterozygote. The genomic coincidence elements ancient, deeply coalescing haplotypes, which pepper otherwise homogeneous genomes these animals, raises questions about how apparent gene-drive persist for long periods time. Here, I investigate mating system affects evolution their paternal-effect counterparts, peels. Despite an intuition antagonistic should induce balancing selection by killing homozygotes, models show that, under partial selfing, experience positive frequency dependence: common allele drives rare one extinct, even if is more penetrant. Analytical results threshold required to invade population very weakly penetrant allele, whose effects would escape laboratory detection, could nevertheless prevent much from invading high rates selfing. Ubiquitous weak Medeas peels then localized barriers gene flow between populations, generating islands deep coalescence. Analysis expression data, however, suggests this cannot be whole story. A complementary explanation ordinary ecological generates ancient haplotypes on can evolve, while homozygosity selfers minimizes role drive evolution.

Language: Английский

Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation DOI Creative Commons
Kohta Yoshida, Christian Rödelsperger, Waltraud Röseler

et al.

Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 30, 2023

Abstract Large-scale genome-structural evolution is common in various organisms. Recent developments speciation genomics revealed the importance of inversions, whereas role other rearrangements, including chromosome fusions, have not been well characterized. We study genomic divergence and reproductive isolation closely related nematodes: androdioecious (hermaphroditic) model Pristionchus pacificus its dioecious sister species exspectatus . A chromosome-level genome assembly P. using single-molecule Hi-C sequencing a chromosome-wide rearrangement relative to Strikingly, characterization cytogenetic studies outgroup occultus indicated two independent fusions involving same chromosome, ChrIR, between these species. Genetic linkage analysis that altered pattern recombination, resulting large low-recombination regions probably facilitated coevolution some ~14.8% genes across entire genomes. Quantitative trait locus analyses for hybrid sterility all three sexes major quantitative loci mapped fused ChrIR. While abnormal segregations partially explain female sterility, hybrid-specific recombination breaks region was associated with male sterility. Thus, recent repatterned rate drove during speciation.

Language: Английский

Citations

44
Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities DOI
Sonya A. Widen, Israel Campo Bes, Alevtina Koreshova

et al.

Science, Journal Year: 2023, Volume and Issue: 380(6652)

Published: June 29, 2023

Horizontal gene transfer, the movement of genetic material between species, has been reported across all major eukaryotic lineages. However, underlying mechanisms transfer and their impact on genome evolution are still poorly understood. While studying evolutionary origin a selfish element in nematode Caenorhabditis briggsae, we discovered that Mavericks, ancient virus-like transposons related to giant viruses virophages, one long-sought vectors horizontal transfer. We found Mavericks gained novel herpesvirus-like fusogen nematodes, leading widespread exchange cargo genes extremely divergent bypassing sexual barriers spanning hundreds millions years. Our results show how union causes ultimately incompatibilities natural populations.

Language: Английский

Citations

43
CaeNDR, the Caenorhabditis Natural Diversity Resource DOI Creative Commons
Timothy A. Crombie, Ryan McKeown, Nicolas D. Moya

et al.

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D850 - D858

Published: Oct. 19, 2023

Abstract Studies of model organisms have provided important insights into how natural genetic differences shape trait variation. These discoveries are driven by the growing availability genomes and expansive experimental toolkits afforded to researchers using these species. For example, Caenorhabditis elegans is increasingly being used identify measure effects variants on traits quantitative genetics. Since 2016, C. Natural Diversity Resource (CeNDR) has facilitated many studies providing an archive wild strains, genome-wide sequence variant data for each strain, a association (GWA) mapping portal community. Here, we present updated platform, (CaeNDR), that enables genetics genomics across three species: elegans, briggsae tropicalis. The CaeNDR platform hosts several databases continually addition new whole-genome annotated variants. Additionally, provides interactive tools explore variation enable GWA mappings. All accessible through freely available web located at caendr.org.

Language: Английский

Citations

32
Ancient diversity in host-parasite interaction genes in a model parasitic nematode DOI Creative Commons
Lewis Stevens, Isaac Martínez-Ugalde, Erna King

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 27, 2023

Host-parasite interactions exert strong selection pressures on the genomes of both host and parasite. These can lead to negative frequency-dependent selection, a form balancing that is hypothesised explain high levels polymorphism seen in many immune parasite antigen loci. Here, we sequence several individuals Heligmosomoides bakeri, model house mice, polygyrus, closely related wood mice. Although H. bakeri commonly referred as polygyrus literature, their show divergence are consistent with at least million years independent evolution. The species contain hyper-divergent haplotypes enriched for proteins interact response. Many these originated prior between suggesting they have been maintained by long-term selection. Together, our results suggest exerted response played key role shaping patterns genetic diversity parasitic nematodes.

Language: Английский

Citations

25
Novel and improved Caenorhabditis briggsae gene models generated by community curation DOI Creative Commons
Nicolas D. Moya, Lewis Stevens, Isabella R. Miller

et al.

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Aug. 25, 2023

Abstract Background The nematode Caenorhabditis briggsae has been used as a model in comparative genomics studies with elegans because of their striking morphological and behavioral similarities. However, the potential C. for is limited by quality its genome resources. resources laboratory strain AF16 have not developed to same extent . recent publication new chromosome-level reference QX1410, wild closely related AF16, provided first step bridge gap between Currently, QX1410 gene models consist software-derived predictions that contain numerous errors structure coding sequences. In this study, team researchers manually inspected over 21,000 underlying transcriptomic data repair errors. Results We designed detailed workflow train nine students curate using RNA read alignments. models, proposed corrections sequences 8,000 genes, modeled thousands putative isoforms untranslated regions. exploited conservation protein sequence length quantify improvement protein-coding showed manual curation led substantial improvements accuracy genes. Additionally, collinear alignment analysis genomes revealed 1,800 genes affected spurious duplications inversions are now resolved genome. Conclusions Community-based, transcriptome an effective approach improve protocols work can be useful future large-scale projects other species. Our efforts brought comparable level extensively curated models. improved provide reliable tools study biology nematodes.

Language: Английский

Citations

12
Inferring inter-chromosomal rearrangements and ancestral linkage groups from synteny DOI Creative Commons
Alexander Mackintosh, Pablo Manuel González De la Rosa, Simon H. Martin

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 17, 2023

Abstract Chromosome rearrangements shape the structure of genome and influence evolutionary processes. Inferring ancestral chromosomes across a phylogenetic tree is therefore an important analysis within genetics. One approach to this inference problem focus on synteny information, i.e. co-occurrence loci same chromosome. Although algorithms for inferring linkage groups (ALGs) inter-chromosomal from have been previously described, they seldom applied modern data. Here we implement these in command-line tool, syngraph , evaluate their performance using simulations that include mix different types error. We show ALGs can be recovered when rearrangement frequency per-branch well below number chromosomes. demonstrate competing models inferred by comparing observed results simulations. Finally, reanalyse assemblies rhabditid nematodes find independent fusions pose challenge difficult overcome without gene-order information. Our real data both promise limitations information infer patterns evolution.

Language: Английский

Citations

11
Transposon-mediated genic rearrangements underlie variation in small RNA pathways DOI Creative Commons
Gaotian Zhang,

Marie-Anne Félix,

Erik C. Andersen

et al.

Science Advances, Journal Year: 2024, Volume and Issue: 10(38)

Published: Sept. 20, 2024

Transposable elements (TEs) can alter host gene structure and expression, whereas organisms develop mechanisms to repress TE activities. In the nematode Caenorhabditis elegans , a small interfering RNA pathway dependent on helicase ERI-6/7 primarily silences retrotransposons recent genes of likely viral origin. By studying expression variation among wild C. strains, we found that structural variants transposon remnants underlie in eri-6/7 targets. We further multiple insertions DNA transposons, Polintons, reshuffled locus induced inversion eri-6 some strains. inverted configuration, function was previously shown be repaired by unusual trans-splicing mediated direct repeats. identified these repeats originated from terminal Polintons . Our findings highlight role host-transposon interactions driving rapid genome diversification natural populations shed light evolutionary novelty splicing mechanisms.

Language: Английский

Citations

2
Molecular patterns of evolutionary changes throughout the whole nervous system of multiple nematode species DOI Creative Commons
Itai Antoine Toker, Lidia Ripoll-Sánchez, Luke T. Geiger

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 25, 2024

One avenue to better understand brain evolution is map molecular patterns of evolutionary changes in neuronal cell types across entire nervous systems distantly related species. Generating whole-animal single-cell transcriptomes three nematode species from the

Language: Английский

Citations

2
Ancient diversity in host-parasite interaction genes in a model parasitic nematode DOI Creative Commons
Lewis Stevens, Isaac Martínez-Ugalde, Erna King

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: April 17, 2023

Abstract Host-parasite interactions exert strong selection pressures on the genomes of both host and parasite. These can lead to increased fitness rare alleles, resulting in negative frequency-dependent selection, a form balancing that is hypothesised explain high levels polymorphism seen many immune parasite antigen loci. Despite their economic ecological importance, there limited evidence for parasitism-relevant genes parasitic nematodes. Here, we sequenced several individuals Heligmosomoides bakeri , house mice well-established model nematode, polygyrus closely related wood mice. We combined our single nematode genome assemblies with chromatin conformation capture (Hi-C) libraries derived from pools generate chromosome-level reference species. Although H. commonly referred as literature, show divergence are consistent millions years independent evolution. found genome, which expected be highly homozygous through inbreeding, contained hundreds hyper-divergent haplotypes, similar those recently reported free-living Within these an enrichment protein families interact response, including protease inhibitors transthyretin-related proteins. also haplotypes originated prior between suggesting they have been maintained since last common ancestor two species by long-term selection. Together, results suggest exerted parasites hosts led unexpected modes genetic diversity economically ecologically important

Language: Английский

Citations

6
DNA Polymerase Diversity Reveals Multiple Incursions of Polintons During Nematode Evolution DOI Creative Commons
Dae‐Eun Jeong, Sameer Sundrani, Richard Nelson Hall

et al.

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(12)

Published: Dec. 1, 2023

Polintons are double-stranded DNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses consistent with the hypothesis that invade host genomes through infectious viral particles. Nematode contain multiple copies and provide an opportunity to explore natural distribution evolution during this process. We performed extensive search across nematode genomes, identifying full-length Polinton several species. evidence both ancient integrations recent mobility strains same In addition major family, we identified a group overall closely related family but encode distinct protein-primed DNA polymerase B (pPolB) is homologs from different present outside Nematoda. Phylogenetic analyses on pPolBs support evolutionary scenarios which these extrinsic seem derive families oomycetes molluscs replaced canonical pPolB subsets terrestrial marine nematodes, respectively, suggesting interphylum horizontal gene transfers. The oomycete share unique feature, insertion HNH nuclease domain, whereas VSR domain mollusc pPolBs. hypothesize transfer occurs among cohabiting hosts.

Language: Английский

Citations

6