The libraries that made SUCEST

Vettore, André Luiz; Silva, Felipe Rodrigues da; Kemper, Edson L.; Arruda, Paulo

doi:10.1590/s1415-47572001000100002

Cited by 186 publications

(167 citation statements)

References 14 publications

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“…4). Interestingly, the library HR1 (Vettore et al, 2001) accounted for most of the cold-inducible ESTs. This library was constructed from bacteriuminfected sugarcane tissues (Vettore et al, 2001) and could be a good source for the discovery of biotic and abiotic stress-related genes.…”

Section: Identification and Functional Classification Of Coldresponsimentioning

confidence: 99%

“…Sixteen 96-well plates containing EST plasmid clones were randomly sampled from the following sugarcane cDNA libraries: heat-and coldtreated and untreated callus (CL6), sugarcane plantlets infected with H. rubrisubalbicans (HR1) or A. diazotroficans (AD1), and leaf row tissue (LR1; Vettore et al, 2001). The plasmid DNA was denatured in 0.2 n NaOH for 15 min at 37°C and then spotted onto Hybond-N filters (Amersham Biosciences, Piscataway, NJ) with a hand-held 96-pin printhead tool (V&P Scientific, San Diego, CA).…”

Section: High-density Filter Arrays and Probe Preparationmentioning

confidence: 99%

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RNA Expression Profiles and Data Mining of Sugarcane Response to Low Temperature

et al. 2003

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Tropical and subtropical plants are generally sensitive to cold and can show appreciable variation in their response to cold stress when exposed to low positive temperatures. Using nylon filter arrays, we analyzed the expression profile of 1,536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp. cv SP80-3280) exposed to cold for 3 to 48 h. Thirty-four cold-inducible ESTs were identified, of which 20 were novel cold-responsive genes that had not previously been reported as being cold inducible, including cellulose synthase, ABI3-interacting protein 2, a negative transcription regulator, phosphate transporter, and others, as well as several unknown genes. In addition, 25 ESTs were identified as being down-regulated during cold exposure. Using a database of cold-regulated proteins reported for other plants, we searched for homologs in the sugarcane EST project database (SUCEST), which contains 263,000 ESTs. Thirty-three homologous putative coldregulated proteins were identified in the SUCEST database. On the basis of the expression profiles of the cold-inducible genes and the data-mining results, we propose a molecular model for the sugarcane response to low temperature.

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Section: Identification and Functional Classification Of Coldresponsimentioning

confidence: 99%

Section: High-density Filter Arrays and Probe Preparationmentioning

confidence: 99%

RNA Expression Profiles and Data Mining of Sugarcane Response to Low Temperature

et al. 2003

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“…The SUCEST database contains sugarcane cDNA partial sequences of 37 libraries from different tissues, physiological and stressed conditions (Vettore et al, 2001). Sequence comparisons against GenBank were available for keyword searching .…”

Section: Sucest Ests Database Screeningmentioning

confidence: 99%

Survey of transposable elements in sugarcane expressed sequence tags (ESTs)

Rossi¹,

Araujo²,

Sluys³

2001

Genet. Mol. Biol.

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The sugarcane expressed sequence tag (SUCEST) project has produced a large number of cDNA sequences from several plant tissues submitted or not to different conditions of stress. In this paper we report the result of a search for transposable elements (TEs) revealing a surprising amount of expressed TEs homologues. Of the 260,781 sequences grouped in 81,223 fragment assembly program (Phrap) clusters, a total of 276 clones showed homology to previously reported TEs using a stringent cut-off value of e-50 or better. Homologous clones to Copia/Ty1 and Gypsy/Ty3 groups of long terminal repeat (LTR) retrotransposons were found but no non-LTR retroelements were identified. All major transposon families were represented in sugarcane including Activator (Ac), Mutator (MuDR), Suppressor-mutator (En/Spm) and Mariner. In order to compare the TE diversity in grasses genomes, we carried out a search for TEs described in sugarcane related species O.sativa, Z. mays and S. bicolor. We also present preliminary results showing the potential use of TEs insertion pattern polymorphism as molecular markers for cultivar identification.

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“…A basic local alignment search tool TBLASTN search (protein sequence against 6-frame nucleotide translated database sequences) was carried out against 81,223 consensi from the fragment assembly program (phrap, Altschul et al, 1997) clustering of 260,781 ESTs (reference: ) contained in the SUCEST database which were sequenced mostly from the 5' end and derived from 37 cDNA libraries constructed from distinct sugarcane tissues grown under different conditions (Vettore et al, 2001). The EST reads were generated by a consortium of laboratories and deposited and managed at the bioinformatics laboratory at the university of Campinas .…”

Section: Methodsmentioning

confidence: 99%

Sugarcane genes related to mitochondrial function

et al. 2001

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Mitochondria function as metabolic powerhouses by generating energy through oxidative phosphorylation and have become the focus of renewed interest due to progress in understanding the subtleties of their biogenesis and the discovery of the important roles which these organelles play in senescence, cell death and the assembly of iron-sulfur (Fe/S) centers. Using proteins from the yeast Saccharomyces cerevisiae, Homo sapiens and Arabidopsis thaliana we searched the sugarcane expressed sequence tag (SUCEST) database for the presence of expressed sequence tags (ESTs) with similarity to nuclear genes related to mitochondrial functions. Starting with 869 protein sequences, we searched for sugarcane EST counterparts to these proteins using the basic local alignment search tool TBLASTN similarity searching program run against 260,781 sugarcane ESTs contained in 81,223 clusters. We were able to recover 367 clusters likely to represent sugarcane orthologues of the corresponding genes from S. cerevisiae, H. sapiens and A. thaliana with E-value ≤ 10 -10 . Gene products belonging to all functional categories related to mitochondrial functions were found and this allowed us to produce an overview of the nuclear genes required for sugarcane mitochondrial biogenesis and function as well as providing a starting point for detailed analysis of sugarcane gene structure and physiology.

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The libraries that made SUCEST

Cited by 186 publications

References 14 publications

RNA Expression Profiles and Data Mining of Sugarcane Response to Low Temperature

RNA Expression Profiles and Data Mining of Sugarcane Response to Low Temperature

Survey of transposable elements in sugarcane expressed sequence tags (ESTs)

Sugarcane genes related to mitochondrial function

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