Multiple sequence alignment and phylogenetic analysis

Multiple sequence alignment of PIN proteins was done using the Clustal Omega program (https://www.ebi.ac.uk/Tools/msa/clustalo/) with default parameters, and the phylogenetic tree ( Figure 1A ) was generated according to the maximum likelihood (ML) method (Truszkowski and Goldman, 2016), and 1,000 replicates were used for bootstrap analysis by using MEGA-11 software. For Figure 2 , the phylogenetic tree was constructed by IQ-Tree v.2.1.2 (Minh et al., 2020) with 1,000 ultrafast bootstrap replicates using the alignment file generated through MAFFT tool v.7 (Katoh et al., 2019) with default parameters. The tree was visualized and edited using iTOL (v.6) (Letunic and Bork, 2019).

Phylogeny, chromosomal location, gene structure, and protein domains in 12 PINs of rice. (A) The phylogenetic tree of PIN proteins showing relative evolutionary relationships among themselves. (B) Genome organization of rice PIN genes on eight chromosomes of rice. (C) Exon-intron distribution of rice PIN genes. (D) Conserved protein domains identified in rice PIN proteins. Out of 10 motifs, seven were common in all of the PIN proteins.

The phylogenetic relationship of PIN proteins of different plant species across the plant kingdom. A maximum likelihood method using 1,000 ultrafast bootstrap replicates was used to construct the tree. The OsPINs are labeled in red. The phylogenetic tree clustered into eight major groups was depicted in different colors.