Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

By Nicholas H. Putnam, Brendan L. O’Connell, Jonathan Stites, Brandon J. Rice, M. Blanchette, Robert Calef, Christopher J. Troll, Andrew Fields, Paul D. Hartley, Charles W. Sugnet and 3 more. Genome Research, 2015

724 citations recorded by the source corpus.

Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can address this problem, dramatically increasing the scaffold contiguity of assemblies. Here, we describe a simpler approach (“Chicago”) based on in vitro reconstituted chromatin. We generated two Chicago data sets with human DNA and developed a statistical model and a new software pipeline (“HiRise”) that can identify poor quality joins and produce accurate, long-range sequence scaffolds. We used these to construct a highly accurate de novo assembly and scaffolding of a human genome with scaffold N50 of 20 Mbp. We also demonstrated the utility of Chicago for improving existing assemblies by reassembling and scaffolding the genome of the American alligator. With a single library and one lane of Illumina HiSeq sequencing, we increased the scaffold N50 of the American alligator from 508 kbp to 10 Mbp.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/656f75f4b421b522d6731c6ed19b06d7afd0bec1

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Citations in the corpus

YaHS: yet another Hi-C scaffolding tool (2022, neutral): “…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 al. , 2021).”
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds (2016, methodology): “Indeed, Hi-C has been used to improve draft genome assemblies (7, 9) and to create chromosome-length scaffolds for large genomes (10).”
A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas (2020, neutral): “7 [51], the assembled genome sequence initially comprised a total of ∼633 Mb, with a scaffold and contig N50 of 57.”
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies (2017, methodology): “Although generating Hi-C data requires intact cells, Putnam et al. (2016) recently described a proximity ligation method using in vitro reconstituted chromatin from high-molecular-weight DNA.”
Pathways to de‐extinction: how close can we get to resurrection of an extinct species? (2017, background): “…either sequence long DNA molecules [e.g. Pacific Biosciences long-read sequencing technology (English et al. 2012)] or that require long molecules to prepare DNA sequencing libraries for short-read sequencing platforms (e.g. ‘Chicago’ libraries; Putnam et al. 2016) are not available to ancient DNA.”
Direct determination of diploid genome sequences (2016, neutral): “…are inconsistent (includes bona fide sample/reference differences). r Run time (days) for assemblies using a single server having 28 cores and 384 GB available memory (booted with “ mem =384G ” ), exclusive of subsampling to 1200 M reads, sorting by barcode and trimming of barcodes (total 2 – 5 h).”
Integrating Hi-C links with assembly graphs for chromosome-scale assembly (2018, methodology): “The other library was from [43], are in 344 vitro chromatin sequencing library (Chicago) generated by Dovetail Genomics (L1).”