Data from: Diurnal transcriptional regulation of endosymbiotically derived genes in the chlorarachniophyte Bigelowiella natans

Chlorarachniophyte algae possess complex plastids acquired by the
secondary endosymbiosis of a green alga, and the plastids harbor a relict
nucleus of the endosymbiont, the so-called nucleomorph. Due to massive
gene transfer from the endosymbiont to the host, many proteins involved in
plastid and nucleomorph are encoded by the nuclear genome. Genome
sequences have provided a blueprint for the fate of endosymbiotically
derived genes; however, transcriptional regulation of these genes remains
poorly understood. To gain insight into the evolution of endosymbiotic
genes, we performed genome-wide transcript profiling along the cell cycle
of the chlorarachniophyte Bigelowiella natans, synchronized by light and
dark cycles. Our comparative analyses demonstrated that transcript levels
of 7,751 nuclear genes (35.7% of 21,706 genes) significantly oscillated
along the diurnal/cell cycles, and those included 780 and 147 genes for
putative plastid and nucleomorph-targeted proteins, respectively.
Clustering analysis of those genes revealed the existence of
transcriptional networks related to specific biological processes such as
photosynthesis, carbon metabolism, translation, and DNA replication.
Interestingly, transcripts of many plastid-targeted proteins in B. natans
were induced before dawn, unlike other photosynthetic organisms. In
contrast to nuclear genes, 99% nucleomorph genes were found to be
constitutively expressed during the cycles. We also found that the
nucleomorph DNA replication would be controlled by a nucleus-encoded
viral-like DNA polymerase. The results of this study suggest that
nucleomorph genes have lost transcriptional regulation along the diurnal
cycles, and nuclear genes exert control over the complex plastid including
the nucleomorph.