Citation: T. Schmutzer (2016-08-03): Large data tables for gene prediction, gene annotation and the genetic map of rye (Lo7). DOI:10.5447/ipk/2016/57

Abstract: This DOI contains 4 data sets related to the publication by Bauer et al., entitled ‘Towards a whole-genome sequence for rye (Secale cereale L.)’. File 1: Assignment of 27,784 rye gene models to Lo7 WGS contigs (‘Assignment_RyeGeneModels_to_Lo7Contigs.xlsx’). File 2: Rye gene model candidates with divergent PAV patterns (‘PAV_analysis_2934_gene_model_candidates.xlsx’). Candidates were detected using read coverage analysis of all gene models. A gene model was defined as absent if less than 5% of the gene length was covered with reads. Subsequently, a gene model was considered as strong candidate for divergent PAV patterns, if more than 25% of the studied genotypes (>3) were absent. Among all 2,934 candidates depicted in this table, 1,251 are strong candidates showing interesting patterns of divergence between rye genotypes. File 3: Annotation of rye gene models with AHRD (a human readable description) and Blast2GO (‘AHRD_Blast2GO_Annotation_RyeGeneModels.xlsx’). This file contains two spreadsheets. In the first AHRD annotation, a total of 23,271 rye gene models were linked to a human readable description for their putative function. In the second Blast2GO annotation, 16,275 sequences were mapped, 12,716 sequences annotated and 3,247 sequences were assigned to an EC number. File 4: High-density genetic map with 88k markers for the Lo7 x Lo225 RIL population (‘Lo7Lo225_88k_geneticmap.xlsx’).

License: CC BY 4.0 (Creative Commons Attribution)

DOI: 10.5447/ipk/2016/57