Long-read sequence assembly of the gorilla genome

Gordon, D. Benjamin; Huddleston, John; Chaisson, Mark; Hill, Curtis; Kronenberg, Zev; Munson, Katherine M.; Malig, Maika; Raja, Archana; Fiddes, Ian T.; Hillier, La Deana W.; Dunn, Christopher; Baker, Carl; Armstrong, Joel; Diekhans, Mark; Paten, Benedict; Shendure, Jay; Wilson, Richard K.; Haussler, David; Chin, Chen-Shan; Eichler, Evan E.

doi:10.1126/science.aae0344

Cited by 364 publications

(328 citation statements)

References 62 publications

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“…Recent studies have highlighted the improvements of SMRT-only assemblies compared to Illumina-only assemblies [Bickhart et al, 2017], [Gordon et al, 2016], [Jiao et al, 2017], [Zhang et al, 2016], [Shi et al, 2016]. Here we found that both the pooled Illumina assembly (with mixed read length) and the PacBio SMRT-only assembly resulted in substantially improved assembly statistics compared to the two published hamster genome assemblies (Table 1), with an order of magnitude fewer scaffolds and 2–4x larger N50 values.…”

Section: Resultsmentioning

confidence: 99%

“…The acquisition of such contiguous sequences is possible now with third generation sequencing technologies, such as Single Molecule Real Time (SMRT) sequencing technology [Eid et al, 2009], which provide mean read lengths that are more than an order of magnitude larger than earlier sequencing technologies. The reads can span repetitive elements, resulting in longer contigs and minimal gaps within scaffolds [Bickhart et al, 2017], [Jiao et al, 2017], [Gordon et al, 2016]. This enables the routine assembly of mammalian genomes approaching the current quality of the human genome.…”

Section: Introductionmentioning

confidence: 99%

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A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp

MacDonald

et al. 2018

Biotech & Bioengineering

102

119

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Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read based assemblies. Here, we completely resequenced C. griseus using Single Molecule Real Time (SMRT) sequencing and merged this with Illumina-based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28-fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up- and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important CHO cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp

MacDonald

et al. 2018

Biotech & Bioengineering

102

119

View full text Add to dashboard Cite

show abstract

“…Although it is more expensive than short-read sequencing approaches, singlemolecule real-time (SMRT) sequencing improved the contiguity and repeat representation of mammalian (Pendleton et al 2015;Gordon et al 2016;Bickhart et al 2017) and diploid grass genomes (Zimin et al 2017). SMRT technologies are also being used to generate the complete sequence of transcripts, increasing the accuracy of splicing isoform definition (Abdel-Ghany et al 2016).…”

mentioning

confidence: 99%

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

Clavijo¹,

Venturini²,

Schudoma³

et al. 2017

Genome Res.

363

311

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Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.

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“…This de novo assembly process is difficult for large and complex genomes (Istrail et al 2004;Chaisson et al 2015a;Gordon et al 2016;Steinberg et al 2016). A core challenge is the correct representation of highly similar sequences, which range in scale from single base repeats (homopolymers) to large complex events including segmental duplications (Bailey et al 2002).…”

mentioning

confidence: 99%

Direct determination of diploid genome sequences

et al. 2017

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Determining the genome sequence of an organism is challenging, yet fundamental to understanding its biology. Over the past decade, thousands of human genomes have been sequenced, contributing deeply to biomedical research. In the vast majority of cases, these have been analyzed by aligning sequence reads to a single reference genome, biasing the resulting analyses, and in general, failing to capture sequences novel to a given genome. Some de novo assemblies have been constructed free of reference bias, but nearly all were constructed by merging homologous loci into single "consensus" sequences, generally absent from nature. These assemblies do not correctly represent the diploid biology of an individual. In exactly two cases, true diploid de novo assemblies have been made, at great expense. One was generated using Sanger sequencing, and one using thousands of clone pools. Here, we demonstrate a straightforward and low-cost method for creating true diploid de novo assemblies. We make a single library from ∼1 ng of high molecular weight DNA, using the 10x Genomics microfluidic platform to partition the genome. We applied this technique to seven human samples, generating low-cost HiSeq X data, then assembled these using a new "pushbutton" algorithm, Supernova. Each computation took 2 d on a single server. Each yielded contigs longer than 100 kb, phase blocks longer than 2.5 Mb, and scaffolds longer than 15 Mb. Our method provides a scalable capability for determining the actual diploid genome sequence in a sample, opening the door to new approaches in genomic biology and medicine.

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Long-read sequence assembly of the gorilla genome

Cited by 364 publications

References 62 publications

A reference genome of the Chinese hamster based on a hybrid assembly strategy

A reference genome of the Chinese hamster based on a hybrid assembly strategy

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

Direct determination of diploid genome sequences

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