Protein sequence analysis

Consensus amino acid (aa) sequence for LS and SS were generated through multiple sequence alignment of aa sequences belonging to all the orthologs through Geneious software ver 6.6.1 with default settings (http://www.geneious.com). An aa at a particular position present in majority of the orthologs was used for generating the consensus sequence. If a different aa was present at a particular position, aa in the maize reference was used for the consensus sequence. The insertions in any of the other species relative to the reference species were also added to the consensus sequence (Navarro et al., 2015). For sequence similarity, aa at different positions in a particular species were compared with the consensus sequence. In monocots, a similarity scale of 0–10 (a separate scale for each wheat homoeologue), and in dicots, a scale of 0–3 was used. A value of zero indicated complete lack of similarity with the consensus, while a value of 10 in monocots and 3 in dicots suggested conservation of aa in all of the species. Domains and motifs in the consensus protein sequence were identified through CDD analysis (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi).