title: 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 divergence between host plant specialized biotypes. Analysis of the contigs obtained from assembling the unmapped reads pooled by biotype allowed us to recover some divergent genomic regions previously excluded from analysis and to discover putative novel sequences of A. pisum and its symbionts. In conclusion, this study emphasizes the interest of the unmapped component of re-sequencing data sets and the potential loss of important information. We here propose strategies to aid the capture and interpretation of this information.
authors.affiliation: 1] INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France [2] INRIA/IRISA/GenScale, Campus de Beaulieu, Rennes, France.
authors.forename: A
authors.initials: A
authors.lastname: Gouin
authors.affiliation: 1] INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France [2] INRIA/IRISA/GenScale, Campus de Beaulieu, Rennes, France.
authors.forename: F
authors.initials: F
authors.lastname: Legeai
authors.affiliation: INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France.
authors.forename: P
authors.initials: P
authors.lastname: Nouhaud
authors.affiliation: Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK.
authors.forename: A
authors.initials: A
authors.lastname: Whibley
authors.affiliation: INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France.
authors.forename: J-C
authors.initials: JC
authors.lastname: Simon
authors.affiliation: INRIA/IRISA/GenScale, Campus de Beaulieu, Rennes, France.
authors.forename: C
authors.initials: C
authors.lastname: Lemaitre
mesh_terms: D000818:Animals; D001042:Aphids / Q000235:genetics*; D020635:Buchnera / Q000235:genetics; D002874:Chromosome Mapping; D016680:Genome, Bacterial; D049750:Genome, Insect; D054629:Genome, Mitochondrial; D017422:Sequence Analysis, DNA / Q000379:methods*; D013559:Symbiosis