Sugarcane ORF finder: the web-application for mining genes from sugarcane genome

Abstract

Sugarcane is one of the most important multi-purpose crops that are native to tropical regions. As commercial sugarcane is an interspecific hybrid between Saccharum officianarum and Saccharum spontaneum, the genome size of sugarcane has been reported around 10 Gbase. From this reason, it has been hard to build the reference level assembly resulting in partial contigs. With the advance of third generation sequencers and assembly strategies, recently, two sugarcane genome assemblies were published representing monoploidy of sugarcane cultivar and whole genome of S. spontaneum. Synergetically, the genome-editing technology is advanced that can eventually facilitate the sugarcane breeding and the necessity of utilizing genome sequence is also arising for sugarcane researchers to find guide-RNA binding site by the machine learning algorithms or human inspection. Here, we built web-application for the researchers to find the open reading frame (ORF) of sugarcane genes easily with a query gene ID and catalog candidate gene list by query sentences (http://pgl.gnu.ac.kr/sugarcane_orf_finder/). This enables the researchers to find their genes of interest and directly observe the ORF structure of the query gene and design precise guide RNA for genome editing.