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.