2.3. Phylogenetic Analysis and Classification of the TcNAC Gene Family

MEGA 7.0 (http://www.megasoftware.net/) was used for constructing an individual phylogenetic tree of the TcNAC gene family [43]. Based on their aggregation with the AtNAC genes, the TcNAC genes were divided into different subgroups, and a comprehensive phylogenetic tree including Arabidopsis and Theobroma cacao was constructed using MEGA 7.0. All of the sequences were firstly aligned using ClustalW (http://www.ebi.ac.uk/clustalw/) with the default parameters [44]. Since not all NAC family members are necessarily homologous, to increase the reliability of the analysis, we deleted gaps and built a more conservative phylogenetic tree. Both of the phylogenetic trees were built using MEGA 7.0 using the maximum parsimony (MP) method [45] with 1000 repetitions for the bootstrap test [46].