Despite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most of the sugarcane transcriptomic studies have been based on Saccharum officinarum gene indices (SoGI), expressed sequence tags (ESTs) and de novo assembled transcript contigs from short-reads; hence knowledge of the sugarcane transcriptome is limited in relation to transcript length and number of transcript isoforms. The sugarcane transcriptome was sequenced using PacBio isoform sequencing (Iso-Seq) of a pooled RNA sample derived from leaf, internode and root tissues, of different developmental stages, from 22 varieties, to explore the potential for capturing full-length transcript isoforms. A total of 107,598 unique transcript isoforms were obtained, representing about 71% of the total number of predicted sugarcane genes. The majority of this dataset (92%) matched the plant protein database, while just over 2% was novel transcripts, and over 2% was putative long non-coding RNAs. About 56% and 23% of total sequences were annotated against the gene ontology and KEGG pathway databases, respectively. Comparison with de novo contigs from Illumina RNA-Sequencing (RNA-Seq) of the internode samples from the same experiment and public databases showed that the Iso-Seq method recovered more full-length transcript isoforms, had a higher N50 and average length of largest 1,000 proteins; whereas a greater representation of the gene content and RNA diversity was captured in RNA-Seq. Only 62% of PacBio transcript isoforms matched 67% of de novo contigs, while the non-matched proportions were attributed to the inclusion of leaf/root tissues and the normalization in PacBio, and the representation of more gene content and RNA classes in the de novo assembly, respectively. About 69% of PacBio transcript isoforms and 41% of de novo contigs aligned with the sorghum genome, indicating the high conservation of orthologs in the genic regions of the two genomes. The transcriptome dataset should contribute to improved sugarcane gene models and sugarcane protein predictions; and will serve as a reference database for analysis of transcript expression in sugarcane.

Productivity of sugarcane (Saccharum spp.) relies upon sucrose production in leaves and movement to sinks. The feedback regulatory effect of sugar upon photosynthesis balances this process involving Phosphoenolpyruvate carboxylase (PEPCase) and Rubisco where greater understanding in this area may allow manipulation to achieve higher yields. Accumulation of sucrose in leaves and decreased photosynthesis are early symptoms of the condition called yellow canopy syndrome (YCS) in sugarcane, which presents as a system in which to study sucrose feedback regulation. This work investigates changes in gene expression and protein abundance which coincide with the sugar accumulation in the leaves of YCS symptomatic sugarcane. During the early-stage of sugar accumulation, the levels of the Photosystem II core protein D1, and PsbQ of the oxygen-evolving complex decreased significantly. Transcript levels of these proteins also decreased, suggesting both nuclear and chloroplast gene expression were affected early in sugar build-up of YCS development. Transcript level of primary carbon fixation reactions enzyme NADP malate dehydrogenase was especially downregulated. However, PEPCase, decarboxylation and re-fixation (Rubisco) enzymes were not negatively regulated at the transcript or protein abundance level. Phosphoenolpyruvate carboxykinase was upregulated in both gene expression and protein abundance. The Calvin cycle in the bundle sheath was sensitive through the CP12 protein. Two isoforms of CP12 were found, one of which showed downregulation which coincided with a decrease in CP12 protein. This suggests transcript and protein decrease of PEPCase and Rubisco may be secondary regulation points of the sugar feedback regulation process upon photosynthesis in sugarcane leaves.

Background: The composition of biomass determines its suitability for different applications within a biorefinery system. The proportion of the major biomass fractions (sugar, cellulose, hemicellulose and lignin) may vary in different sugarcane genotypes and growth environments and different parts of the plant. This study investigated the composition of mature and immature internodes, roots and mature leaves of sugarcane. Results: Internodes were found to have a significantly larger alcohol-soluble component than leaves and roots. The primary difference between the immature and mature internodes was the ratio of soluble sugars. In mature tissues, sucrose content was significantly higher, whereas in immature internodal tissues there was lower sucrose and heightened concentrations of reducing sugars. Carbon (C) partitioning in leaf tissues was characterised by low levels of soluble components and high “other” and cell wall fractions. Root tissue had low ratios of soluble fractions relative to their cell wall contents, indicating a lack of storage of soluble carbon. There was no significant difference in the ratio of the major cell wall fractions between the major organ types. Characterisation of individual non-cellulosic monomers indicated leaf and root tissues had significantly higher arabinose and galactose fractions. Significantly larger proportions of syringyl lignin compounds and the hydroxycinnamic compound, p-coumaric acid were observed in mature internodal tissues compared to the other tissue types. Tissue-specific differences in composition were shown to greatly affect the recalcitrance of the cell wall to enzymatic saccharification. Conclusions: Overall, this study displayed clear evidence of the differential partitioning of C throughout the sugarcane plant in specific organs. These organ-specific differences have major implications in their utility as a bioproduct feedstock. For example, the inclusion of trash (leaves) with the culms (internodes) may alter processing efficiency.

The relationship between metabolic changes occurring in the developing internodes of sugarcane and the final yield and sugar characteristics is poorly understood due to the lack of integration between phenotypic and metabolic data. To address this issue, a study was conducted where sugarcane metabolism was modeled based on the measurement of cellular components in the top internodes, at two stages of crop development. The study also looked at the effects of Trinexapac-ethyl (Moddus^®) on growth inhibition. The metabolome was measured using GC-analysis, while LC-MS/MS was used to measure proteome changes in the developing internodes. These data were then integrated with the metabolic rates. Regardless of the growth rate, internode elongation was restricted to the top five internodes. In contrast, sucrose and lignin accumulation was sensitive to the growth rate. Crossover plots showed that sucrose accumulation only occurred once the cell wall synthesis had slowed down. These data suggest that sucrose accumulation controlled a reduction in sucrose breakdown for metabolic activity and a reduction in demand for carbon for cell wall polysaccharide synthesis. This study also found that nucleotide sugar metabolism appears to be a key regulator in regulating carbon flow during internode development.

Photosynthesis, stomatal conductance, electron transport, internal CO2 and sugar levels were determined in the leaves of Yellow Canopy Syndrome (YCS) symptomatic sugarcane (Saccharum spp.) plants. Two varieties from two different geographic regions in Australia, KQ228 and Q200 were used. Although visual yellowing was only evident in the lower leaves of the canopy (older than Leaf 5), photosynthesis and stomatal conductance were lower in both the yellowing leaves and those not yet showing any visible symptoms. On a canopy basis, photosynthesis was reduced by 14% and 36% in YCS symptomatic KQ228 and Q200 plants, respectively. Sucrose levels increased significantly in the leaves, reflecting some of the earliest changes induced in YCS symptomatic plants. The electron transport characteristics of dark-adapted leaves showed disruptions on both the electron acceptor and donor side of PSII. Some of these changes are characteristic of a degree of disruption to the protein structure associated with the electron transport chain. Based on the results, we propose that the first change in metabolism in the YCS symptomatic plants was an increase in sucrose in the leaves and that all the other changes are secondary effects modulated by the increased sugar levels.

Sugarcane growth and its subsequent yield are linked to plant height. The increase in sugarcane height is controlled by elongation of the top 6 to 7 internodes. The elongation of the internodes can be significantly reduced by an application of the Trinexapac-ethyl (Moddus®) which is a known disruptor of GA synthesis. In this study, the growth and composition of the internodes were analysed following the treatment. We found that the strong inhibitory effect of Moddus® on internode size was due to a strongly suppressed rate of internode elongation, with no effect on the duration of the elongation period. The Moddus® inhibition of internode elongation was not due to a lack of an osmotic potential gradient but probably reflects a higher pressure potential of the tissue. A consequence of the reduced internode size was a significant reduction in carbon flow (sink strength) of the internode. It was not only the rate of internode growth that was altered by Moddus®, but also partitioning within the internode. Partitioning of carbon into components other than the soluble sugars and cell wall was significantly reduced by the Moddus® treatment. The high reducing sugar content in the Moddus® treatment suggests that sucrose mobilisation (hydrolysis by invertases and cleavage by sucrose synthase) might, like the duration of elongation, be controlled by thermal time. No accumulation of reducing sugars was evident in the control internodes probably due to the rapid mobilisation to other cellular processes. Sucrose accumulation in the internode reflected a cessation of sugar utilisation to support growth and maintenance.