Whole genome sequence comparisons in taxonomoy

Abstract

This chapter is devoted to application of whole genome sequence comparisons in taxonomy. Driven by the rapid progress in sequencing technologies, “low budget” bacterial genomes become increasingly available in a nearly unlimited number. During finalizing this chapter, completed genomes representing 1,604 bacterial and 85 archaeal species were present in the public data bank (http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi) reflecting the enormous progress made within sequencing microbial genomes in the last years. With the advent of next generation sequencing, whole genome sequence comparisons will be more and more important for taxonomy, especially valuable in elucidating relationship of groups of closely related bacterial strains which might form a single taxon, a subspecies or just an ecovar within a given species. The aim of this chapter is to hand out a tool set for applying genomics to the interested taxonomist. Using these tools might prove as being useful especially in refining groups of closely related strains, which are not resolved by their 16S rRNA sequence. Here, we will exemplify this approach by selecting a specific group of plant – associated Bacillus amyloliquefaciens strains with plant growth promoting properties. In recent years, those strains were increasingly applied as biological substitutes of agrochemicals, mainly used as biofertilizer and for biocontrol of phytopathogenic microorganisms, and nematodes (Chen et al., 2007).