SeeDev-binary@ldeleger:SeeDev-binary-21635767-3 JSONTXT

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the entire coexpression network is useful for network topology analysis, isolation\nof a subnetwork (or cluster) makes it more accessible to biologists [40,58]. More importantly, a subnetwork in the large coexpression network is often more biologically\nrelevant in a pathway context. Hence, we extracted subnetworks from this gene coexpression\nnetwork for genes relevant to the accumulation of seed storage reserves (Figure 4). Of the 48 genes known to encode enzymes involved in FA biosynthesis [17,59], we identified 44 (or ~92%) genes represented on the ATH1 array, and all of them\nwere found in one subnetwork (Figure 4A). This subnetwork cluster consists of 1854 genes (Additional File 1), which is in general agreement with an interactive correlation network generated\ngenome-wide in Arabidopsis using a heuristic clustering algorithm [41]. Such a gene list can be used to identify interactors of genes in FA synthesis in\ndeveloping seeds. Consistent with the coexpression subnetwork analysis, the majority\nof genes involved in FA biosynthesis were associated with Cluster 1 (Figure 3). Their expression levels increased steadily from the globular embryo stage, generally\nreached the peak at the expanded cotyledon stage, and dramatically declined subsequently\nthroughout late seed maturation (Figure 4B). Such a unified expression pattern for most FA biosynthetic genes supports earlier\nstudies showing that FA supply can be a limiting factor for triacylglycerol (TAG)\naccumulation in developing embryos of Brassica napus [60], olive (Olea europaea L.) and oil palm (Elaeis guineensis Jacq.)[61], as well as cuphea lanceolata and other oil species [62]. Recent studies of metabolic flux in developing embryos of B. napus, however, indicated that TAG assembly was more limiting than FA biosynthesis in regulating\nthe flow of carbon into TAG [63]. The majority of genes encoding oilbody oleosins and SSPs were found in another subnetwork\nwith a distinct expression pattern (Figure 4C). The subnetwork encompassing genes encoding oleosins and SSPs is comprised of 1392\ngenes (Additional File 2). Genes encoding oleosins and SSPs were in Cluster 2 (Figure 3), and their expression profiles were strikingly similar. These genes were virtually\nunexpressed at the globular stage, increased rapidly (\u003e1000-fold in many cases) from\nthe globular stage to the bilaternal stage, and remained at the elevated expression\nlevel throughout the remaining stages of seed maturation (Figure 4D). Transcripts for OLEOSIN and SSP genes are most abundant in the seed transcriptome late during seed development. In\ncontrast, most genes in the TAG assembly pathway were found in different subnetworks,\nexhibiting various expression profiles during seed development (Figure 5). DIACYLGLYCEROL ACYLTRANSFERASE 1 (DGAT1), FATTY ACID DESATURASE 2 (FAD2), FATTY ACID ELONGASE 1 (FAE1) and STEAROYL DESATURASE (SAD) genes were identified in this subnetwork, albeit expressed at substantially lower\nlevels compared to genes encoding oleosins and SSPs (Additional File 3). DGAT catalyzes the acyl-CoA-dependent acylation of sn-1,2-diacylglycerol to produce TAG and CoA [64]. FAD2 catalyzes the introduction of a second double bond into acyl groups in phospholipid\nwhereas SAD catalyzes the formation of monounsaturated FA in the plastid [65]. FAE1 catalyzes the elongation oleoyl-CoA in the endoplasmic reticulum [65]. Our analysis determined that AT1G48300, which was named DGAT3, is the putative gene encoding a cytosolic DGAT in Arabidopsis. The amino acid sequence\nof AT1G48300 has a significantly high degree of similarity (expect value \u003c 1 × 10-21) to the soluble DGAT in peanut (Arachis hypogaea), where the cytosolic DGAT gene in plants was first discovered [66]. Notably, DGAT3 exhibited a similar expression pattern with DGAT1, but expressed higher during late seed maturation. In earlier studies, quantification\nof DGAT activity during seed maturation in B. napus indicated that enzyme activity was maximal during the rapid phase of oil accumulation\nwith a substantial decrease in activity occurring as oil levels reached a plateau\n[67,68]. Assuming DGAT activity shows a similar profile during seed development in Arabidopsis,\nthis suggests that DGAT may be down-regulated post-transcriptionally and/or post-translationally\nduring the latter stages of seed development.\n"}