Table 1.
Primers used in this study.
Figure 1.
Phylogenetic tree inferred from rhodopsin amino acid sequences.
Shown at nodes are bootstrap values from Neighbor-Joining (left), SH-like value of maximum likelihood (medium) and Bayesian analysis (right); only values ≥70%/0.7 at critical nodes are shown. The thickest branches denote bootstrap values of>90%, medium-thick branches values of 70 to 90%, and thin branches values of <70%. The scale bar indicates the substitutions rate per nucleotide. Tree is rooted with Plecoglossus altivelis. The two major types, the proton-pumping (PR) and the sensory type (SR), are indicated on the far right while subgroups within PR are shown next. Pie slices indicate the relative transcript abundances of the two major types (with subtypes within each type combined) in terms of the percentage of reads. Asterisks depict sequences obtained in this study that were either new or matched previously reported sequences (accession numbers indicated).
Figure 2.
Growth curve (A), cell volume (B), prey 18S rRNA percentage (C), cellular total RNA content (D) of starved O. marina.
RT-qPCR was carried out to quantify the 18S rRNA level of both O. marina and D. tertiolecta in the cDNA libraries from both conditions. Y-axis in (C) indicates the ratio of prey 18S rRNA and O. marina 18S rRNA. LD, cultures grown under light: dark cycle; DD, cultures grown under continuous darkness; error bars, standard deviation. Significant differences between LD and DD groups were marked with “*”. Arrow in the figure denotes time when food was supplied.
Figure 3.
Expression levels of rhodopsin genes as normalized to 18S rRNA cDNA.
LD, cultures grown under light: dark cycle; DD, cultures grown under continuous darkness; error bars, standard deviation. (A) PR; (B) SR1; (C) SR2; (D) SR3. Significant differences between LD and DD groups were marked with “*”.
Figure 4.
Expression levels of rhodopsin genes as normalized to cox1 cDNA.
LD, cultures grown under light: dark cycle; DD, cultures grown under continuous darkness; error bars, standard deviation. (A) PR; (B) SR1; (C) SR2; (D) SR3. Significant differences between LD and DD groups were marked with “*”.
Figure 5.
Ratio of expression levels between proton-pump rhodopsin (PR) and sensory rhodopsins (SR1, SR2 and SR3).
LD, cultures grown under light: dark cycle; DD, cultures grown under continuous darkness; error bars, standard deviation. (A) PR/SR1; (B) PR/SR2; (C) PR/SR3. Significant differences between LD and DD groups were marked with “*”.