ArticleGenetics2015
Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856.
Article in Genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed, 148 citations in OpenAlex.
- Genomic sequence and structural variations accumulating between laboratory lineages of wild typebioRxiv : 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
- Natural variation suggests candidate genes underlyingbioRxiv : the preprint server for biology · 2025Article
- The Caenorhabditis elegans spe-21 gene that encodes a palmitoyltransferase is necessary for spermiogenesis.Developmental biology · 2025Article
- Outcrossing Complicates Mutation Purging by Trapping Single Nucleotide Polymorphisms in Structural Variant Mutations.bioRxiv : the preprint server for biology · 2025Article
- Gain and Loss of Heterozygosity in the Genome of the Asexual Nematode Halicephalobus mephisto.Journal of molecular evolution · 2025Article
- Transposable elements and heterochromatic regions are enriched for structural variation and sequence divergence in the genome of wild-type Caenorhabditis elegans.G3 (Bethesda, Md.) · 2025Article
- Genetic mapping of lifespan and mitochondrial stress response inbioRxiv : the preprint server for biology · 2025Article
- Dynamic molecular architecture of the synaptonemal complex.Science advances · 2025Article
- Parental-effect gene-drive elements under partial selfing, or why do Caenorhabditis genomes have hyperdivergent regions?Genetics · 2025Article
- eQTL mapping in transgenic alpha-synuclein carrying Caenorhabditis elegans recombinant inbred lines.Human molecular genetics · 2024Article
- High-content phenotypic analysis of a C. elegans recombinant inbred population identifies genetic and molecular regulators of lifespan.Cell reports · 2024Article
- Parental-effect gene-drive elements under partial selfing, or why dobioRxiv : the preprint server for biology · 2024Article
- Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes.Genome biology · 2024Article
- High-content phenotypic analysis ofbioRxiv : the preprint server for biology · 2024Article
- Identifying transgene insertions inPeerJ · 2024Article
- Ancient diversity in host-parasite interaction genes in a model parasitic nematode.Nature communications · 2023Article
- Comprehensive detection of structural variation and transposable element differences between wild type laboratory lineages ofbioRxiv : the preprint server for biology · 2023Article
- Beyond the reference: gene expression variation and transcriptional response to RNA interference in Caenorhabditis elegans.G3 (Bethesda, Md.) · 2023Article
29 more citing papers are in PubMed but not listed here.
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Authors and funding
20 authors at 9 institutions in 6 countries.
Funding
Abstract
The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population, and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. When compared against the N2 reference, the CB4856 genome has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events that result in a total of 3.3 Mb of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 but not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, which have a greatly elevated SNV density, ranging from 2 to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors, suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.
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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.