True Mate Pair NGS libraries and Applications

Mate-pair Libraries are critically important tools for scaffolding and closing genomes.  Current technologies cannot resolve repeats or segmentally duplicated sequences, which results in large missing segments of eukaryotic genomes and failure to close small prokaryotic genomes. These limitations make it very difficult and expensive to assemble large or small genomes de novo.  Lucigen will present a fresh approach to solving some of the challenges associated with constructing large insert mate pair libraries. The efficient construction of large insert libraries >5 kb was not practical until the development of the pNGS fosmid system for 40 kb mate pair libraries by Lucigen. We will introduce a novel clone free technology for constructing 2-50 kb mate pair libraries. Our strategy involves the use of multiple methods to prevent chimera formation, including the incorporation of Chimera Codes™ that allow one to distinguish true mate pairs from false junctions for de novo sequence assembly. Sequence data from 8kb and 20kb E. coli mate-pair libraries confirmed our expected results of 90% assembled reads (114,869 of 126,930) showing consistent alignment across the entire genome.   We have used this technology to close the 22 contig draft Thermus aquaticus genome as well as assemble BAC clones efficiently using Illumina and Ion Torrent platforms. We will also highlight DNASTAR Genomics Suite software, which is uniquely suited for use with data generated by sequencing of Lucigen mate-pair libraries to build scaffolds and close genomes.