Improving Genomes for Agricultural Species

High quality reference genome sequences are the foundation of genetic analyses.  Even “high quality” draft genome sequences have thousands of gaps remaining that adversely impact the annotation and assessment of genes and other functional elements.  The current sequencing technologies are relatively inexpensive, making sequencing for de novo genome assemblies within the budgets of more researchers, resulting in hundreds of genome assemblies in need of sequence improvement.  With the long reads provided by Pacific Bioscience’s PacBios RS technology and our PBJelly software we upgraded several draft genomes, including new de novo genomes assembled with Illumina short read data, Roche 454 and Sanger sequences.  Our latest PBJelly 2 software leverages the current SMRT analysis pipeline and adds scaffolding to fill inter-scaffold gaps as well as the intra-scaffold gaps addressed by PBJelly 1.  Other improvements increased the accuracy of the gap-filling sequence.   We have improved the contiguity of the genome assemblies for primates (P. anubis, M. murinus, C. atys, P. coquereli, M. mulata), rat, sheep and other non-mammalian species.  Using data with an N50 read length of 8.4 kb, at 19x coverage, the sheep genome Contig N50 improved 12 fold.  Earlier data with an N50 of only 1.9 kb at 10x improved the contiguity of the rat genome two fold.    Improvements for the other mammalian genomes fell between these extremes.  Transcripts align better to the PBJelly treated genomes than to the starting assemblies, suggesting gene based analyses will benefit from the more contiguous genome sequences.