*4.4. Phylogenetic Analysis and Gene Structure*

To analyzethe phylogenetic relationships between *TCP* genes in *G. hirsutum* and other species, the protein sequences of the identified *GhTCP* genes, Arabidopsis *TCP* genes, and rice *TCP* genes, were used to generate aphylogenetic tree. The ClustalX program was used to align the TCP domains. Phylogenetic trees were constructed by MEGA6.0 using the NJ and Minimal Evolution (ME) methods. For both methods, the bootstrap test of phylogeny was performed with 1000 replications. The exon/intron structures for each *GhTCP* gene was determined by aligning the CDS sequences to their corresponding genomic DNA sequences. The structures were shown using the Gene Structure Display Server 2.0 (http://gsds.cbi.pku.edu.cn/).
