Re-examination of two diatom reference genomes using long-read sequencing
Abstract Background The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group. Their reference genomes, published in 2004 and 2008, respectively, were the product of traditio...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-05-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-07666-3 |
| _version_ | 1819047312990666752 |
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| author | Gina V. Filloramo Bruce A. Curtis Emma Blanche John M. Archibald |
| author_facet | Gina V. Filloramo Bruce A. Curtis Emma Blanche John M. Archibald |
| author_sort | Gina V. Filloramo |
| collection | DOAJ |
| description | Abstract Background The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group. Their reference genomes, published in 2004 and 2008, respectively, were the product of traditional Sanger sequencing. In the case of T. pseudonana, optical restriction site mapping was employed to further clarify and contextualize chromosome-level scaffolds. While both genomes are considered highly accurate and reasonably contiguous, they still contain many unresolved regions and unordered/unlinked scaffolds. Results We have used Oxford Nanopore Technologies long-read sequencing to update and validate the quality and contiguity of the T. pseudonana and P. tricornutum genomes. Fine-scale assessment of our long-read derived genome assemblies allowed us to resolve previously uncertain genomic regions, further characterize complex structural variation, and re-evaluate the repetitive DNA content of both genomes. We also identified 1862 previously undescribed genes in T. pseudonana. In P. tricornutum, we used transposable element detection software to identify 33 novel copia-type LTR-RT insertions, indicating ongoing activity and rapid expansion of this superfamily as the organism continues to be maintained in culture. Finally, Bionano optical mapping of P. tricornutum chromosomes was combined with long-read sequence data to explore the potential of long-read sequencing and optical mapping for resolving haplotypes. Conclusion Despite its potential to yield highly contiguous scaffolds, long-read sequencing is not a panacea. Even for relatively small nuclear genomes such as those investigated herein, repetitive DNA sequences cause problems for current genome assembly algorithms. Determining whether a long-read derived genomic assembly is ‘better’ than one produced using traditional sequence data is not straightforward. Our revised reference genomes for P. tricornutum and T. pseudonana nevertheless provide additional insight into the structure and evolution of both genomes, thereby providing a more robust foundation for future diatom research. |
| first_indexed | 2024-12-21T10:58:22Z |
| format | Article |
| id | doaj.art-959c405dad7842b4a33fa11772ec1c3a |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T10:58:22Z |
| publishDate | 2021-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-959c405dad7842b4a33fa11772ec1c3a2022-12-21T19:06:25ZengBMCBMC Genomics1471-21642021-05-0122112510.1186/s12864-021-07666-3Re-examination of two diatom reference genomes using long-read sequencingGina V. Filloramo0Bruce A. Curtis1Emma Blanche2John M. Archibald3Department of Biochemistry and Molecular Biology, Dalhousie UniversityDepartment of Biochemistry and Molecular Biology, Dalhousie UniversityDepartment of Biochemistry and Molecular Biology, Dalhousie UniversityDepartment of Biochemistry and Molecular Biology, Dalhousie UniversityAbstract Background The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group. Their reference genomes, published in 2004 and 2008, respectively, were the product of traditional Sanger sequencing. In the case of T. pseudonana, optical restriction site mapping was employed to further clarify and contextualize chromosome-level scaffolds. While both genomes are considered highly accurate and reasonably contiguous, they still contain many unresolved regions and unordered/unlinked scaffolds. Results We have used Oxford Nanopore Technologies long-read sequencing to update and validate the quality and contiguity of the T. pseudonana and P. tricornutum genomes. Fine-scale assessment of our long-read derived genome assemblies allowed us to resolve previously uncertain genomic regions, further characterize complex structural variation, and re-evaluate the repetitive DNA content of both genomes. We also identified 1862 previously undescribed genes in T. pseudonana. In P. tricornutum, we used transposable element detection software to identify 33 novel copia-type LTR-RT insertions, indicating ongoing activity and rapid expansion of this superfamily as the organism continues to be maintained in culture. Finally, Bionano optical mapping of P. tricornutum chromosomes was combined with long-read sequence data to explore the potential of long-read sequencing and optical mapping for resolving haplotypes. Conclusion Despite its potential to yield highly contiguous scaffolds, long-read sequencing is not a panacea. Even for relatively small nuclear genomes such as those investigated herein, repetitive DNA sequences cause problems for current genome assembly algorithms. Determining whether a long-read derived genomic assembly is ‘better’ than one produced using traditional sequence data is not straightforward. Our revised reference genomes for P. tricornutum and T. pseudonana nevertheless provide additional insight into the structure and evolution of both genomes, thereby providing a more robust foundation for future diatom research.https://doi.org/10.1186/s12864-021-07666-3Diatom genomicsOxford Nanopore long-read sequencingBionano optical mappingLong-terminal repeat retrotransposonsPhaeodactylum tricornutumThalassiosira pseudonana |
| spellingShingle | Gina V. Filloramo Bruce A. Curtis Emma Blanche John M. Archibald Re-examination of two diatom reference genomes using long-read sequencing BMC Genomics Diatom genomics Oxford Nanopore long-read sequencing Bionano optical mapping Long-terminal repeat retrotransposons Phaeodactylum tricornutum Thalassiosira pseudonana |
| title | Re-examination of two diatom reference genomes using long-read sequencing |
| title_full | Re-examination of two diatom reference genomes using long-read sequencing |
| title_fullStr | Re-examination of two diatom reference genomes using long-read sequencing |
| title_full_unstemmed | Re-examination of two diatom reference genomes using long-read sequencing |
| title_short | Re-examination of two diatom reference genomes using long-read sequencing |
| title_sort | re examination of two diatom reference genomes using long read sequencing |
| topic | Diatom genomics Oxford Nanopore long-read sequencing Bionano optical mapping Long-terminal repeat retrotransposons Phaeodactylum tricornutum Thalassiosira pseudonana |
| url | https://doi.org/10.1186/s12864-021-07666-3 |
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