Tandem gene duplication analysis

We extracted sequences of 144 rice SDRLK family proteins from the Gramene (http://gramene.org). We then built a sequence similarity tree to identify subgroups of genes that are most similar using Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo) (Sievers et al., 2011) software (set to default parameters). The tree file saved from Clustal Omega was exported to the Interactive Tree of Life (iToL; https://itol.embl.de) (Letunic & Bork, 2016) website to visualize and add data layers. We further investigated if genes that show high sequence similarity are in the same genomic neighborhood. We uploaded Gene IDs on the O. sativa genome browser available at Gramene and then manually inspected the genomic location and flanking regions of individual genes. We defined tandem duplicates based on sequence similarity and genomic location (<5 genes in between).