Figure 6

Hierarchical clustering of coffee cDNA libraries and clusters based on EST distribution. a) C. canephora hierarchical clustering of 443 clusters differentially expressed vs. the eight cDNA library assemblies. b) C. arabica hierarchical clustering of 331 clusters differentially expressed vs. the 23 cDNA library assemblies. Hierarchical clustering was performed using a correlation matrix constructed from EST frequencies for differentially expressed C. arabica and C. canephora contigs. Black intensity designates relative transcript abundance in a given library, as inferred from EST frequency within each contig. Library abbreviations correspond to the following descriptions: C. canephora: LF; young leaves, PP1; pericarp, all developmental stages; SE1; whole cherries,18 and 22 weeks after pollination; SE2, whole cherries,18 and 22 weeks after pollination; SE3: endosperm and perisperm, 30 weeks after pollination SE4; endosperm and perisperm, 42 and 46 weeks after pollination; EC1: embriogenic calli; SH1: leaves from water deficit stressed plants; and SH3: leaves from water deficit stressed plants (drought resistant clone). C. arabica: PC1, C. arabica non-embryogenic cell line induced with 2,4-D; CA1, non-embryogenic calli; IC1, C. arabica non-embryogenic cell line without 2,4-D; EA; EA2, C. arabica embryogenic calli; IA2, C. arabica embryogenic cell line induced with 2,4-D; PA1, primary embryogenic C. arabica calli; EM1, zygotic embryo from mature germinating seeds; SI3, germinating whole seeds; LV4, young leaves from orthotropic branches; LV5, young leaves from orthotropic branches; LV8, mature leaves from plagiotropic branches; LV9, mature leaves from plagiotropic branches; FB1, floral buds at developmental stages 1 and 2; FB2, floral buds at developmental stages 1 and 2; FB4, floral buds at developmental stages 3 and 4; FR1, floral buds, pinhead fruits, fruit developmental stages 1 and 2; FR2, floral buds, pinhead fruits, fruit developmental stages 1 and 2; SS1, well-watered field plant tissues; SH2, water-stressed plant tissues; CB1, suspension cells treated with acibenzolar-S-methyl and brassinosteroids; CS1, suspension cells under osmotic stress; AR1, leaves treated with arachidonic acid; LP1, plantlets treated with arachidonic acid; RT5, roots with acibenzolar-S-methyl; CL2, hypocotyls treated with acibenzolar-S-methyl; BP1, suspension cells treated with acibenzolar-S-methyl; RT8, root suspension cells under aluminum stress; RX1, Xyllela spp.-infected stems; NS1, nematode-infected roots; and RM1, leaves infected with leaf miner and coffee leaf rust.