*2.2. Chromosomal Location, Phylogenetic Analysis, Prediction of Subcellular Localization, Gene Structure, Cis-Acting Elements, and Conserved Motifs Analyses*

For gene location visualization on the respective chromosomes, the retrieved gene ID information in gtf3 file format of all the *GhSAMSs* was used in Tbtools software to map the genes onto the chromosomes. The coding sequence of *GhSAMS* members was downloaded from the official website of Phytozome (https://Phytozome.jgi.doe.gov; accessed on 9 June 2020). Homolog genes from closely related plant species (Table S1) were also downloaded from the Phytozome website and later used to perform the phylogenetic analysis via the neighbor-joining method in the MEGA 7.0 program, with the specification of 1000 bootstrap replicates [26]. ClustalX software was used to align all the protein sequences before generating a phylogenetic tree diagram for evolutionary relationships analysis [27]. The Poisson correction was applied to estimate the distance between sequences. WoLF Psort online software was used to predict *GhSAMS* genes' subcellular localization (https://wolfpsort.hgc.jp; accessed on 15 June 2020) [28].

*GhSAMS* genes' structure analysis was conducted via the Gene Structure Display Server website (http://gsds.cbi.pku.edu.cn; accessed on 19 June 2020) [29]. In-depth prediction of the cis-regulatory DNA elements in the *GhSAMS* promoter region (2000 bp upstream nucleotide sequence) was achieved by the online PlantCARE server software (Bristol, England) [30]. MEME server (https://meme-suite.org, version 5.4.1; accessed on 13 Jully 2020), with the default setting, was used to predict conserved motifs within the gene structures ().
