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

  1. Junho Lee1,2,3
  1. 1Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea 08826;
  2. 2Department of Biological Sciences, Seoul National University, Seoul, Korea 08826;
  3. 3Research Institute of Basic Sciences, Seoul National University, Seoul, Korea 08826;
  4. 4Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA;
  5. 5Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
  1. 6 These authors contributed equally to this work.

  • Corresponding author: elegans{at}snu.ac.kr
  • 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.

    Footnotes

    • [Supplemental material is available for this article.]

    • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.246082.118.

    • Freely available online through the Genome Research Open Access option.

    • Received December 19, 2018.
    • Accepted April 22, 2019.

    This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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