Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations
Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat content. Here we report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis. Our approach also provides an accurate method with...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2020
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/110094 |
| _version_ | 1855528465151819776 |
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| author | Zhou, C. Olukolu, B. Gemenet, D. Wu, S. Grüneberg, W.J. Cao, M.D. Fei, Z. Zeng, Z.B. George, A.W. Khan, A. Yencho, George Craig Coin, L.J.M. |
| author_browse | Cao, M.D. Coin, L.J.M. Fei, Z. Gemenet, D. George, A.W. Grüneberg, W.J. Khan, A. Olukolu, B. Wu, S. Yencho, George Craig Zeng, Z.B. Zhou, C. |
| author_facet | Zhou, C. Olukolu, B. Gemenet, D. Wu, S. Grüneberg, W.J. Cao, M.D. Fei, Z. Zeng, Z.B. George, A.W. Khan, A. Yencho, George Craig Coin, L.J.M. |
| author_sort | Zhou, C. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat content. Here we report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis. Our approach also provides an accurate method with which to detect and fix assembly errors. Using simulated data, we demonstrate that our approach is of high accuracy and outperforms three existing state-of-the-art genetic mapping tools. Particularly, our approach is more robust to the presence of missing genotype data and genotyping errors. We used our method to construct pseudomolecules for allotetraploid lawn grass utilizing PacBio long reads in combination with restriction site-associated DNA sequencing, and for diploid Ipomoea trifida and autotetraploid potato utilizing contigs assembled from Illumina reads in combination with genotype data generated by single-nucleotide polymorphism arrays and genotyping by sequencing, respectively. We resolved 13 assembly errors for a published I. trifida genome assembly and anchored eight unplaced scaffolds in the published potato genome. |
| format | Journal Article |
| id | CGSpace110094 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1100942025-11-29T05:22:17Z Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations Zhou, C. Olukolu, B. Gemenet, D. Wu, S. Grüneberg, W.J. Cao, M.D. Fei, Z. Zeng, Z.B. George, A.W. Khan, A. Yencho, George Craig Coin, L.J.M. genetic linkage genomes software polyploidy plant genetics Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat content. Here we report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis. Our approach also provides an accurate method with which to detect and fix assembly errors. Using simulated data, we demonstrate that our approach is of high accuracy and outperforms three existing state-of-the-art genetic mapping tools. Particularly, our approach is more robust to the presence of missing genotype data and genotyping errors. We used our method to construct pseudomolecules for allotetraploid lawn grass utilizing PacBio long reads in combination with restriction site-associated DNA sequencing, and for diploid Ipomoea trifida and autotetraploid potato utilizing contigs assembled from Illumina reads in combination with genotype data generated by single-nucleotide polymorphism arrays and genotyping by sequencing, respectively. We resolved 13 assembly errors for a published I. trifida genome assembly and anchored eight unplaced scaffolds in the published potato genome. 2020-10-30 2020-11-09T20:29:02Z 2020-11-09T20:29:02Z Journal Article https://hdl.handle.net/10568/110094 en Limited Access Springer Zhou, C., Olukolu, B., Gemenet, D., Wu, S., Gruneberg, W.J., Cao, M.D., Fei, Z., Zeng, Z.B., George, A.W., Khan, A., Yencho, G.C. and Coin, L.J.M. (2020). Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations. Nature Genetics. ISSN 1546-1718. v52: 1256–1264 |
| spellingShingle | genetic linkage genomes software polyploidy plant genetics Zhou, C. Olukolu, B. Gemenet, D. Wu, S. Grüneberg, W.J. Cao, M.D. Fei, Z. Zeng, Z.B. George, A.W. Khan, A. Yencho, George Craig Coin, L.J.M. Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations |
| title | Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations |
| title_full | Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations |
| title_fullStr | Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations |
| title_full_unstemmed | Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations |
| title_short | Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations |
| title_sort | assembly of whole chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations |
| topic | genetic linkage genomes software polyploidy plant genetics |
| url | https://hdl.handle.net/10568/110094 |
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