Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics

Lewis Stevens, Nicolas D. Moya, Robyn E. Tanny, Sophia B. Gibson, Alan Tracey, Huimin Na, Rojin Chitrakar, Job Dekker, Albertha J.M. Walhout, L. Ryan Baugh, Erik C. Andersen

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
JournalGenome biology and evolution
Volume14
Issue number4
DOIs
StatePublished - Apr 10 2022

Keywords

  • Caenorhabditis briggsae
  • comparative genomics
  • genetic diversity
  • genome rearrangement
  • reference genomes
  • selfing

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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