Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning

Abstract

Oil palm can accumulate up to 90% oil in its mesocarp, the highest level observed in the plant kingdom. In contrast, the closely related date palm accumulates almost exclusively sugars. To gain insight into the mechanisms that lead to such an extreme difference in carbon partitioning, the transcriptome and metabolite content of oil palm and date palm were compared during mesocarp development. Compared with date palm, the high oil content in oil palm was associated with much higher transcript levels for all fatty acid synthesis enzymes, specific plastid transporters, and key enzymes of plastidial carbon metabolism, including phosphofructokinase, pyruvate kinase, and pyruvate dehydrogenase. Transcripts representing an ortholog of the WRI1 transcription factor were 57-fold higher in oil palm relative to date palm and displayed a temporal pattern similar to its target genes. Unexpectedly, despite more than a 100-fold difference in flux to lipids, most enzymes of triacylglycerol assembly were expressed at similar levels in oil palm and date palm. Similarly, transcript levels for all but one cytosolic enzyme of glycolysis were comparable in both species. Together, these data point to synthesis of fatty acids and supply of pyruvate in the plastid, rather than acyl assembly into triacylglycerol, as a major control over the storage of oil in the mesocarp of oil palm. In addition to greatly increasing molecular resources devoted to oil palm and date palm, the combination of temporal and comparative studies illustrates how deep sequencing can provide insights into gene expression patterns of two species that lack genome sequence information.

Fig. 1.

Oil palm and date palm fruits show a completely different carbon-partitioning pattern. (A) Phylogenic tree constructed with RBCL gene sequences. Bar indicates the percentage of divergence. (B) Open fruits and mesocarp composition (% dry weight) (SI Materials and Methods). (C) Fatty acid and soluble sugar content of mesocarp during fruit ripening. (D) Transmission electron micrograph of cell containing oil droplets from oil palm mesocarp, harvested 20 WAP. See also Fig. S1.

Fig. 2.

Lipid subcategories except for fatty acid synthesis show similar expression pattern in oil palm and date palm. (A) The ratio of ESTs in oil palm versus date palm for each lipid category (calculated per enzyme to account for different number of enzymes per pathway). (B) Temporal profile of ESTs for lipid categories in developing mesocarp of oil palm. See Dataset S2A for the list of genes included in each category. Pt, plastid; TAG, triacylglycerol; ExPL, extraplastidial polar lipids; PL, polar lipids; Mt, mitochondria; SphL, sphingolipids; β-ox, β-oxidation.

Fig. 3.

Transcript patterns for enzymes involved in plastidial and extraplastidial reactions of oil synthesis differ greatly. Values in red indicate the ratio of oil palm to date palm ESTs, calculated as the ratio of sum of ESTs for five stages. Values in green indicate fold increase in ESTs during oil palm ripening, which are calculated as ratio of ESTs at 23 versus 15 WAP. Ratios ≥ twofold and significant at P value < 0.05 are indicated in boldface type. ESTs for enzymes with multiple subunits or isoforms were summed. For details on abbreviations, annotations, and EST levels at each stage, see Dataset S2A. 16:0, palmitic acid; 18:0, stearic acid; 18:1, oleic acid.

Fig. 4.

Temporal pattern of EST levels for palm orthologs of Wrinkled1 (WRI1) (At3g54320) and select enzymes that are known to be WRI1-regulated (+) or not (−). pPK, plastid pyruvate kinase (At5g52920); PDH-α, pyruvate dehydrogenase (At1g01090); BCCP1, biotin carboxyl carrier protein1 (At5g16390); ENR, enoyl-ACP reductase (At2g05990); HXK2, hexokinase (At2g19860).

Fig. 5.

Transcript patterns for enzymes involved in generating pyruvate from sucrose. Values in red indicate the ratio of oil palm to date palm ESTs, calculated as the ratio of sum of ESTs for five stages. Values in green indicate temporal changes during oil palm ripening, which is calculated as the ratio of ESTs at 23 versus 15 WAP. Ratios ≥ twofold significance at P value < 0.05 are indicated in boldface type. ESTs for enzymes with multiple subunits or isoforms were summed. For details on abbreviations, annotations, and EST levels at each stage, see Dataset S2B.

Fig. 6.

Plastid glycolytic enzymes and transporters. (A) Average EST levels for select plastidial glycolytic enzymes and (B) plastid transporters and (C) temporal profile of glucose-6-phosphate transporter (GPT2) expression in five stages of oil palm and date palm mesocarp. For details on EST levels for cytosolic enzymes, abbreviations, annotations, and EST levels for each stage, see Dataset S2B.