ArticleGenome biology and evolution2022
Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics.
Article in Genome biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 41 citations in OpenAlex.
- T2T genomes ofGenome research · 2026Article
- A gap-free, telomere-to-telomere genome assembly for the Caenorhabditis briggsae reference strain AF16.G3 (Bethesda, Md.) · 2026Article
- Population structure and punctuated genomic hyper-diversity in Caenorhabditis briggsae.Molecular biology and evolution · 2026Article
- Programmed DNA elimination was present in the last common ancestor ofbioRxiv : the preprint server for biology · 2026Article
- Genome evolution in parthenogenetic nematodes shaped by chromosome rearrangements and introgression.Genome research · 2026Article
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- Origins of Self-Fertility in ThreeBiology · 2026Review
- Evaluating beta-tubulin variants as predictors of benzimidazole resistance across Caenorhabditis nematodes.PLoS pathogens · 2026Article
- A gap-free, telomere-to-telomere genome assembly for thebioRxiv : the preprint server for biology · 2026Article
- Global genomic diversity of the selfing nematodebioRxiv : the preprint server for biology · 2026Article
- Natural variation suggests candidate genes underlying Caenorhabditis elegans susceptibility to diverse toxicants.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
- Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility.Genome research · 2026Article
- Allelic Variation at tRNA Genes in Three Nematode Species Indicates Mutation Load Despite Strong Purifying Selection.Genome biology and evolution · 2026Article
- High-Throughput Toxicity Screening withEnvironmental science & technology · 2026Review
- Article
- Natural variation suggests candidate genes underlyingbioRxiv : the preprint server for biology · 2025Article
- Divergence in neuronal signaling pathways despite conserved neuronal identity among Caenorhabditis species.Current biology : CB · 2025Article
- Heat tolerance and genetic adaptations in Caenorhabditis briggsae: insights from comparative studies with Caenorhabditis elegans.Genetics · 2025Article
- TeloSearchLR: an algorithm to detect novel telomere repeat motifs using long sequencing reads.G3 (Bethesda, Md.) · 2025Article
- Dynamic Birth and Death of Argonaute Gene Family Functional Repertoire Across Caenorhabditis Nematodes.Genome biology and evolution · 2025Article
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Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
Abstract
The publication of the Caenorhabditis briggsae reference genome in 2003 enabled the first comparative genomics studies between C. elegans and C. briggsae, shedding light on the evolution of genome content and structure in the Caenorhabditis genus. However, despite being widely used, the currently available C. briggsae reference genome is substantially less complete and structurally accurate than the C. elegans reference genome. Here, we used high-coverage Oxford Nanopore long-read and chromosome-conformation capture data to generate chromosome-level reference genomes for two C. briggsae strains: QX1410, a new reference strain closely related to the laboratory AF16 strain, and VX34, a highly divergent strain isolated in China. We also sequenced 99 recombinant inbred lines generated from reciprocal crosses between QX1410 and VX34 to create a recombination map and identify chromosomal domains. Additionally, we used both short- and long-read RNA sequencing data to generate high-quality gene annotations. By comparing these new reference genomes to the current reference, we reveal that hyper-divergent haplotypes cover large portions of the C. briggsae genome, similar to recent reports in C. elegans and C. tropicalis. We also show that the genomes of selfing Caenorhabditis species have undergone more rearrangement than their outcrossing relatives, which has biased previous estimates of rearrangement rate in Caenorhabditis. These new genomes provide a substantially improved platform for comparative genomics in Caenorhabditis and narrow the gap between the quality of genomic resources available for C. elegans and C. briggsae.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.