Gene coexpression network analysis of galactomannan biosynthesis and endosperm maturation in species of the genus Coffea

In a few important plant families and genera, including Arecaceae, Fabaceae and the genus Coffea, the main seed storage polysaccharide is not starch but cell wall galactomannans. Such seeds are albuminous with a persistent copious living endosperm that accumulates galactomannans. However, our understanding of the regulation of endosperm maturation, cell wall formation and galactomannan biosynthesis in albuminous seeds remains very limited. To gain insights into these processes, a large RNA-seq dataset was produced (14 coffee species x 5 endosperm developmental stages) and scrutinized using gene coexpression network analysis. The network revealed tight transcriptional coordination of the core galactomannan biosynthetic machinery for sucrose import, glycolysis, nucleotide sugar synthesis and transport, arabinogalactan protein and cellulose synthesis, and regulation of the trans-Golgi network. The orchestration of galactomannan and oil accumulation during endosperm maturation appeared to be exerted by the transcription factors FUSCA3, WRINKLED1, SHINE2 and DREB2D. The latter was the only coexpression partner of galactomannan biosynthetic genes. Numerous key genes of galactomannan biosynthesis were significantly upregulated in coffee somatic embryos overexpressing DREB2D, which showed increased production of UDP-galactose and diversion towards raffinose family oligosaccharides. Further, most genes of the galactomannan coexpression module were identified as DREB2D target genes by DAP-seq analysis. HighlightGene coexpression network analysis of the maturing endosperm identified the AP2/ERF transcription factor DREB2D as a major regulator of galactomannan accumulation in the cell walls of albuminous coffee seeds.