June 1, 2021

Best practices for diploid assembly of complex genomes using PacBio: A case study of Cascade Hops

Author(s): Kingan, S., and Peluso, P., and Rank, D., and Henning, J., and Hendrix, D.

A high quality reference genome is an essential resource for plant and animal breeding and functional and evolutionary studies. The common hop (Humulus lupulus, Cannabaceae) is an economically important crop plant used to flavor and preserve beer. Its genome is large (flow cytometrybased estimates of diploid length >5.4Gb1), highly repetitive, and individual plants display high levels of heterozygosity, which make assembly of an accurate and contiguous reference genome challenging with conventional short-read methods. We present a contig assembly of Cascade Hops using PacBio long reads and the diploid genome assembler, FALCON-Unzip2. The assembly has dramatically improved contiguity and completeness over earlier short-read assemblies. The genome is primarily assembled as haplotypes due to the outbred nature of the organism. We explore patterns of haplotype divergence across the assembly and present strategies to deduplicate haplotypes prior to scaffolding

Organization: PacBio
Year: 2018

View Conference Poster

Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.