Orthology guided transcriptome assembly of Italian ryegrass and meadow fescue (update data set)
- 1. Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research
- 2. Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit – Growth and Development
- 3. Institute of Agricultural Sciences, Forage Crop Genetics, ETH Zurich
- 4. Department of Environmental Stress Biology, Institute of Plant Genetics of the Polish Academy of Sciences
Description
Transcriptome sequencing was performed on ten samples (corresponding to six genotypes) of Festuca pratensis and ten samples (corresponding to six genotypes) of Lolium multiflorum and fourteen samples of Lolium perenne (corresponding to fourteen genotypes). Using the OGA approach, 18,952 non-redundant F. pratensis transcripts were assembled by combining the contigs of all six genotypes based on orthology with the Brachypodium distachyon proteome. Similarly, 19,036 non-redundant L. multiflorum 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 L. perenne 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).
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