Sequencing Plant Genomes by Combining Illumina and PacBio Technologies

Although with tremendous success, current second generation short read sequencing technologies are still highly limited in producing high quality draft reference plant genomes. To assemble short genome sequences into large-sized scaffolds, many mate-pair libraries of different sized are usually created to jump over the repeats. This process is cubersome and costly. With the advance of single molecule third generation sequencing, a recent trend is to combine second and third generation technologies (eg, Illumina and PacBio) in de novo genome assembly, which fully utilizes their respective advantages in base accuracy and long read length, to save both workload and cost. We have tested this strategy in rice and some other plant species.

On the other hand, there are many large repeat regions, eg, >30kb, even in medium-sized plant genomes. They are still hard to resolve with the above combined method. We investigated the usage of BAC libaries (BAC sequencing vs. BAC physical map) in filling the  gap.