Studying the interactions between arbuscular mycorrhizal fungi (AMFs) and their symbiotic endobacteria has potentially strong impacts on the development of new biotechnology applications. The analysis of genomic data and syntenies is a key technique for acquiring information about phylogenetic relationships and metabolic functions of such organisms. In this paper, we describe a modular architecture meant to support in-silico genome sequence analysis, which is being developed within the project BIOBITS. In particular, we focus on a flexible genome retrieval tool, which supports optimized and customized comparative genomics searches.