Single-molecule sequencing and conformational capture enable<i>de novo</i>mammalian reference genomes

Abstract

Abstract The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat ( Capra hircus ), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most contiguous de novo mammalian assembly to date, with chromosome-length scaffolds and only 663 gaps. Our assembly represents a &gt;250-fold improvement in contiguity compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, supporting the most complete repeat family and immune gene complex representation ever produced for a ruminant species.

Keywords

Affiliated Institutions

• South China Agricultural University CN
• BioNano Genomics (United States) US
• University of Minnesota US
• Agricultural Research Service US
• The Pirbright Institute GB
• Recombinetics (United States) US
• University of Washington US
• Cornell University US
• Howard Hughes Medical Institute US
• Virginia State University US
• Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria IT
• National Human Genome Research Institute US

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