2.4 | Optimizing the method by searching conservedin silico mate pairs
We used a map method to search for conserved in silico mate pairs (Fig. 3). First, mate-pair reads generated using the first reference were mapped to another reference with BWA-MEM (Li, 2013) and default settings, as described above. Then, an in-house python script (Sam2fq.py) was used to select the mate-pair reads mapped within 20 percent deviation of insert sizes and in the same direction (not reversed). To distinguish conserved mate pairs generated from the original in silico method, these were named as ‘species1-species2**’ using two reference genomes,‘species1-species2-species3**’ using three reference genomes, and ‘species1-species2-species3-species4**’ using four reference genomes.