Serial analysis of gene expression in sugarcane (Saccharum spp.) leaves revealed alternative C4 metabolism and putative antisense transcripts

Abstract

Sugarcane (Saccharum spp.) is a highly efficient biomass and sugar producing crop. Leaf reactions have been considered as potential rate-limiting step for sucrose accumulation in sugarcane stalks. To characterize the sugarcane leaf transcriptome, field-grown mature leaves from cultivar "SP80-3280" were analyzed using Serial Analysis of Gene Expression (SAGE). From 480 sequenced clones, 9,482 valid tags were extracted, with 5,227 unique sequences, from which 3,659 (70%) matched at least a sugarcane assembled sequence (SAS) with putative function; while 872 tags (16.7%) matched SAS with unknown function; 523 (10%) matched SAS without a putative annotation; and only 173 (3.3%) did not match any sugarcane ESTs. Based on gene ontology (GO), photosystem (PS) I reaction center was identified as the most frequent gene product location, followed by the remaining sites of PS I, PS II and thylakoid complexes. For metabolic processes, photosynthesis light harvesting complexes; carbon fixation; and chlorophyll biosynthesis were the most enriched GO-terms. Considering the alternative photosynthetic C(4) cycles, tag frequencies related to phosphoenolpyruvate carboxykinase (PEPCK) and aspartate aminotransferase compared to those for NADP(+)-malic enzyme (NADP-ME) and NADP-malate dehydrogenase, suggested that PEPCK-type decarboxylation appeared to predominate over NADP-ME in mature leaves, although both may occur, opposite to currently assumed in sugarcane. From the unique tag set, 894 tags (17.1%) were assigned as potentially derived from antisense transcripts, while 73 tags (1.4%) were assigned to more than one SAS, suggesting the occurrence of alternative processing. The occurrence of antisense was validated by quantitative reverse transcription amplification. Sugarcane leaf transcriptome provided new insights for functional studies associated with sucrose synthesis and accumulation.

C4 Cycles: Past, Present, and Future Research on C4 Photosynthesis

“…These include proteome comparisons between isolated BS and M cell chloroplasts (Majeran et al, 2005;Friso et al, 2010), microarray analysis of BS and M cell transcriptomes (Sawers et al, 2007), transcriptome profiling of mature sugarcane leaves (Calsa and Figueira, 2007), transcriptome and proteome profiling in a single-cell C 4 species (Park et al, 2010) and across a developmental gradient in the maize leaf (Li et al, 2010a;Majeran et al, 2010), comparative transcriptomics between closely related C 4 and C 3 species , and genome-scale models of flux distribution between BS and M cells (Dal'Molin et al, 2010). All of these studies have generated a substantial amount of data, and more is on the way.…”

Identification of Suitable Internal Control Genes for Quantitative Real-Time PCR Expression Analyses in Peanut (Arachis hypogaea)

“…Significantly different Student's t-test groups are indicated as well. with the reduction of NAD+ to NADH, and also plays an important role in lowering the toxicity of the cell (Yokoyama and Harry, 1993 (Calsa et al, 2007). Yls8 encodes for the mitosis protein YLS8.…”

Biological Activity of Essential Oils from Leaves and Fruits of Pepper Tree (Schinus molle L.) to Control Rice Weevil (Sitophilus oryzae L.)

“…On the other hand, with open systems there is no need for previous knowledge of the genome or transcriptome of the organism. cDNA-AFLP (cDNA-Amplified fragment length polymorphism), MPSS (massively parallel signature sequencing), and specially SAGE (serial analysis of gene expression) have been successfully used to quantify transcript abundance and generate expression data across different tissue types or developmental stages in higher plants ( Fizames ( Fizames et al, 2004;Meyers et al, 2004;Calsa and Figueira, 2007;Chen et al, 2007;Leymarie et al, 2007;McIntosh et al, 2007;Song et al, 2007;Ritter et al, 2008). �orth mentioning are 454-sequencing .…”