De novo Assembly of Eukaryotic Genomes from Illumina TruSeq Synthetic Long-Reads

The recent emergence of long-read sequencing technology has improved the accuracy of de novo assembly in complex eukaryotic genomes. We have developed the methodology for de novo assembly of eukaryotic genomes from Illumina TruSeq Synthetic Long-Reads (TSLRs). Approximately 10-kb fragments in length are prepared and then sequenced on HiSeq 2500 platform. After assembling unique barcode reads, on average 6.8-kb long reads (7.5-kb of N50 size) are generated. We have recently assembled unknown genomes, a industrial fungus genome, Lichtheimia ramosa, and a flowering plant genome, Platycodon grandiflorum, using TSLRs as well as short insert and long-mate pair reads in a variety of sizes. The analyses revealed the de novo assemblies of 32.2 Mb in L. ramosa and 633.4 Mb in P. grandiflorum. More than 96% short insert reads were aligned to scaffolds of each of assembled genome, suggesting the high coverage of assembled scaffolds. Additionally, a high portion of complete gene models were analyzed through ab initio gene prediction, transcriptome alignment, and homology-based search. TSLR data with paired reads in a variety of sizes is likely to offer a powerful approach to improve de novoassembly of unknown genomes.