Citation: International Wheat Genome Sequencing Consortium (2018-03-29): Gene family expansion and contraction in the genome of bread wheat cv. Chinese Spring. DOI:10.5447/ipk/2018/5

Abstract: Gene families were inferred using a phylogenomics approach utilizing the OrthoFinder software incorporating the predicted protein sequences from bread wheat (RefSeq Annotation v1.0), nine other grasses and four Viridiplantae genomes. Wheat sub-genomes were handled as independent taxa. Gene family expansions and contractions in either one of the wheat sub-genomes, the wheat A- or D-lineage or the wheat genome in general were inferred using a previously established phylogenomic approach. Log-transformed gene family sizes among the 10 grasses were compared using phylogenetic comparative one-way ANOVA correcting for phylogenetic interdependency using a species tree that was computed by coalescence analysis of 14,275 orthologue-only subfamily clades extracted from the gene family trees derived by OrthoFinder. To account for hexaploidy in the bread wheat genome, all three sub-genomes were treated as separate entities i.e. taxa. Gene family sizes were log-scaled. 1) gene_family_analysis_results.xlsx Microsoft Excel file with five sheets containing the results of an analysis for the expansion and contraction of gene families in the genome of bread wheat cultivar Chinese Spring. The fifth sheet provides further details on the contents of sheet 1 to 4. 2) Traits.orthologs.xlsx Microsoft Excel file with two sheets. First sheet provides a detailed description of the columns of sheet 2, which lists all Plant Trait ontology term associations for V1.0 loci, including the originally mapped ortholog and information whether they are part of an expanded or contracted gene family. For more details or questions, contact Manuel.Spannagl@helmholtz-muenchen.de and Daniel.Lang@helmholtz-muenchen.de.

License: CC BY-SA 4.0 (Creative Commons Attribution-ShareAlike)

DOI: 10.5447/ipk/2018/5