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

Dudchenko, Olga; Batra, Sanjit Singh; Omer, Arina D.; Nyquist, Sarah K.; Hoeger, Marie; Durand, Neva C.; Shamim, Muhammad S.; Machol, Ido; Lander, Eric S.; Aiden, Aviva Presser; Aiden, E

doi:10.1126/science.aal3327

Cited by 1,953 publications

(1,774 citation statements)

References 38 publications

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“…Hi-C is a relatively new approach that is gaining rapid acceptance because of the resulting useful arrangements of contigs in chromosome-scale scaffolds (Korbel and Lee, 2013;Bickhart et al, 2017;Dudchenko et al, 2017;Mascher et al, 2017). Hi-C was originally developed to detect intra-and interchromosomal interactions such as those between enhancers and promoter regions, but it has proven to be useful for long-range scaffolding of sequence contigs as well.…”

Section: Enhancement By Combination With Other Methods Including Hi-cmentioning

confidence: 99%

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

Udall

Dawe

2017

Plant Cell

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ORCID ID: 0000-0003-0978-4764 (J.A.U.)Long-read single-molecule sequencing, Hi-C sequencing, and improved bioinformatic tools are ushering in an era where complete genome assembly will become common for species with few or no classical genetic resources. There are no guidelines for how to proceed in such cases. Ideally, such genomes would be sequenced by two different methods so that one assembly serves as confirmation of the other; however, cost constraints make this approach unlikely. Overreliance on synteny as a means of confirming and ordering contigs will lead to compounded errors. Optical mapping is an accessible and relatively mature technology that can be used for genome assembly validation. We discuss how optical mapping can be used as a validation tool for genome assemblies and how to interpret the results. In addition, we discuss methods for using optical map data to enhance genome assemblies derived from both traditional sequence contigs and Hi-C pseudomolecules.

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Section: Enhancement By Combination With Other Methods Including Hi-cmentioning

confidence: 99%

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

Udall

Dawe

2017

Plant Cell

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“…Recently, we developed Juicebox, a system for the visual exploration of Hi-C data (Durand, Robinson et al 2016), and 3D-DNA, an automated pipeline for using Hi-C data to assemble genomes (Dudchenko et al 2017). Here, we introduce "Assembly Tools," a new module for Juicebox, which provides a point-and-click interface for using Hi-C heatmaps to identify and correct errors in a genome assembly.…”

mentioning

confidence: 99%

The Juicebox Assembly Tools module facilitatesde novoassembly of mammalian genomes with chromosome-length scaffolds for under $1000

Dudchenko

Shamim

Batra

et al. 2018

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Hi-C contact maps are valuable for genome assembly (Lieberman-Aiden, van Berkum et al. 2009; Burton et al. 2013; Dudchenko et al. 2017). Recently, we developed Juicebox, a system for the visual exploration of Hi-C data (Durand, Robinson et al. 2016), and 3D-DNA, an automated pipeline for using Hi-C data to assemble genomes (Dudchenko et al. 2017). Here, we introduce “Assembly Tools,” a new module for Juicebox, which provides a point-and-click interface for using Hi-C heatmaps to identify and correct errors in a genome assembly. Together, 3D-DNA and the Juicebox Assembly Tools greatly reduce the cost of accurately assembling complex eukaryotic genomes. To illustrate, we generated de novo assemblies with chromosome-length scaffolds for three mammals: the wombat, Vombatus ursinus (3.3Gb), the Virginia opossum, Didelphis virginiana (3.3Gb), and the raccoon, Procyon lotor (2.5Gb). The only inputs for each assembly were Illumina reads from a short insert DNA-Seq library (300 million Illumina reads, maximum length 2x150 bases) and an in situ Hi-C library (100 million Illumina reads, maximum read length 2x150 bases), which cost <$1000.

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“…Early anecdotal experience shows that this results in scaffolds well over 10 Mbp. Some large gaps will remain unspanned, and therefore we will use the long-range Hi-C paired-end data to link the 10X scaffolds into large super-scaffolds and separate these into chromosomal units (127,128) with the aid of syntenic mapping to a phylogenetically close relative.…”

Section: The Bat1k Proposalmentioning

confidence: 99%

Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species

Teeling

Vernes

Dávalos

et al. 2018

Annu. Rev. Anim. Biosci.

194

191

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Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene. Despite their great numbers and diversity, many species are threatened and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n ∼ 1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any interested individuals committed to a better understanding of the genetic and evolutionary mechanisms that underlie the unique adaptations of bats. Our aim is to catalog the unique genetic diversity present in all living bats to better understand the molecular basis of their unique adaptations; uncover their evolutionary history; link genotype with phenotype; and ultimately better understand, promote, and conserve bats. Here we review the unique adaptations of bats and highlight how chromosome-level genome assemblies can uncover the molecular basis of these traits. We present a novel sequencing and assembly strategy and review the striking societal and scientific benefits that will result from the Bat1K initiative.

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

Cited by 1,953 publications

References 38 publications

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

The Juicebox Assembly Tools module facilitatesde novoassembly of mammalian genomes with chromosome-length scaffolds for under $1000

Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species

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