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. 2017 Sep 27;8:1629. doi: 10.3389/fpls.2017.01629

FIGURE 2.

FIGURE 2

Transporter-gene expression networks for Shiraz berries during development associated with veraison. The networks were obtained using Cytoscape 3.5.1 (http://www.cytoscape.org/index.html) (Shannon et al., 2003) with the RNAseq data of Sweetman et al. (2012), where all transporter genes plus sucrose synthases and invertases were selected giving a total of 260 detected transcripts. Those with very low expression (value of zero during any stage) or those without an associated Genoscope identification were excluded giving a total of 188 transcripts that were log (Ln2) transformed before analysis with Cytoscape (ExpressionCorrelation plugin). Using the classifications of clusters determined by Sweetman et al. (2012), nodes were selected as Early veraison or Veraison up-regulated or Veraison onwards. Networks were then generated from the first nodes connected to these selected clusters using only positive interactions with better than 0.98 (Pearson Correlation Coefficient). Three networks were extracted as shown. (A,B) Networks associated predominately with Veraison upregulated or Early veraison, (C) Network associated with Veraison onwards that includes the Sweetman et al. (2012) cluster Increasing. The size of the nodes indicates the Betweenness Centrality of the node indicative of how central the node is in the overall network. The thickness of the edges (lines connecting the nodes) indicates the strength of the positive relationship. Selected highly expressed transcripts related to sugar transport and cation transport, in each network include; (A) bidirectional sugar transporter SWEET10 (SWEET10 VIT_17s0000g00830), cyclic nucleotide-gated ion channel 4-like (ATCNGC4 VIT_19s0014g03700), sodium/hydrogen exchanger 2(NHX4 VIT_05s0020g01960) and potassium transporter 11-like (KUP11 VIT_01s0011g01510). The most highly expressed gene is probable aquaporin PIP2-5 (PIP2;3 VIT_08s0040g01890). (B) Sodium/hydrogen exchanger 2-like (VIT_14s0128g00020), bidirectional sugar transporter SWEET4 (VIT_02s0025g02080). The most highly expressed gene is aquaporin PIP1-2 (PIP1;3 VIT_02s0025g03390). (C) Bidirectional sugar transporter SWEET15 (SAG29, VIT_01s0146g00260), probable cyclic nucleotide-gated ion channel 5 (VIT_11s0037g00230), chloride channel protein CLC-f (CLC-F VIT_19s0015g01850). The most highly expressed gene is sucrose synthase 2 (VIT_07s0005g00750). Gene IDs (in brackets) were found by blasting nucleotide sequence from the Vitis vinifera 8x assembly (From Genoscope ID provided by Sweetman et al. (2012)) then blasting this nucleotide sequence against the Vitis vinifera IGGP_12x in Ensembl Plants. Annotations provided by Sweetman et al. (2012) are in italics.