Mobilomics-acyrthosiphon pisum-Materials and Methods

MATERIALS AND METHODS

Annotation and data mining

We used the set of scaffolds provided by the first assembling of the Pea aphid Acyrthosiphon pisum LSR1.AC.F1 strain genome to map transposable element (TE) features, as described in (IAGC 2010). Among the different mobile genetic elements (MGEs) characterized we identified 549 LTR retroelement-like features belonging or related to the Ty3/Gypsy, Bel/Pao and Ty1/Copia families. The sequences were curated via BLASTx, tBLASTn and BLASTp (Altschul et al. 1997) searches on the basis of their similarities to other LTR retroelements classified at GyDB (LLorens et al. 2011) and RepBase (Jurka et al. 2005) by combining the version of Apollo (Lewis et al. 2003) distributed by International Aphid Genomics Consortium (IAGC) and the GPRO (Gypsy Database Professional) software (Futami et al. 2011) which implements a bioinformatic annotation pipeline.

Mobilomics Server design

The Mobilomics was programed as a PHP/JavaScript module completely integrated on the GyDB wiki system as a dynamic set of templates that queries a MySQL database which contains the complete set of mobilomes organized by organisms.