title: In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.
abstract: We describe a method that exploits contiguity preserving transposase sequencing (CPT-seq) to facilitate the scaffolding of de novo genome assemblies. CPT-seq is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to > 1 megabase. These pools are "subhaploid," in that the lengths of fragments contained in each pool sums to ∼5% to 10% of the full genome. The scaffolding approach described here, termed fragScaff, leverages coincidences between the content of different pools as a source of contiguity information. Specifically, CPT-seq data is mapped to a de novo genome assembly, followed by the identification of pairs of contigs or scaffolds whose ends disproportionately co-occur in the same indexed pools, consistent with true adjacency in the genome. Such candidate "joins" are used to construct a graph, which is then resolved by a minimum spanning tree. As a proof-of-concept, we apply CPT-seq and fragScaff to substantially boost the contiguity of de novo assemblies of the human, mouse, and fly genomes, increasing the scaffold N50 of de novo assemblies by eight- to 57-fold with high accuracy. We also demonstrate that fragScaff is complementary to Hi-C-based contact probability maps, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps. Finally, we demonstrate CPT-seq as a means of anchoring unplaced novel human contigs to the reference genome as well as for detecting misassembled sequences.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA;
authors.forename: Andrew
authors.initials: A
authors.lastname: Adey
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA;
authors.forename: Jacob O
authors.initials: JO
authors.lastname: Kitzman
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA;
authors.forename: Joshua N
authors.initials: JN
authors.lastname: Burton
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA;
authors.forename: Riza
authors.initials: R
authors.lastname: Daza
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA;
authors.forename: Akash
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA.
authors.forename: Lena
authors.initials: L
authors.lastname: Christiansen
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA.
authors.forename: Mostafa
authors.initials: M
authors.lastname: Ronaghi
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA.
authors.forename: Sasan
authors.initials: S
authors.lastname: Amini
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA.
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Gunderson
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA.
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Steemers
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA; shendure@uw.edu.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D015723:Gene Library; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D051379:Mice; D012984:Software; D019895:Transposases / Q000378:metabolism*
chemical_list: D019895:Transposases