Genome Center bioinformatics script finds new life in study of gene silencing in stone fruit

Recently, researchers from Kyoto and Iwate Universities in Japan published a report of successful induction of virus-induced gene silencing in trees of seven Prunus species: almond, Armenian and Japanese apricot, cherry, peach, and European and Japanese plum. In this technique, a modified version of a plant’s own gene is expressed as part of a recombinant vector based on a virus, in this case apple latent spherical virus (ALSV). The plant’s innate immune system recognizes the virus and takes steps to neutralize it, via the production of small, 21-nucleotide RNA that mark both the native and the engineered messenger RNA for destruction. In this study, led by Professor Ryutaro Tao of Kyoto University, the target was phytoene desaturase, an enzyme involved in the synthesis of carotenoid pigments, so that mutations could easily be detected in the form of leaf discoloration. A project such as this generates a tremendous amount of sequence information, whose analysis frequently requires custom bioinformatic tools, most commonly scripts written in Python. These scripts filter, annotate, and categorize the raw Illumina data so that if the haystack does contain one or more needles, they are more likely to be identified. Rather than reinvent the wheel, in this case the researchers chose to use scripts created at the Genome Center in Professor Luca Comai’s lab. Their original function was elucidation of the mechanism of sex determination in persimmon, a collaborative effort of Comai and Tao. These scripts are freely available for download. The study was published in Scientia Horticulturae: Virus-induced gene silencing in various Prunus species with the Apple latent spherical virus vector