Comparative analysis of predicted gene expression among deep-sea genomes

Deep-sea species live in an environment that is specifically characterized by extreme temperature and hydrostatic pressure. In this work, predicted highly expressed (PHX) genes are comparatively analyzed for six deep-sea microbes, which allows us to pinpoint the common highly expressed genes shared by them. The relationships between gene expression level and some basic properties such as genomic G + C content, optimal growth temperature (OGT), and environmental hydrostatic pressure of the six deep-sea species are also investigated. We find that the percentage of PHX genes out of a whole genome positively correlates to OGT for the deep-sea genomes, whereas such positive correlation seems not to exist between environmental hydrostatic pressure and percentage of PHX genes. Moreover, there exists a negative correlation between genomic G + C content and diversity of gene expression level for the deep-sea genomes, which is in sharp contrast to land-living microbes. We report the top 20 PHX genes for the six deep-sea genomes and find no common highly expressed genes shared by them except for ribosomal proteins, transcription factors, and translation factors. Our present work proffers a paradigm for studying the relationship between environmental factors and microbes' predicted gene expression level. (C) 2007 Elsevier B.V. All rights reserved.