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Background  Whole and partial chromosome losses or gains and structural chromosome changes are hallmarks of human tumors. Guanine-rich DNA, which has a potential to form a G-quadruplex (G 4 ) structure, is particularly vulnerable to changes. In  Caenorhabditis elegans , faithful transmission of G-rich DNA is ensured by the DOG-1/FANCJ deadbox helicase.    Results  To identify a spectrum of mutations, after long-term propagation, we combined whole genome sequencing (WGS) and oligonucleotide array Comparative Genomic Hybridization (oaCGH) analysis of a  C. elegans  strain that was propagated, in the absence of DOG-1 and MDF-1/MAD1, for a total of 470 generations, with samples taken for long term storage (by freezing) in generations 170 and 270. We compared the genomes of F 170  and F 470  strains and identified 94 substitutions, 17 InDels, 3 duplications, and 139 deletions larger than 20 bp. These homozygous variants were predicted to impact 101 protein-coding genes. Phenotypic analysis of this strain revealed remarkable fitness recovery indicating that mutations, which have accumulated in the strain, are not only tolerated but also cooperate to achieve long-term population survival in the absence of DOG-1 and MDF-1. Furthermore, deletions larger than 20 bp were the only variants that frequently occurred in G-rich DNA. We showed that 126 of the possible 954 predicted monoG/C tracts, larger than 14 bp, were deleted in  unc-46 mdf-1 such-4; dog-1  F 470  (JNC170).    Conclusions  Here, we identified variants that accumulated in  C. elegans’  genome after long-term propagation in the absence of DOG-1 and MDF-1. We showed that DNA sequences, with G 4 -forming potential, are vulnerable to deletion-formation in this genetic background.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1402-y) contains supplementary material, which is available to authorized users.

Spectrum of variations in dog-1/FANCJ and mdf-1/MAD1 defective Caenorhabditis elegans strains after long-term propagation