The Comparison of Aegilops tauschii Sequence Assembled By NRGene's DeNovoMAGIC and Pacbio-Illumina Hybrid Assembly with the MaSuRCA Mega-Reads Algorithm

There are various genome sequencing technologies and assembly methods. The DeNovoMAGIC by the NRGene and Pacbio-Illumina Hybrid assembly with the MaSuRCA mega-reads algorithm are newly emerged assembly pipelines. With the availability of the both assemblies for the same Aegilops tauschii accession, it is possible now to assess how the two assembly methods behave for large and complex genome. The alignment of assembled sequences with BioNano genome map reveals overall good contiguity for both assemblies. When comparing sequences at base pair level, there are notable discrepancy between the two assemblies, including “SNPs”, indels and structural variations (SVs) which were not detected with BioNano genome map due to its limited resolution. The BAC-based Illumina’s MiSeq sequence assembly is also available for the accession; the regions harboring “SNPs”, indels and SVs were then aligned to BAC-based sequence assembly. The results indicate that the “SNPs”, indels and SVs were largely caused by mis-assembly with the NRGene’s DeNovoMAGIC. This work is a part of the NSF-funded Project IOS-1238231 to generate a reference sequence for the genome of Ae. tauschii (http://aegilops.wheat.ucdavis.edu/ATGSP/).