From Multi-Genome Assembly to Capturing Full Diversity Using Denovomagic 3.0

Whole genome shotgun sequencing using 180X coverage of Illumina reads and assembly using NRGene’s DeNovoMAGIC-2.0 software was successfully completed for the bread wheat strain Chinese Spring. Intensive in-depth analysis of the sequence data performed by the International Wheat Genome Sequencing Consortium (IWGSC) reconfirmed top sequence quality with accurate contigs and very long scaffolds (N50=7 Million bp, N90>1 Million bp). Additional 9 diploid, tetraploid and hexaploid wheat strains and related wild ancestors were also assembled with the same level of quality, together enabling the detection of broad genomic diversity, including SNPs, indels, SVs, gene PAVs, gene CNVs, haplotype resolution, and a pangenome view.

These fast and robust de novo assemblies have increased the efficiency of capturing diversity. Until now every new assembled genome required a separate analysis to detect assembly chimeras and order the scaffolds into pseudochromosomes, delaying the diversity elucidation process.

Here we describe DeNovoMAGIC-3.0, a cloud-based tool that assembles short and long reads produced using high-throughput Illumina X-series machines. The updated software version delivers multiple advantages, including reduced sequencing costs, a more robust assembly, a sharp increase in scaffold N50, and, most importantly, the elimination of assembly chimeras.

The N50 produced by DeNovoMAGIC-3.0 for homozygote bread wheat and maize genotypes was improved three-fold to 28.9 Mbp and 35.5 Mbp, respectively. Moreover, DeNovoMAGIC-3.0 is most efficient for whole genome assembly and sequence diversity discovery from 30-60X coverage only, making the analysis and comparison of hundreds of genomes both immediate and affordable.

Gil Ronen1, C.J. Pozniak², Nils Stein³ Jesse Poland⁴, Andrew Sharpe⁵, Assaf Distelfeld⁶, Jizeng Jia⁷, Tom Brutnell⁸, Kelly Dawe⁹, Alvaro Hernandez¹⁰, Guy Kol¹, Omer Barad¹, Kobi Baruch¹,

¹NRGene Technologies, Nes Tziyona, Israel

²Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

³IPK Gatersleben, Gatersleben, Germany

⁴Department of Agronomy, Kansas State University, Manhattan, Kansas, USA

⁵Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

⁵Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland

⁶Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel

⁷Institute of Crop Sciences, Chinese Academy of Agricultural sciences, Beijing, China

⁸Donald Danforth Plant Science Center, St. Louis, MO, USA

⁹Department of Plant Biology, University of Georgia, Athens, GA, USA

¹⁰Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, USA