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De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.


ABSTRACT: 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 Aeaegypti 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.

SUBMITTER: Dudchenko O 

PROVIDER: S-EPMC5635820 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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De novo assembly of the <i>Aedes aegypti</i> genome using Hi-C yields chromosome-length scaffolds.

Dudchenko Olga O   Batra Sanjit S SS   Omer Arina D AD   Nyquist Sarah K SK   Hoeger Marie M   Durand Neva C NC   Shamim Muhammad S MS   Machol Ido I   Lander Eric S ES   Aiden Aviva Presser AP   Aiden Erez Lieberman EL  

Science (New York, N.Y.) 20170323 6333


The Zika outbreak, spread by the <i>Aedes aegypti</i> 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 <i>Ae</i><i>aegypti</i  ...[more]

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