FvJAZ, FvMYC2 and FvMYC2-like genes conserve synteny in F. vesca genome
JAZ and MYC along with COI1 co-receptor establish the core of JA signalling pathway [10,46]. Eleven to eighteen JAZ genes have been identified in the genome of higher plant species: thirteen JAZ protein members belonging to TIFY family in Arabidopsis [10,17], 15 members in rice [45], 14 members in wheat [47], 13 members in tomato [48], 18 members in apple and bamboo [49,50] and 11 members in grape [51]. We identified 12 non-redundant JAZ genes in F. vesca genome, FvJAZ1, FvJAZ4-1, FvJAZ4-2, FvJAZ4-3, FvJAZ5, FvJAZ7, FvJAZ8.1, FvJAZ8.2, FvJAZ9, FvJAZ10, FvJAZ11 and FvJAZ12 (Table 1). On the other hand, there are four MYC members involved in the JA signalling pathway in Arabidopsis: MYC2, MYC3, MYC4 and MYC5 [23–25]. Nevertheless, we only found two genes encoding for MYC TFs in F. vesca genome: MYC2 and MYC2-like (Table 1). The number of MYC2-like genes is variable between species, for instance M. × domestica contains five MYC2–like TFs (S2 Table) [52,53], but others species such as V. vinifera, Nicotiana tabacum, Nicotiana attenuata, Salvia miltiorrhiza, and S. lycopersicum contain two MYC2-like TFs [51,54–56] like in F. vesca (Table 1 and S2 Table). In the case of apple, which belongs to Rosaceae family and is evolutionary related to strawberry, contains five MYC2-like encoding genes defined as MdMYC2a [52], MdMYC2b, MdMYC2-like1, MdMYC2-like2 and MdMYC2-like3 [53].
Tandem, segmental and whole duplication are key processes in the expansion of gene families [57,58] and genome comparisons provide information about roles and evolutionary relationships between genes [59]. Tandemly duplicated genes were considered as adjacent homologous in the same chromosome according to observed in rice and apple [45,50]. Specifically, gene duplications play an important role in expansion of the TIFY family [21], to which belongs JAZ subfamily as observed for JAZ7, JAZ8 and JAZ9, JAZ10 in V. vinifera and S. lycopersicum genomes, respectively [48,51], similar to that observed in apple JAZ genes [50]. These results indicate that FvJAZ, AtJAZ, FvMYC2 and AtMYC2 syntenic genes share likely a common ancestor and tandemly and segmental gene duplications were important for the expansion of JAZ subfamily [50]. In the case of FvPPD genes, they did not show syntenic regions within A. thaliana genome.
Exon-intron organization plays a role in diversification and evolution of gene families through gain/loss and insertion/deletions [58]. FvJAZ genes showed variable lengths and number of introns with their respective Arabidopsis orthologs (Fig 2A). These differences could be a consequence of rearrangements and fusions similar to that observed in apple TIFY gene family [50]. The presence of introns allows expanding the repertoire of some JAZ proteins, as reported for the different splice variants for AtJAZ10 with different stability in their encoded proteins and roles in JA responses [60]. In contrast to FvJAZ genes, FvMYC2 and FvMYC2-like genes lack introns as Arabidopsis MYC-like orthologs (Fig 2B). In some cases, introns could have additional functions related to gene expression regulation [61], and this could be related with a key role in JAs responses [62–64], because their absence could be related with faster and efficient expression [65].