Sequences of target genes and probes for construction of exon-targeted libraries for Prunus spp.

(Files) "baits-selection-15171.fas": Sequences of 15,171 baits used for hybridization reaction. "Targets_mume.15171.xlsx": Sequences of target genes used for design baits. (Protocol for bait design) To selectively retrieve libraries with exons, 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 P. mume (Zhang et al., 2012). We subjected 29,621 non-redundant coding loci to search for single hits with BLAST+ (MEGABLAST with -p 70) against the P. mume 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 15,171 coding loci.

文件列表："baits-selection-15171.fas"：用于核酸杂交反应的15171条诱饵序列；"Targets_mume.15171.xlsx"：用于诱饵设计的靶基因序列。

诱饵设计方案：为选择性富集包含外显子的文库，本研究采用myBaits Custom定制化设计试剂盒（美国密歇根州安阿伯市Arbor Biosciences公司）合成1~20千碱基的寡核苷酸探针（Gnirke等，2009），该试剂盒借助生物素标记的RNA探针富集携带目标序列的DNA片段。本研究基于已发表的梅花（Prunus mume，简称P. mume）基因组及编码序列（Zhang等，2012），通过BLAST+序列比对工具（采用参数-p 70的MEGABLAST算法）比对梅花基因组，对29621个非冗余编码位点开展唯一匹配位点筛选，以支撑后续诱饵设计工作。针对每个筛选得到的位点，随机设计GC含量介于25%~55%之间的120碱基长度诱饵序列，最终获得靶向15171个编码位点的诱饵集。