In silico evaluation of the Eucalyptus transcriptome

Abstract

The expressed sequence tags (ESTs) produced in the Forests project provide an invaluable opportunity to assess the Eucalyptus transcriptome. Besides providing information on the different proteins produced by this plant, it is possible to infer gene expression profiles because non-normalized cDNA libraries were used. The EST frequency from any gene is correlated to the transcript levels in the tissues from which the cDNA libraries were constructed. The goal of this work was to identify Eucalyptus genes that showed either differential expression pattern or were ubiquitously expressed in the tissues sampled in the Forests project. Six robust statistical tests and very restrictive rules were applied to gain confidence in the in silico data aiming to avoid false positives. Several genes with interesting expression profiles were identified and some of them were validated by RT-PCR.

Validation of housekeeping genes for gene expression studies in an ice alga Chlamydomonas during freezing acclimation

“…ICE-L. This observation corroborates the quantification of GAPDH expression in Coffea Arabica (BarsalobresCavallari et al 2009), sugarcane (Iskandar et al 2004) and Eucalyptus (Vicentini et al 2005). Czechowski et al (2005) compared traditional and novel reference genes in Arabidopsis and found that GAPDH was ranked among the 100 most stably expressed genes after omission of seed and pollen samples.…”

Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus

“…Several different platforms were employed, e.g., microarrays (Barros et al 2009;Solomon et al 2010), in silico analysis of EST databases (Vicentini et al 2005), sequencing of cDNA libraries on next-generation sequencers (Külheim 2010), serial analysis of gene expression (De Carvalho et al 2008;Moon et al 2007) and cDNA-amplified fragment length polymorphism (Ranik et al 2006). Several of these studies aimed at providing candidate genes to be tested in association genetics experiments (see Section "Gene discovery and association genetics").…”

Eucalyptus applied genomics: from gene sequences to breeding tools

“…that were later annotated and used in expression QTL studies (Kirst et al ., 2004). Other mostly private EST databases for Eucalyptus were built between 2002 and 2004 in the Genolyptus project (Grattapaglia, 2004; Grattapaglia et al ., 2004b) and the ForEST project (Vicentini et al ., 2005) in Brazil and in Japan (S. Sato, unpublished). The different species planted around the world and the hybrid breeding system adopted in Eucalyptus have driven a distinctive multi‐species approach to EST sequencing efforts.…”