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.
Xu
Ke
K
College of Mathematics and Information Science, Shandong University of Technology, Zibo, PR China.
Ma
Bin-Guang
BG
D001105:Archaea / Q000235:genetics / Q000302:isolation & purification; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D001482:Base Composition; D019641:DNA, Archaeal / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D015870:Gene Expression; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D006874:Hydrostatic Pressure; D008386:Marine Biology; D013045:Species Specificity
D019641:DNA, Archaeal; D004269:DNA, Bacterial