*4.3. Analyses of Exon–Intron Structure, Distribution of Conserved Motifs and Characteristic Domain Architecture*

Exon–intron structures of the grapevine B3 genes were analyzed using aligned transcribed sequences and corresponding genomic sequences, and diagrams were created using the online Gene Structure Display Server 2.071 [62]. Conserved motifs and domains of proteins were analyzed using MEME 4.11.2 (http://meme-suite.org/tools/meme), searching up to 20 conserved motifs, and SMART (http://smart.embl-heidelberg.de). Protein domains were identified using the NCBI Conserved Domain Database (https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml).

## *4.4. Synteny Analysis of Grape, Tomato and Arabidopsis B3 Genes*

Tandem and segmental duplications of B3 genes in the grapevine genome were identified based on chromosomal locations. For synteny analysis, adjacent homologous grape B3 genes on a single chromosome without the presence of intervening genes was considered as a tandem duplication, whereas gene duplication events occurring on different chromosomes were defined as segmental duplications [68]. The list of grape B3 genes in duplicated genomic regions and a comparison of grape and Arabidopsis as well as grape and tomato genomes were retrieved from the Plant Genome Duplication Database [34]. Diagrams were generated using the program Circos version 0.63 (http://circos.ca/).
