De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective way. Here we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
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American Association for the Advancement of Science (AAAS)
2018
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| Online Access: | http://hdl.handle.net/1721.1/116720 |
| _version_ | 1811081814123479040 |
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| author | Dudchenko, Olga Batra, Sanjit S. Omer, Arina D. Hoeger, Marie Durand, Neva C. Shamim, Muhammad S. Machol, Ido Aiden, Aviva Presser Aiden, Erez Lieberman Nyquist, Sarah Kate Lander, Eric Steven |
| author2 | Massachusetts Institute of Technology. Computational and Systems Biology Program |
| author_facet | Massachusetts Institute of Technology. Computational and Systems Biology Program Dudchenko, Olga Batra, Sanjit S. Omer, Arina D. Hoeger, Marie Durand, Neva C. Shamim, Muhammad S. Machol, Ido Aiden, Aviva Presser Aiden, Erez Lieberman Nyquist, Sarah Kate Lander, Eric Steven |
| author_sort | Dudchenko, Olga |
| collection | MIT |
| description | The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective way. Here we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67× coverage). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Ae. aegypti and Culex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that almost all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, and accurate, and can be applied to many species. |
| first_indexed | 2024-09-23T11:52:53Z |
| format | Article |
| id | mit-1721.1/116720 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T11:52:53Z |
| publishDate | 2018 |
| publisher | American Association for the Advancement of Science (AAAS) |
| record_format | dspace |
| spelling | mit-1721.1/1167202022-10-01T06:42:06Z De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds Dudchenko, Olga Batra, Sanjit S. Omer, Arina D. Hoeger, Marie Durand, Neva C. Shamim, Muhammad S. Machol, Ido Aiden, Aviva Presser Aiden, Erez Lieberman Nyquist, Sarah Kate Lander, Eric Steven Massachusetts Institute of Technology. Computational and Systems Biology Program Massachusetts Institute of Technology. Department of Biology Nyquist, Sarah Kate Lander, Eric Steven The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective way. Here we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67× coverage). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Ae. aegypti and Culex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that almost all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, and accurate, and can be applied to many species. 2018-07-02T17:37:55Z 2018-07-02T17:37:55Z 2017-03 2018-06-28T13:44:07Z Article http://purl.org/eprint/type/JournalArticle 0036-8075 1095-9203 http://hdl.handle.net/1721.1/116720 Dudchenko, Olga, Sanjit S. Batra, Arina D. Omer, Sarah K. Nyquist, Marie Hoeger, Neva C. Durand, Muhammad S. Shamim, et al. “De Novo Assembly of the Aedes Aegypti Genome Using Hi-C Yields Chromosome-Length Scaffolds.” Science 356, no. 6333 (March 23, 2017): 92–95. http://dx.doi.org/10.1126/SCIENCE.AAL3327 Science Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf American Association for the Advancement of Science (AAAS) PMC |
| spellingShingle | Dudchenko, Olga Batra, Sanjit S. Omer, Arina D. Hoeger, Marie Durand, Neva C. Shamim, Muhammad S. Machol, Ido Aiden, Aviva Presser Aiden, Erez Lieberman Nyquist, Sarah Kate Lander, Eric Steven De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds |
| title | De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds |
| title_full | De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds |
| title_fullStr | De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds |
| title_full_unstemmed | De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds |
| title_short | De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds |
| title_sort | de novo assembly of the aedes aegypti genome using hi c yields chromosome length scaffolds |
| url | http://hdl.handle.net/1721.1/116720 |
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