Dissecting the sugarcane expressed sequence tag (SUCEST) database: unraveling flower-specific genes

Abstract

There are almost 260,000 independent clones sequenced from the 5' end in the Sugarcane Expressed Sequence Tag (SUCEST) database, which have been obtained from 37 cDNA libraries prepared from different tissues. This large number of expressed sequence tags (ESTs) provides an opportunity, unprecedented in plants, to perform 'digital differential screening' on selected cDNA libraries. In general, the frequency of a particular EST correlates with transcript accumulation in the tissues from which the cDNA libraries were constructed, so it is possible to compare the whole transcriptome from different tissues using computer-assisted analysis of an EST database. In our research we analyzed sugarcane ESTs according to tissue expression and identified more than 1,000 putative flower-specific genes. The fact that using this technique we were able to identify sugarcane homologues of several genes previously described as pollen-specific justifies this method of assessing tissue specificity. In addition, ESTs similar to genes specific to reproductive organs were detected e.g. a sugarcane gene encoding a meiotic protein essential for assembly of the synaptonemal complex and normal synapsis. This approach also allowed the identification of many flower-specific anonymous sequences that are good candidates for being novel genes involved in plant reproduction. This paper describes the analysis of the gene expression levels of 24 EST clusters during flower development using a 'digital northern blot' constructed from direct EST counts made on the non-normalized sugarcane cDNA libraries.

In silico evaluation of the Eucalyptus transcriptome

“…A striking difference was observed for FB1 library, corresponding to flowers, flower buds and fruits, which had the highest number of differentially expressed genes. The presence of a high number of genes preferentially expressed in flower tissues was also observed in silico in sugarcane (Figueiredo et al, 2001), indicating that this organ has special features that require a wide range of protein functions.…”

In silico prediction of gene expression patterns in Citrus flavedo

“…Together with the 10,429 singletons, we conclude that 13,281 expressed sequences are exclusive from flavedo and could be considered as candidates to flavedo-specific genes. Indeed, in silico EST sequence analysis has been used to identify tissue-specific genes in diverse plant species (Figueiredo et al, 2001;Dornelas and Rodriguez, 2004;Hecht et al, 2005;Laitinen et al, 2005;. When ESTs are generated from nonnormalized cDNA libraries, gene expression patterns normally can be inferred from the relative abundance of these sequences among different libraries (Ewing et al, 1999) and the indication of tissue-specific sequences is based on a simplified rule.…”

A proposed model for the flowering signaling pathway of sugarcane under photoperiodic control

“…The Sugarcane EST project (Figueiredo et al, 2001), SUCEST, encompasses a collection of 240,000 ESTs generated from 26 cDNA libraries constructed from different organs and/or tissues at different developmental stages, including apical meristem, flowers, leaf roll, seeds, internode, stem bark, etiolated leaves, and lateral buds (Vettore et al, 2001).…”