Identification of Key Genes Related to Speciation and Adaptation
To explore the differentiation mechanism in the early stage of speciation, SNPs related to selection were identified. Candidate SNPs were mapped to the corresponding genes to check whether these genes were included in DEGs. The genes obtained using the above filtration procedure were considered driver genes in the early speciation ofA. viridiflora . Next, the clusterProfiler package in R was used to perform KEGG enrichment analysis on candidate genes (Yu et al., 2012). Additionally, environment-related genes that were selected and differentially expressed were regarded as candidate genes that differentiated by adapting to the environment in the early stages of speciation. The coding sequence (CDS) regions of candidate genes were analyzed to identify whether the mutations in the CDS regions were synonymous or nonsynonymous. Additionally, Multiple Em for Motif Elicitation (MEME) v.5.3.3 (https://meme-suite.org/meme/tools/meme) (Bailey & Elkan, 1994) was used to identify transcription factor binding sites in the 2 kb region upstream and downstream of the gene, and Motif Comparison Tool (Tomtom) v.5.3.3 (https://meme-suite.org/meme/tools/tomtom) (Gupta, Stamatoyannopoulos, Bailey, & Noble, 2007) was used to annotate the motif functions.