*2.3. Conserved Sequence Alignment and Motif Analysis*

Multiple sequence alignments were created by Jalview for the 21 LiNAC proteins to investigate the presence and locations of conserved protein domains (Figure 2) and Weblogo displayed the conserved domains with five subdomains (A–E) (Figure 3). All LiNAC family members contained a NAM domain (Figure 4C), which contains a highly conserved A–E subdomain. To further analyze the structural diversity in LiNAC proteins, conserved motifs were searched using the MEME program. In total, 20 distinct motifs were identified (Figure 4B). Most LiNAC proteins contained motif 3 (representing subdomain A), motif 4 (representing subdomain B), motif 2 (representing subdomain C), motif 1 (representing subdomain D), and motif 5 (representing subdomain E) (Figure S2). Additionally, the majority of the members in the phylogenetic tree that were closely linked displayed comparable motifs in the same alignment and location (Figure 4A). Members in the TERN subgroup had nearly identical motifs. Interestingly, some motifs were identified in a certain subgroup. For example, compared with Group I, the number of motifs in Group II was small. Motif 14 was found only in the NAC1 subgroup and motif 16 in the ONAC022 subgroup. The results revealed that LiNAC proteins clustering in the same subgroup may have comparable biological roles and that specific motifs may be associated with specific functions of different subgroups.

**Figure 1.** NAC phylogenetic tree of *L. indica* and *A. thaliana*. Each subgroup is distinguished by a different color.

**Figure 2.** Amino acid sequence alignment of *L. indica*. The black box lines represent the five subdomains (**A**–**E**) of LiNAC.

**Figure 3.** Conserved domain of LiNAC family by Jalview software and Weblogo. (A–E) represent five subdomains.

**Figure 4.** Evolutionary trees (**A**), conserved motifs (**B**), and conserved domain (**C**) of *LiNAC* genes.
