Sequences of target genes and probes for construction of exon-targeted libraries in rice

(Files) "Rice-baits-selection-16462.txt": Sequences of 16,462 baits used for hybridization reaction. "Rice-input-seq.fas": Sequences of target loci used for design baits. (Protocol for bait design) To selectively retrieve libraries with target sites, a myBaits Custom design kit was used to design 1–20-K probes (Arbor Biosciences, Ann Arbor, MI, USA), which uses biotinylated RNA probes to concentrate fragments carrying sequences of interest (Gnirke et al., 2009), based on the published genomic and coding sequences of IRGSP-Npb. We subjected 19,109 non-redundant coding loci to search for single hits with BLAST+ (MEGABLAST with -p 80) against the IRGSP-Npb genome, for the subsequent bait design. A 120-mer bait with 25–55 GC% per locus was randomly designed for each locus, and finally we obtained a bait set targeting 16,462 coding loci.