A database for the provisional identification of species using only genotypes: web-based genome profiling

Abstract

Correspondence: Koichi Nishigaki. E-mail: koichi@fms.saitama-u.ac.jp Abstract Background: For a long time one could not imagine being able to identify species on the basis of genotype only as there were no technological means to do so. But conventional phenotype-based identification requires much effort and a high level of skill, making it almost impossible to analyze a huge number of organisms, as, for example, in microbe-related biological disciplines. Comparative analysis of 16S rRNA has been changing the situation, however. We report here an approach that will allow rapid and accurate phylogenetic comparison of any unknown strain to all known type strains, enabling tentative assignments of strains to species. The approach is based on two main technologies: genome profiling and Internet-based databases.

Systematic genome sequence differences among leaf cells within individual trees

“…GP has been used as a tool for universal species identification [ 21 , 24 , 27 , 28 , 33 ] and as an accurate detector of mutation [ 34 , 35 ]. In this study, we applied the GP method to a new challenge: detection of extremely small genomic differences between very closely related cells with the aim of examining within-organism sequence variation.…”