Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans

Abstract

Long-read sequencing technologies have contributed greatly to comparative genomics among species and can also be applied to study genomics within a species. In this study, to determine how substantial genomic changes are generated and tolerated within a species, we sequenced a C. elegans strain, CB4856, which is one of the most genetically divergent strains compared to the N2 reference strain. For this comparison, we used the Pacific Biosciences (PacBio) RSII platform (80×, N50 read length 11.8 kb) and generated de novo genome assembly to the level of pseudochromosomes containing 76 contigs (N50 contig = 2.8 Mb). We identified structural variations that affected as many as 2694 genes, most of which are at chromosome arms. Subtelomeric regions contained the most extensive genomic rearrangements, which even created new subtelomeres in some cases. The subtelomere structure of Chromosome VR implies that ancestral telomere damage was repaired by alternative lengthening of telomeres even in the presence of a functional telomerase gene and that a new subtelomere was formed by break-induced replication. Our study demonstrates that substantial genomic changes including structural variations and new subtelomeres can be tolerated within a species, and that these changes may accumulate genetic diversity within a species.

Tightly linked antagonistic-effect loci underlie polygenic phenotypic variation inC. elegans

“…CB4856, isolated from a pineapple field in Maui in 1972, was for many years the C. elegans isolate most different from N2, and these two strains have been the subject of an enormous number of genetic studies. Both strains have exceptional highquality genome assemblies (Consortium 1998; Thompson et al 2015;Kim et al 2019;Yoshimura et al 2019). Population genetic studies have revealed that the similarity of most wild isolates to N2 results from very recent partial selective sweeps and migration events that have homogenized much of the species, while CB4856 retains alleles that were lost in the swept populations Andersen et al 2012).…”

Caenorhabditis elegansdauers vary recovery in response to bacteria from natural habitat

“…Since the three worm strains responded differently to the range of bacteria, we sought to characterize molecular polymorphisms in these conserved dauer-controlling pathways. N2 and CB4856 already had sequenced and assembled genomes ( Kim et al, 2019 ), so we sequenced JU1395’s genome to allow for comparisons between the three strains. The assembled sequence was 103,053,620 nucleotides in 161 contiguous pieces.…”

Repair and Reconstruction of Telomeric and Subtelomeric Regions and Genesis of New Telomeres: Implications for Chromosome Evolution

“…In particular, analysis of the newly identified genomes of yeasts and C. elegans by long‐read sequencing showed that subtelomeres experienced significant changes including extensive SVs and interchromosomal reshuffling following telomere damage, even in the presence of the telomerase gene. [ 23,24,127 ]…”

“…Signatures of DSB repair have also been observed in subtelomeres of the two most divergent strains of C. elegans , CB4856 and N2. [ 24 ] In these strains, the right end of chromosome V contains the subtelomeric region with the largest difference; the Hawaiian CB4856 strain has a new sequence of ≈200 kb after the telomere of the Bristol N2 strain ( Figure 2 ). The newly added sequence starts with about one tenth of the telomeric repeat sequences of C. elegans average telomere length; this observation suggests that ancient telomere damage occurred that telomerase could not repair.…”

“…The process of subtelomere evolution, and the repair mechanisms involved, can be inferred by assembling subtelomeric regions from sequencing data, and by creating accurate and contiguous subtelomeric sequences. [ 23,24 ] However, the repetitive sequences of subtelomeric regions severely impede correct sequencing and assembly. Indeed, only 10 of the 14 highly contiguous genomes (number of scaffolds <100; 14 out of 202 total genomes registered in the Ensemble database) have been assembled up to telomeric repeats including subtelomeric regions (ensemble does not include recent long‐read sequencing data).…”