Orthology Guided Transcriptome Assembly Of Italian Ryegrass And Meadow Fescue For Single Nucleotide Polymorphisms Discovery (Data Set)

Transcriptome sequencing was performed on ten samples (corresponding to six genotypes) of <em>Festuca pratensis</em> and ten samples (corresponding to six genotypes) of <em>Lolium multiflorum</em> and fourteen samples of<em> Lolium perenne</em> (corresponding to fourteen genotypes). Using the OGA approach, 18,952 non-redundant <em>F. pratensis</em> transcripts were assembled by combining the contigs of all six genotypes based on orthology with the <em>Brachypodium distachyon </em>proteome. Similarly, <em>19,036</em> non-redundant<em> L. multiflorum</em> transcripts were assembled and annotated. In total, 17,455 orthologous transcripts were shared between the transcriptomes of the two species. Out of these, 16,613 orthologous transcripts overlap with the previously published<em> L. perenne</em> transcriptome containing 19,279 non-redundant transcripts(fasta files). We identified SNPs, the following criteria were used to classify it as one of following three classes (1) intraspecific SNPs (INTRA), (2) interspecific SNPs in two-way comparison (INTER-2W) and (3) interspecific SNPs in three-way comparison (INTER-3W) (GFF files).本研究对草地羊茅（Festuca pratensis）的10个样本（对应6个基因型）、多花黑麦草（Lolium multiflorum）的10个样本（对应6个基因型）以及多年生黑麦草（Lolium perenne）的14个样本（对应14个基因型）进行了转录组测序。采用OGA方法，基于与二穗短柄草（Brachypodium distachyon）蛋白质组的直系同源关系，整合全部6个基因型的重叠群序列，组装得到18952条非冗余的草地羊茅转录本。同理，组装并注释得到19036条非冗余的多花黑麦草转录本。两个物种的转录组中共共享17455个直系同源转录本；其中16613个直系同源转录本与已发表的包含19279条非冗余转录本的多年生黑麦草转录组（fasta格式文件）相重叠。本研究鉴定了单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs），并采用以下标准将其划分为三类：(1) 种内SNPs（INTRA）；(2) 双向比较种间SNPs（INTER-2W）；(3) 三向比较种间SNPs（INTER-3W），相关分类结果存储于GFF格式文件中。