Whole genome re-sequencing : lessons from unmapped reads

Unmapped reads are often discarded from the analysis of whole genome re-sequencing, while, opposingly, new biological information can be discovered from their analysis. In this pa- per, we investigated these reads from the re-sequencing data of thirty-three aphid genomes. The unmapped reads for each individual were retrieved from the results of the mapping of the sets of reads against the Acyrthosyphon Pisum reference genome, its mitochondrion genome and several known or putative symbiont genomes. These sets of unmapped reads were then cross-compared, this pointed out that a significant number of these sequences were conserved among individuals, especially when the latter are adapted to a same specific host plant, revealing that they may share crucial and functional material. Moreover, the analysis of the contigs resulting from the assem- blies of the unmapped reads gathered by biotype allowed us to discover putative novel sequences absent from the reference genomes and highlighted the possible presence of other symbionts in the pea aphid genome whose existence were not known previously. As a conclusion, this study emphasizes that using a default strategy (e.g for the mapping) may lead to the loss of important information, and must be accompanied by specific analyses depending on the biological model.