Gross chromosomal rearrangements in kluyveromyces marxianus revealed by illumina and oxford nanopore sequencing

Lin Ding, Harrison D. Macdonald, Hamilton O. Smith, Clyde A. Hutchison, Chuck Merryman, Todd P. Michael, Bradley W. Abramson, Krishna Kannan, Joe Liang, John Gill, Daniel G. Gibson, John I. Glass

Research output: Contribution to journalArticlepeer-review

Abstract

Kluyveromyces marxianus (K. marxianus) is an increasingly popular industrially relevant yeast. It is known to possess a highly efficient non-homologous end joining (NHEJ) pathway that promotes random integration of non-homologous DNA fragments into its genome. The nature of the integration events was traditionally analyzed by Southern blot hybridization. However, the precise DNA sequence at the insertion sites were not fully explored. We transformed a PCR product of the Saccharomyces cerevisiae URA3 gene (ScURA3) into an uracil auxotroph K. marxianus otherwise wildtype strain and picked 24 stable Ura+ transformants for sequencing analysis. We took advantage of rapid advances in DNA sequencing technologies and developed a method using a combination of Illumina MiSeq and Oxford Nanopore sequencing. This approach enables us to uncover the gross chromosomal rearrangements (GCRs) that are associated with the ScURA3 random integration. Moreover, it will shine a light on understanding DNA repair mechanisms in eukaryotes, which could potentially provide insights for cancer research.

Original languageEnglish (US)
Article number7112
Pages (from-to)1-10
Number of pages10
JournalInternational journal of molecular sciences
Volume21
Issue number19
DOIs
StatePublished - Oct 1 2020
Externally publishedYes

Keywords

  • Gross chromosomal rearrangements
  • Illumina MiSeq
  • Kluyveromyces marxianus
  • Non-homologous end joining
  • Oxford Nanopore
  • Saccharomyces cerevisiae
  • Translocation
  • URA3 gene

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry

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