De Novo Assembly of Plant Genomes: Hybrid Approaches for Heterogeneous NGS Data

Pacific Biosciences (PacBio), Moleculo, and Oxford Nanopore, among other third generation single molecule sequencing technologies, are revolutionizing research in the area of genomics and transcriptomics with their capability to sequence long individual molecules of DNA and RNA. One major advantage is the ability to generate longer sequences: thousands or tens of thousands of base pairs instead of mere hundreds. With the rapid advancements in second and third generation sequencing technologies, hybrid genome assembly approaches using the strengths of both of these technologies is gaining impetus. While the hybrid approaches have been shown to work well largely in the microbial world, recently there has been greater push to extend them beyond microbes and into larger and complex eukaryotes like plants, animals, and humans.

We will present preliminary results toward generating de novo genome assemblies for our plant genomes of interest using a multi-platform sequencing strategy (Illumina HiSeq, PacBio RSII, and BioNano Whole Genome Maps). One of our key goals is to generate accurate high quality de novo reconstructions of genomes, which requires accurate long-range contiguity. We have used hybrid assembly workflow to integrate HiSeq and PacBio RSII and BioNano Whole Genome Map data. The pipeline exploits the base call accuracy and read pair linkage of Illumina data and the long read contiguity of PacBio data and the extremely long range sequence information from BioNano whole genome map data.