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

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 (RILs) 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 (RNA-seq) 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.

Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities

“…To test whether the msft-1/tlpr-1 TA is indeed mobile in nature, we assembled the genomes of three additional C. briggsae wild isolates using Nanopore long-05 reads (Figure S6). Analysis of these three and two additional genomes [31] revealed that the insertion site of msft-1/tlpr-1 varied between natural isolates. msft-1/tlpr-1 was located on Chr.…”

Genetic architecture and temporal analysis of Caenorhabditis briggsae hybrid developmental delay

“…elegans and C . briggsae , where crossing-over rarely occurs [ 19 , 20 , 54 ]. Thus, absence of a perfect genotype-phenotype correlation could be interpreted in at least two not mutually exclusive ways.…”

“…This interval also contains the PCR genotyping assay at 4.0 Mbp that was previously used to map delay, at which 1 of 41 delayed individuals did not contain a homozygous AF16 genotype [12]. Genetic mapping is notoriously difficult in the central recombination domains in C. elegans and C. briggsae, where crossing-over rarely occurs [19,20,54]. Thus, absence of a perfect genotype-phenotype correlation could be interpreted in at least two not mutually exclusive ways.…”

“…The AF16 and HK104 wild isolates are routinely used in C . briggsae genetic studies, the genome assembly of this species was originally based on the AF16 sequence [ 19 ], and more recent work using the isolates QX1410 and VX34 have improved the quality of the genome assembly [ 20 ]. C .…”

“…Natural populations ("wild isolates") of C. briggsae collected from around the world form at least three genetically distinct phylogeographic clades (temperate, tropical circles of latitude, and equatorial) that correlate with isolate latitude [16][17][18]. The AF16 and HK104 wild isolates are routinely used in C. briggsae genetic studies, the genome assembly of this species was originally based on the AF16 sequence [19], and more recent work using the isolates QX1410 and VX34 have improved the quality of the genome assembly [20]. C. briggsae, like C. elegans, is a primarily selfing species, having an androdioecious mating system (separate male and hermaphrodite individuals, where males are rare in nature).…”