I am using exome capture kit from Roche for exome capture in alfalfa. I wanted to know what is the significance of addition of two adapter (one command and the other unique) during sample library preparation. The final sequencing after hybridization with the exome capture probes will be Illumina paired end reads. is it because we are doing the paired end read, and through read overlaps we will confirm the reads, the two adapters were used.

I am new to this field and would appreciate your answers.