Gross Chromosomal Rearrangements in <i>Kluyveromyces marxianus</i> Revealed by Illumina and Oxford Nanopore Sequencing
<i>Kluyveromyces marxianus</i> (<i>K. marxianus</i>) 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. T...
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MDPI AG
2020-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/19/7112 |
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| author | Lin Ding 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 John I. Glass |
| author_facet | Lin Ding 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 John I. Glass |
| author_sort | Lin Ding |
| collection | DOAJ |
| description | <i>Kluyveromyces marxianus</i> (<i>K. marxianus</i>) 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 <i>Saccharomyces cerevisiae URA3</i> gene (<i>ScURA3</i>) into an uracil auxotroph <i>K. marxianus</i> 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 <i>ScURA3</i> random integration. Moreover, it will shine a light on understanding DNA repair mechanisms in eukaryotes, which could potentially provide insights for cancer research. |
| first_indexed | 2024-03-10T16:02:16Z |
| format | Article |
| id | doaj.art-ef0f81f287e645d69f8477effdeb094f |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T16:02:16Z |
| publishDate | 2020-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-ef0f81f287e645d69f8477effdeb094f2023-11-20T15:13:52ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-09-012119711210.3390/ijms21197112Gross Chromosomal Rearrangements in <i>Kluyveromyces marxianus</i> Revealed by Illumina and Oxford Nanopore SequencingLin Ding0Harrison D. Macdonald1Hamilton O Smith2Clyde A. Hutchison III3Chuck Merryman4Todd P. Michael5Bradley W. Abramson6Krishna Kannan7Joe Liang8John Gill9Daniel G. Gibson10John I. Glass11J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USAJ. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USAJ. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USAJ. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USAJ. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USAJ. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USAJ. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USACodex DNA, 9535 Waples St #100, San Diego, CA 92121, USACodex DNA, 9535 Waples St #100, San Diego, CA 92121, USACodex DNA, 9535 Waples St #100, San Diego, CA 92121, USAJ. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USAJ. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA<i>Kluyveromyces marxianus</i> (<i>K. marxianus</i>) 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 <i>Saccharomyces cerevisiae URA3</i> gene (<i>ScURA3</i>) into an uracil auxotroph <i>K. marxianus</i> 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 <i>ScURA3</i> random integration. Moreover, it will shine a light on understanding DNA repair mechanisms in eukaryotes, which could potentially provide insights for cancer research.https://www.mdpi.com/1422-0067/21/19/7112gross chromosomal rearrangementsnon-homologous end joiningtranslocationIllumina MiSeqOxford NanoporeKluyveromyces marxianus |
| spellingShingle | Lin Ding 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 John I. Glass Gross Chromosomal Rearrangements in <i>Kluyveromyces marxianus</i> Revealed by Illumina and Oxford Nanopore Sequencing International Journal of Molecular Sciences gross chromosomal rearrangements non-homologous end joining translocation Illumina MiSeq Oxford Nanopore Kluyveromyces marxianus |
| title | Gross Chromosomal Rearrangements in <i>Kluyveromyces marxianus</i> Revealed by Illumina and Oxford Nanopore Sequencing |
| title_full | Gross Chromosomal Rearrangements in <i>Kluyveromyces marxianus</i> Revealed by Illumina and Oxford Nanopore Sequencing |
| title_fullStr | Gross Chromosomal Rearrangements in <i>Kluyveromyces marxianus</i> Revealed by Illumina and Oxford Nanopore Sequencing |
| title_full_unstemmed | Gross Chromosomal Rearrangements in <i>Kluyveromyces marxianus</i> Revealed by Illumina and Oxford Nanopore Sequencing |
| title_short | Gross Chromosomal Rearrangements in <i>Kluyveromyces marxianus</i> Revealed by Illumina and Oxford Nanopore Sequencing |
| title_sort | gross chromosomal rearrangements in i kluyveromyces marxianus i revealed by illumina and oxford nanopore sequencing |
| topic | gross chromosomal rearrangements non-homologous end joining translocation Illumina MiSeq Oxford Nanopore Kluyveromyces marxianus |
| url | https://www.mdpi.com/1422-0067/21/19/7112 |
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