Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads.

ABSTRACT: Unmapped reads are often discarded from the analysis of whole-genome re-sequencing, but new biological information and insights can be uncovered through their analysis. In this paper, we investigate unmapped reads from the re-sequencing data of 33 pea aphid genomes from individuals specialized on different host plants. The unmapped reads for each individual were retrieved following mapping to the Acyrthosiphon pisum reference genome and its mitochondrial and symbiont genomes. These sets of unmapped reads were then cross-compared, revealing that a significant number of these unmapped sequences were conserved across individuals. Interestingly, sequences were most commonly shared between individuals adapted to the same host plant, suggesting that these sequences may contribute to the divergen

SUBMITTER: Gouin A 

PROVIDER: S-EPMC4815510 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature