Additional file 2 of Genome-wide analysis of JAZ family genes expression patterns during fig (Ficus carica L.) fruit development and in response to hormone treatment

Additional file 2: Figure S2. Differentially Co-expressed genes of FcJAZs between the fig female flower and peel tissue. The RNA-seq data for the fig fruit development were used for the WGCNA analysis, see the details in Fig 4. (a) Venn diagram showed the shared and unique Differentially Expressed Genes (DEGs) in the fig female flower and peel tissue, which Co-expressed with the FcJAZs. KEGG analysis suggested that the DEGs with the consistent regulation trend between tissues were represented in (b) and the different regulation trend between tissues were represented in (c

Additional file 9 of Genome-wide analysis of JAZ family genes expression patterns during fig (Ficus carica L.) fruit development and in response to hormone treatment

Additional file 9: Table S4. Ka/Ks analysis for the JAZ duplicated gene

Additional file 5 of Genome-wide analysis of JAZ family genes expression patterns during fig (Ficus carica L.) fruit development and in response to hormone treatment

Additional file 5: Figure S5. BiFCvisualization of FcJAZs and FcMYC2 interactions in tobacco leaf cells. FcJAZs and FcMYC2 were fused with the N- and C-termini of YFP and all ten possible interactions were tested. The interactions between FcMYC2 fused with N-terminal YFP and empty vector with C-terminal YFP were tested as negative controls. The mCherrycarrying a nuclear localization signal was used as the nuclear marker. Bars=50 μ

Additional file 4 of Genome-wide analysis of JAZ family genes expression patterns during fig (Ficus carica L.) fruit development and in response to hormone treatment

Additional file 4: Figure S4. The interaction network of FcJAZs according to the orthologues in Arabidopsis. This network was predicted by online software STRING. FcJAZ protein was shown by gene ID. The cluster was generated using Kmeans clustering algorithm from STRING database. Different colors indicate different clusters. Red boxes indicate proteins that were predicted to interact with FcJAZ1, FcJAZ8, FcJAZ9 and FcJAZ10 protein

Additional file 3 of Genome-wide analysis of JAZ family genes expression patterns during fig (Ficus carica L.) fruit development and in response to hormone treatment

Additional file 3: Figure S3. Multiple sequence alignment of the full-length MYC2 proteins(a)The conserved domains in FcMYC2 which were detected by NCBI Conserved Domains Search. (b) The details of these proteins’ sequence information in the NCBI database were that, FcMYC2 (c5167_g1), MnMYC2 (XP010104300.1), AtMYC2 (At1g32640.1), CsMYC2 (XP030501877.1), VvMYC2 (XP002280253.1), OsMYC2 (XP015614012.1), SlMYC2 (NP001311412.1), AtMYC3 (At5g46760.1) and AtMYC4 (At4g17880.1). The alignments of the JAZ protein sequences were performed by CLUSTAL

Additional file 8 of Genome-wide analysis of JAZ family genes expression patterns during fig (Ficus carica L.) fruit development and in response to hormone treatment

Additional file 8: Table S3. WGCNA of JAZs related to different metabolite

Additional file 6 of Genome-wide analysis of JAZ family genes expression patterns during fig (Ficus carica L.) fruit development and in response to hormone treatment

Additional file 6: Table S1. Primers sequence used in amplification, qPCR, yeast one-hybrid and BiF

Data_Sheet_1_Quantitative Proteome Analysis Reveals Changes in the Protein Landscape During Grape Berry Development With a Focus on Vacuolar Transport Proteins.xlsx

The vacuole plays a central role in fruit growth and quality formation, yet its proteomic landscape is largely unknown. In the present study, a protocol for isolating intact vacuoles from grape flesh tissue was successfully established. Quantitative proteome analysis identified 2533 proteins from five sampling dates along Cabernet Sauvignon berry development from stage I to III; among them, 1443 proteins were identified on all five sampling dates in at least two biological replicates per sample and were designated core proteome, and 1820 were recruited as differentially abundant proteins (DAPs) by sequential pairwise comparisons using arbitrary fold change of >1.5 and P < 0.05. Metabolism consistently constituted the largest category of identified proteins for both core proteome and DAPs, together with a consistently high proportion of protein-fate category proteins, indicating that the classic lytic functions of vegetative cell vacuoles are maintained throughout berry development; accumulation of metabolites involved in high sugar and other berry qualities in the late developmental stage added to the conventional lytic role of the flesh cell vacuoles. Overall increases in abundance of the DAPs were seen in the transporter proteins, membrane fusion/vesicle trafficking, and protein-fate categories, and decreased abundance was seen for DAPs in the stress, energy and cytoskeleton categories as berry development progressed. A very pronounced proteomic change was revealed between late stage I and mid stage II, with 915 increased and 114 decreased DAPs, demonstrating a significant surge of the vacuolar proteome underlying the rather static phenotypical and physiological phase. We identified 161 transport proteins with differential abundance, including proton pumps, aquaporins, sugar transporters, ATP-binding cassette transporters and ion transport proteins, together with organic compound transport proteins, the highest number and variety of berry tonoplast transporters found in grape proteome efforts to date. We further found a pre-positive increment of 96 transport proteins from the middle of stage II, before the berry undergoes its dramatic physiological changes at and following véraison. Our results are the first to describe the proteome of a vacuole-enriched preparation, toward understanding the functions of the largest compartment in berry cells during grape growth and ripening.</p

Additional file 7 of Genome-wide analysis of JAZ family genes expression patterns during fig (Ficus carica L.) fruit development and in response to hormone treatment

Additional file 7: Table S2. Promoter analysis of the Fig JAZ gene famil

Additional file 1 of Genome-wide analysis of JAZ family genes expression patterns during fig (Ficus carica L.) fruit development and in response to hormone treatment

Additional file 1: Figure S1. Multiple sequence alignment of the full-length JAZ proteins from fig, mulberry and Arabidopsis. The alignments of the JAZ protein sequences were performed by CLUSTALW. Red residues indicated the conservation of amino acid identity were at least 50% of the aligned proteins, whereas residues conserved in all protein sequences were highlighted in red-shaded. The conserved sequence of the motif of TIFY, Jas and EAR were indicated at the bottom of the relevant plac