Linked read technology for assembling large complex and polyploid genomes

Short read DNA sequencing technologies have revolutionized sequencing by providing high accuracy and throughput at low cost, but applications are limited due to the difficulties of assembling and identifying unique genomic locations of short reads. The linked read strategy overcomes these limitations because all short reads originating from a single long molecule of DNA share a common barcode. However, the majority of studies to date that have employed linked reads were focused on human haplotype phasing and genome assembly. Here we describe a de novo maize B73 genome assembly generated via linked read technology which contains ~172,000 scaffolds that cover 50% of the genome. Based on comparisons to the B73 reference genome, 91% of linked read contigs are accurately assembled, and errors were identified with >76% accuracy using a machine learning approach, suggesting that it may be possible to identify and potentially correct systematic errors. The linked read assembly contains substantially longer contigs than the assembly constructed without reference to the long molecule information (N50 of 14.5 kb and 238 bp, respectively) with similar proportions of the genome covered and similar accuracies. Complex polyploids represent one of the last grand challenges in genome assembly. Our results demonstrate that linked read technology can successfully resolve the two subgenomes of a recent alloployloid, i.e., proso millet (Panicum miliaceum). Our proso millet assembly covers ~83% of the 1 Gb genome and consists of 30,819 scaffolds with an N50 of 912 kb. Our analysis provides a framework for future de novo genome assemblies using linked reads, and we suggest computational strategies that if implemented have the potential to improve linked read assemblies, particularly for repetitive genomes.