A customized cDNA chip analysis provided the relative expression profiling of 1439 ESTs of Chaetoceros neogracile in culture environments maintained between 4 and 10 degrees C. Among the 1439 probes, 21.5% were differentially regulated (>= 2-fold) by the temperature upshift within three days. Up-regulation was more prominent among cytoprotective genes, whereas down-regulation was featured in photosynthetic genes. A third of the differentially expressed genes had an unknown function or no similarity to known genes, highlighting their potential importance as a resource to identify key players in the acclimation response of polar algae under thermal stress. Our transcriptome analysis also revealed novel aspects of temperature-responsive, coordinated changes in the abundance of specific mRNAs, along with the rapid establishment of molecular homeostasis in polar algae. Unexpectedly, a small set of genes encoding fucoxanthin chlorophyll a/c-binding proteins were rapidly up-regulated by thermal stress, implying that they have different roles other than light harvesting. (C) 2007 Elsevier Inc. All rights reserved.