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Article

Gross Chromosomal Rearrangements in Kluyveromyces marxianus Revealed by Illumina and Oxford Nanopore Sequencing

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J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
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Codex DNA, 9535 Waples St #100, San Diego, CA 92121, USA
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Int. J. Mol. Sci. 2020, 21(19), 7112; https://doi.org/10.3390/ijms21197112
Received: 30 August 2020 / Revised: 16 September 2020 / Accepted: 22 September 2020 / Published: 26 September 2020
(This article belongs to the Section Molecular Biology)
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. View Full-Text
Keywords: gross chromosomal rearrangements; non-homologous end joining; translocation; Illumina MiSeq; Oxford Nanopore; Kluyveromyces marxianus; Saccharomyces cerevisiae; URA3 gene gross chromosomal rearrangements; non-homologous end joining; translocation; Illumina MiSeq; Oxford Nanopore; Kluyveromyces marxianus; Saccharomyces cerevisiae; URA3 gene
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MDPI and ACS Style

Ding, L.; Macdonald, H.D.; Smith, H.O.; Hutchison III, C.A.; Merryman, C.; Michael, T.P.; Abramson, B.W.; Kannan, K.; Liang, J.; Gill, J.; Gibson, D.G.; Glass, J.I. Gross Chromosomal Rearrangements in Kluyveromyces marxianus Revealed by Illumina and Oxford Nanopore Sequencing. Int. J. Mol. Sci. 2020, 21, 7112. https://doi.org/10.3390/ijms21197112

AMA Style

Ding L, Macdonald HD, Smith HO, Hutchison III CA, Merryman C, Michael TP, Abramson BW, Kannan K, Liang J, Gill J, Gibson DG, Glass JI. Gross Chromosomal Rearrangements in Kluyveromyces marxianus Revealed by Illumina and Oxford Nanopore Sequencing. International Journal of Molecular Sciences. 2020; 21(19):7112. https://doi.org/10.3390/ijms21197112

Chicago/Turabian Style

Ding, Lin, Harrison D. Macdonald, Hamilton O Smith, Clyde A. Hutchison III, Chuck Merryman, Todd P. Michael, Bradley W. Abramson, Krishna Kannan, Joe Liang, John Gill, Daniel G. Gibson, and John I. Glass. 2020. "Gross Chromosomal Rearrangements in Kluyveromyces marxianus Revealed by Illumina and Oxford Nanopore Sequencing" International Journal of Molecular Sciences 21, no. 19: 7112. https://doi.org/10.3390/ijms21197112

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