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

By O. Dudchenko, S. Batra, Arina D. Omer, Sarah K Nyquist, Marie Hoeger, Neva C. Durand, Muhammad Saad Shamim, Ido Machol, Eric S. Lander, A. P. Aiden and 1 more. Science, 2016

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Hi-C for mosquito genomes Most genomes sequenced today are determined through the generation of short sequenced bits of DNA that are computationally pieced together like a jigsaw puzzle. This has resulted in the need for funds and additional data to fill in gaps in order to fully assemble the many chromosomes that make up a eukaryotic genome. Dudchenko et al. used the Hi-C method, which measures the distance between contact points within and between chromosomes for scaffold validation, together with correction and ordering to more completely determine the arrangement of short sequencing reads for genome mapping. They validated their approach through the de novo generation of a complete human genome. A comparative analysis of mosquito genomes was made possible by improving the Culex quinquefasciatus genome assembly and generating the genome of Aedes aegypti, the vector of Zika virus. Science, this issue p. 92 The DNA proximity ligation method Hi-C was used to create a genome assembly for the mosquito Aedes aegypti. 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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/9887337bc350ff71b2aa0c1c5a137ae0333244e4

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Citations in the corpus

Piercing the dark matter: bioinformatics of long-range sequencing and mapping (2018, methodology): “Indeed, several ‘reference’ genomes established using older technologies, such as the genomes of maize 15 , fruit fly 16 , mosquito 12 and many others, have been reassembled with the new technologies to fix errors and improve their resolution.”
Integrating Hi-C links with assembly graphs for chromosome-scale assembly (2018, methodology): “3D-DNA uses signatures of chromosome ends (Dudchenko et al., 2017) to identify break positions which are not present in Chicago data.”
YaHS: yet another Hi-C scaffolding tool (2022, neutral): “Several scaffolding tools have been developed for the construction of chromosome-scale assembly with Hi-C data including LACHESIS (Burton et al. , 2013), HiRise (Putnam et al. , 2016), 3D-DNA (Dudchenko et al. , 2017), ALLHiC (Zhang et al. , 2019), SALSA2 (Ghurye et al. , 2019) and pin_hic (Guan et ”
The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000 (2018, methodology): “left to right and top to bottom: (1) hs-1k genome assembly presented in this study; (2) 3D-DNA assembly algorithm (Dudchenko et al. 2017) applied to $1000 data, without Juicebox Assembly Tools review; (3) hg5 genome assembly produced in 2001 by the International Human Genome Consortium (Lander et al”