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.

Differential expression analysis of transcripts related to oil metabolism in maturing seeds of Jatropha curcas L.

“…Since seed oil metabolism is not restricted to the embryo or cotyledonous tissue and is intricately linked to the developmental and metabolic states of other tissues in seeds (Bourgis et al 2011), we used whole seeds belonging to two mid maturation stages for cDNA subtraction and early and mid-to-late maturation stages to monitor changes in transcript expression. A large number of ESTs were sequenced to obtain a good representation of differential transcripts, since the original library that contained about 2,000 clones was stored as plasmid pools and later used for retransformation to isolate individual clones.…”

A comparative transcriptomic approach to understanding the formation of cork

“…Gene expression differences between cork and holm oak contigs with at least 10 mapped reads were statistically analysed, as has previously been done by Bourgis et al (2011), with DEGseq software using the MA-plot-based random sampling model (Wang et al 2009). To consider transcripts as differentially expressed (DE), we established a two-fold cut-off: log 2 fold-change (FC) (−1 ≤ log 2 FC ≥ 1) and statistical significance of q-value < 0.05 (p-value corrected for false discovery rate (Benjamini and Hochberg 1995)).…”

Quantitative trait loci (QTLs) analysis of palm oil fatty acid composition in an interspecific pseudo-backcross from Elaeis oleifera (H.B.K.) Cortés and oil palm (Elaeis guineensis Jacq.)

“…cDNA sequences of these genes were identified from eight Elaeis full-length cDNA libraries of pulp (unpublished) previously made from developing fruits between 60-75 and 150-180 days after pollination. E. guineensis sequences of these genes are available from Bourgis et al (2011) at http://www.biomemb. cnrs.fr/contigs.html in file oil-contigs.doc (Table 4).…”

“…We used the Blast2GO pipeline (Götz et al 2008) to annotate the contigs with the Gene Ontology terms based on our BLAST results. Also, a BLAST analysis was performed with the E. guineensis cDNA libraries of Bourgis et al (2011) and Tranbarger et al (2011). We used the Prot4EST pipeline (Wasmuth and Blaxter 2004) to obtain a protein prediction from our contig sequences.…”

“…More recently, AlShanfari et al (2011) constructed a suppression subtractive hybridization (SSH) library to identify genes involved in fruit ripening in E. guineensis. Bourgis et al (2011) and Tranbarger et al (2011) notably analyzed the gene expression and regulatory mechanisms underlying the fatty acid biosynthesis during the oil palm fruit mesocarp maturation and ripening. Singh et al (2009) identified quantitative trait loci (QTLs) for fatty acid composition using 81 individuals of an Elaeis interspecific cross.…”