A complete genome comparison of two nematode species found that C. nigoni is 29.9% larger than C. briggsae, with satellite DNA making up more than 30% of the sequence differences between them. The gap is uneven across the chromosomes: C. briggsae autosomes were 15.2% to 20.9% smaller, while its X chromosome was 37.4% smaller than the corresponding C. nigoni chromosome.
A fuller map of the genomes
The finding comes from complete telomere-to-telomere, or T2T, assemblies that measured 107.1 megabases for C. briggsae and 139.0 megabases for C. nigoni. The new C. nigoni reference resolved all gaps and unassigned scaffolds.
The primary genomic data came from C. nigoni JU1422 and C. briggsae AF16. The strains were sequenced to at least 40-fold coverage, producing more than 5 gigabases on an Oxford Nanopore MinION device, and the genomes were assembled de novo with Flye. Reads from the additional C. nigoni strain EG5268 were used to confirm some findings.
Repetitive DNA sets the species apart
The size gap was not matched by a comparable gap in the fractions annotated as genic regions or transposable elements. Genic regions covered 67.4 megabases, or 62.9% of the C. briggsae genome, and 86.8 megabases, or 62.4% of the C. nigoni genome. Transposable elements accounted for 8.2% and 7.3%, respectively.
Satellite DNA showed a much larger contrast. C. briggsae had 9.6 megabases less satellite DNA than C. nigoni, while C. nigoni had 2.8 times as many satellite-DNA arrays. On the X chromosome alone, C. nigoni had 4.6 megabases more satellite DNA, accounting for 48.0% of the X-chromosome size difference.
The X chromosome check
The X-chromosome pattern was also visible in a separate measure of DNA staining intensity. The X chromosome accounted for 19.7% of nuclear intensity in C. briggsae and 26.0% in C. nigoni, close to the assembly fractions of 21.0% and 25.8%. The agreement is consistent with the assembly result, but the imaging served as validation rather than an independent sequence assembly.
Rearrangements across the chromosomes
Comparing the order of matching regions across the genomes identified 122 inversions and two translocations larger than 10 kilobases. The analysis estimated approximately 17.4 inversions per million years for the C. briggsae-C. nigoni comparison, 2.5 times the C. briggsae-C. elegans rate of 6.9. The X chromosome had five inversions, and inversions favored chromosome arms.
The inversion-placement analysis used 10,000 bootstrap simulations, a way of repeatedly resampling the data to test how stable a pattern is. The reported rates and placement patterns therefore depend on the inferred matches between the genomes and on the bootstrap procedure.
A second rDNA array
The assembly also revealed two 45S rDNA arrays in C. nigoni. One, on the X chromosome, contained 39 copies and measured 267 kilobases. A second array on chromosome I was estimated at 89 copies and approximately 653 kilobases. The chromosome-I array was partly reconstructed, so its size and copy number remain estimates.
The study does not directly show that the second array is active: its functionality was inferred rather than tested with a direct assay. More broadly, the genome-size comparison cannot by itself establish which lineage gained or lost sequence, or what evolutionary process produced the difference. The satellite-DNA tally also excluded 45S rDNA and some smaller repeats, and no confidence intervals were reported.
What the comparison cannot settle
Those cautions matter because the genomic comparison centered on one reference strain from each species, JU1422 and AF16, with EG5268 providing an additional check. Results from two reference genomes cannot establish that the same chromosome-size pattern occurs across all strains. The homology analysis could also miss local sequence expansion or divergence.
Data access
Raw sequencing reads and genome assembly data were deposited in NCBI BioProject under PRJNA1418286 and PRJNA1427284.
Paper data and sources
Original title: T2T genomes ofandreveal divergence in satellite DNA abundance.
Authors: Ryan Pellow, Manitejus Kotikalapudi, Ofer Rog
Journal/Repository: Genome research
Status: Peer-reviewed
First online: 2026-10-01
DOI: 10.1101/gr.281988.126
Original paper