In silico analysis of Eucalyptus thioredoxins

ABSTRACT

The Eucalyptus Genome Sequencing Project (FORESTs), an initiative from the Brazilian ONSA consortium (Organization for Nucleotide Sequencing and Analysis), has achieved the sequencing of 123.889 EST clones from 18 different cDNA libraries. We have investigated the FORESTs data set to identify EST clusters potentially encoding thioredoxins (TRX). Two types of thioredoxin families described in plants, chloroplastic (TRXm/f/x/y) and cytosolic (TRXh), have been found in the transcriptome. Putative typical TRXs have been identified in fifteen clusters, four m-type, seven h-type, two f-type, one cluster for each x/y-types and one putative homologue of the TDX gene from Arabidopsis thaliana. One cluster presents an atypical active site WCMPS, different from the conserved WCGPC present in the other 15 clusters, and corresponds to a subgroup of cytosolic thioredoxins. Except in specific libraries from callus, roots, seedlings and wood tissues, thioredoxin deduced ESTs are found in all remaining libraries. According to the calculated frequencies of ESTs, chloroplastic thioredoxins are preferentially present in green tissues such as leaves whilst cytoplasmic thioredoxins are more general but demonstrate elevated frequencies in seedlings and flower tissues. TRX frequency patterns in the Eucalyptus transcriptome seem to indicate a good coherence with data from Arabidopsis thaliana gene expression