An EST survey of the sugarcane transcriptome

Abstract

Its large genome and high polyploidy makes sugarcane (Saccharum spp.) a singularly challenging crop to study and improve using genetic approaches. To provide large numbers of functionally characterized candidate genes that might be tested for direct association (rather than distant linkage) with economically important traits, we sequenced the 5' ends of 9,216 clones from three cDNA libraries (apex, leaf and mature internode), representing 3,401 non-redundant sequences. About 57% of these sequences could be assigned a tentative function based on statistically significant similarity to previously characterized proteins or DNA sequences. Another 28% corresponded to previously identified, but uncharacterized, sequences. Some of the remaining unidentified sequences were predicted to be genes which could potentially be new to plants or unique to sugarcane. Comparisons of the sugarcane ESTs to a large sorghum EST database revealed similar compositions of expressed genes between some different tissues. Comparison to a detailed Arabidopsis protein database showed some highly conserved sequences, which might be useful DNA markers for pan-angiosperm comparative mapping. These EST sequences provide a foundation for many new studies to accelerate isolation of agronomically important genes from the cumbersome sugarcane genome.

Sugarcane Genetics and Genomics

“…Research groups in Brazil (Vettore et al 2003), the United States (Ma et al 2004), South Africa (Carson & Botha 2000, and Australia (Casu et al 2001;Casu et al 2003;Bower et al 2005) have developed multiple sugarcane EST databases with a combined total of over 300,000 ESTs. From the Brazil sugarcane EST (SUCEST) database, 42,982 sugarcane aligned sequences (SASs) were comparatively analyzed against protein and DNA sequences from Arabidopsis and rice.…”

“…Compared with different cDNA libraries, 1,234 of the 43,141 SUCEST SASs were suggested to be tissue-specific (Arruda 2001;Vettore et al 2003). The EST analysis for gene expression in source tissues showed genes for cell wall biosynthesis were mainly enzymes involved either in the xyloglucan network or in lignin biosynthesis and were highly expressed in the culm internode (Ma et al 2004).…”

Transcriptomics of Sugarcane Osmoprotectants Under Drought

“…This project regards a large consortium of Brazilian researchers who sequenced approximately 238,000 redundant ESTs from 26 diverse cDNA libraries (Vettore et al, 2001), representing the largest effort to generate information using new technologies for this species. This endeavor brought a broader panel when compared to previous available ESTs produced by other consortia in countries like Australia (Casu et al, 2003(Casu et al, , 2004Bower et al, 2005) and the US (Ma et al, 2004).…”

Analysis of genes controlling biomass traits in the genome of sugarcane (Saccharum spp. hybrids)

“…These sequences were assembled into 42,982 sugarcane assembled sequences representing more than 30,000 unique genes (~90% of the estimated genes of S. officinarum) (Vettore et al, 2003, Hotta et al, 2010, GRASSIUS: Grass Regulatory Information Server, 2015. There are other sugarcane ESTs collections containing fewer EST entries generated in Casu et al (2003) and Casu et al (2004) (8,342 ESTs), in Ma et al (2004) (7,993 ESTs), in Gupta et al (2010) (~35,000 ESTs), and a small number of ESTs in Carson and Botha (2002a) and Carson and Botha (2000).…”