Figure 2

Diagram depicting the two methods of detecting piggyBac insertion sites in Plasmodium berghei genome with Illumina sequencing data. (A) The ‘BLAST method’ is based on BLAST searching with the 13-bp end sequences of piggyBac ITRs in the Illumina reads. All the Illumina sequencing reads were regarded as single-end reads. Each of single reads can be located in P. berghei chromosomes, or in the piggyBac transposable fragments, or at the junctions between the piggyBac inserts and the flanking genomic sequences. Only the reads overlapping the junctions can be used to identify the exact sites of piggyBac insertions. The example read comes from piggyBac insertion at 52719 of chromosome 1. The workflow of ‘BLAST method’ is shown at the right panel. (B) The ‘SOAP method’ is based on aligning the Illumina sequencing reads respectively to the piggyBac transposable fragments and P. berghei reference sequences using the SOAP software. The Illumina reads were sequenced with the paired-end module. Both of the paired-end reads can be located in the P. berghei chromosomes or in the piggyBac transposable fragments, or alternatively, one of the paired-end reads can lie in the piggyBac transposable fragments while the other of the paired-end reads can lie in the flanking genomic sequences. The latter can be used to identify the sites of piggyBac insertions. The workflow of ‘SOAP method’ is shown at the right panel.