Supplementary Information for Diel transcriptional oscillations of light-sensitive regulatory elements in open ocean eukaryotic plankton communities Sacha N. Coesel1*, Bryndan P. Durham2, Ryan D. Groussman1, Sarah K. Hu3, David A. Caron4, Rhonda L. Morales1, François Ribalet1, and E. Virginia Armbrust1. 1School of Oceanography, University of Washington, Seattle, Washington 98195, USA. 2Department of Biology, Genetics Institute, University of Florida, Gainesville, Florida 32610, USA 3Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA 4Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, USA *Sacha N. Coesel Email: [email protected] This PDF file includes: Figures S1 to S10 Table S1 Legends for Datasets S1 to S7 Other supplementary materials for this manuscript include the following: Datasets S1 to S7 1 two-comp system sensor kinase 1 0.870.930.99 0.99 0.910.91 0.99 0.96 0.93 0.98 CYCc 0.99 1 0.96 0.89 10.96 A 0.98 0.89 histidine kinase 0.91 0.93 0.99 10.97 0.97 0.92 0.87 0.92 0.98 0.99 enzyme 0.97 0.88 0.86 0.99 two-comp system sensor kinase 0.99 0.98 0.98 1 0.85 CYCc 1 1 Enzyme rhodopsin 0.96 0.99 0.99 0.92 0.89 0.98 1 0.98 0.99 0.92 11 1 0.92 0.87 0.960.9 0.91 0.98 0.98 0.98 PDE & Guan Cyc 1 1 0.88 0.88 1 1 0.95 0.88 0.96 0.88 0.89 0.98 0.9 0.99 0.92 0.95 0.9 two-comp system sensor kinase 0.99 0.86 1 0.97 0.92 0.99 0.95 1 1 0.87 0.92 Archaea 0.93 0.96 0.97 0.96 0.92 0.9 0.99 0.99 0.991 1 Bacteria 0.921 0.96 two-comp system sensor kinase 0.94 0.95 1 0.94 0.97 0.95 Opisthokonta 0.97 1 0.990.990.87 CYCc 0.97 0.95 0.91 0.85 Rhizaria 0.88 0.97 0.99 0.98 0.97 0.98 0.95 0.9 Alveolata 0.94 0.97 0.88 0.89 0.98 0.99 0.99 0.99 Cryptophyta 0.95 0.95 0.99 1 0.86 0.99 0.87 0.96 0.95 0.99 1 Haptophyta 0.94 1 0.920.95 1 1 0.98 0.941 Stramenopiles 0.88 0.95 0.95 0.97 SMC_N 0.98 0.930.871 0.86 1 1 0.880.950.86 Chlorophyta/Streptophyta 1 0.95 0.940.94 1 Apolipoprotein 0.94 Rhodophyta 0.96 0.850.880.890.90.98 0.85 1 1 0.94 Neuromodulin Glaucophyta 1 0.97 1 0.88 0.95 0.97 0.97 0.97 1 0.9 0.98 Viruses 0.89 1 0.97 0.911 0.91 0.94 0.92 0.89 0.86 C2 domain Other 1 1 0.92 0.85 0.93 0.93 0.97 0.90.94 1 0.97 0.850.90.9 0.97 0.97 0.92 1 0.980.88 - 0.85 1 Chl - pump (archaeal) 0.97 0.98 0.95 1 0.96 0.94 0.9 0.96 1 1 0.97 0.98 B 0.96 1 0.96 0.98 0.9 0.99 1 0.88 0.98 1 Channel rhodopsin (phototaxis) 1 0.98 0.94 0.94 0.87 channel 0.97 0.98 0.940.86 0.86 1 0.92 0.93 0.94 0.93 0.96 1 1 0.970.99 1 0.99 1 0.98 1 1 0.88 1 0.910.87 0.88 1 1 1 0.99 0.890.930.93 1 0.97 0.97 0.950.92 1 0.86 0.89 1 1 0.880.870.99 C 0.91 0.99 0.92 1 1 0.951 0.93 0.97 1 0.94 0.93 0.99 sensory 1 0.99 1 0.910.92 0.91 0.93 0.99 0.97 0.97 0.92 0.950.99 0.930.9 0.9 1 1 0.940.920.96 0.97 0.94 1 0.92 0.96 0.91 1 0.89 1 0.97 0.910.99 0.930.99 1 1 0.99 0.94 0.98 0.92 0.98 0.970.98 1 1 0.97 0.98 1 0.93 0.85 1 0.86 0.97 0.96 0.890.87 0.95 1 0.99 0.90.96 1 Sensory rhodopsin 1 0.94 1 0.98 0.89 0.97 1 1 0.91 0.98 0.99 0.9 0.93 0.91 0.94 1 0.9 0.850.93 1 0.99 0.99 1 + 0.92 0.98 0.99 0.93 0.91 1 Sensory (phototaxis) / H -pump (archaeal) 0.99 1 0.991 0.96 1 0.98 0.96 0.951 Viral rhodopsin 1 0.980.94 0.94 11 0.89 0.910.92 0.96 0.91 1 D 0.96 0.910.94 Proteorhodopsin ( H+ pump) 0.99 0.890.961 0.980.94 1 0.88 1 0.97 0.96 1 ion-pump 0.911 1 0.9 0.97 0.9 0.93 1 0.93 0.9 0.950.930.98 0.95 0.890.98 + - 1 Na and Chl -pump rhodopsins 1 1 0.99 0.96 0.87 0.95 1 0.98 1 0.93 0.96 0.93 0.99 0.97 0.97 1 0.9 0.98 1 0.910.9 0.97 0.99 0.951 0.91 0.91 1 0.851 E 0.9 1 1 0.95 0.97 0.96 0.96 0.930.980.85 1 0.94 0.92 helio 0.98 0.910.9 1 0.99 0.91 1 0.98 0.89 0.850.86 0.93 0.93 0.98 0.910.91 0.94 1 0.94 0.87 1 1 0.98 0.97 Heliorhodopsin (sensory) 0.88 0.95 0.88 0.95 0.950.88 0.99 1 0.96 0.91 0.9 0.99 0.970.96 0.87 1 0.98 0.98 0.98 0.93 0.92 1 0.85 1 1 0.96 0.92 0.91 1 1 0.93 Fig. S1. Marine-relevant reference tree for rhodopsin. A mid-point rooted approximate maximum likelihood tree (Fasttree) of 933 reference sequences with known taxonomy. Local support values (Shimodaira-Hasegawa test, 1,000 resamples) of > 0.85 are indicated. The edges are colored according to taxonomy. The main functional clades (A~E) are grey-shaded. The red circles indicate the JGI and NCBI- derived sequences used to build the HMM-profile, all others are obtained by hmmsearches on marine relevant genomes and transcriptomes. Functional annotations (black text) are based on the NCBI-derived reference sequences, and protein domain annotations (blue text) are derived from cd-hit blast (NCBI) domains of the full-length sequences. The abbreviations are as follows: CYCc, Adenylyl-/guanylyl cyclase, catalytic domain; SMC_N, structural maintenance chromosomes; PDE, rhodopsin phosphodiesterase; Guan cyc, rhodopsin guanylate cyclase. 2 0.99 0.890.96 0.850.97 1 0.99 0.98 0.94 0.99 0.880.96 0.94 0.86 0.9 1 A 0.960.890.87 0.930.86 1 0.99 0.930.89 1 0.98 0.95 0.93 0.91 0.99 0.95 0.99 0.940.9 0.99 1 1 1 0.98 6-4/Dual-function CPF 1 0.97 0.910.95 0.92 0.930.870.89 1 0.95 0.96 0.94 1 0.95 0.98 0.950.89 0.97 0.87 0.95 0.99 0.930.850.95 0.95 0.99 0.95 0.99 0.98 0.87 0.95 0.98 0.88 0.9 0.96 0.990.97 0.94 0.87 0.96 1 0.98 0.99 0 1 0.94 0.91 0.97 0.99 0.86 1 0.99 0.89 1 0.950.88 0.88 1 0.85 0.99 0.99 0.99 6-4 photolyase 0.910.9 1 0.980.93 0.92 1 0.99 0.951 0.98 1 0.89 1 0.940.98 1 0.940.99 0.98 0.97 0.99 1 0.99 0.970.96 0.99 1 0.980.980.95 0.920.980.95 Animal cryptochrome 0.99 1 1 0.92 1 1 1 1 1 0.98 0.9 1 1 1 1 1 1 0.98 1 0.91 0.93 0.95 0.99 0.95 0.96 0.99 0.98 0.911 0.92 0.97 0.98 0.98 Bacterial cryptochrome 1 0.85 0.99 1 0.98 0.91 0.98 0.87 1 0.99 0.95 0.98 B 1 0.99 0.94 0.99 0.890.91 0.95 0.860.88 Cry-DASH-like 0.94 0.91 0.94 0.94 0.98 0.980.92 0.97 1 1 0.9 0.91 0.96 1 0.87 0.93 1 0.85 0.94 0.89 0.95 Archaea 0.93 1 1 0.94 0.98 1 0.93 Bacteria 0.91 1 0.9 0.95 11 0.94 0.85 0.87 0.970.96 1 Opisthokonta 0.95 0.88 0.99 0.92 1 0.95 0.9 0.9 1 0.99 0.93 0.850.87 0.91 Rhizaria 1 0.94 0.97 0.87 0.94 0.99 0.9 1 0.99 0.95 Alveolata 1 0.91 0.930.96 0.86 1 1 1 1 1 0.85 0.96 Cryptophyta 0.99 0.89 0.98 1 1 11 0.85 0.98 0.920.97 Haptophyta 0.88 0.99 0.92 Cry-DASH 0.94 1 0.97 0.910.96 0.98 1 0.89 Stramenopiles 0.9 0.96 0.910.91 1 0.931 Chlorophyta / Streptophyta 0.91 0.99 1 0.98 0.92 0.9 0.991 Rhodophyta 0.98 0.88 0.98 0.91 0.99 0.930.95 0.89 0.94 0.95 0.99 0.970.9 1 0.89 1 Glaucophyta 0.92 0.92 0.96 0.92 1 0.96 0.99 0.96 1 0.98 Viruses 0.980.95 0.98 0.95 0.870.91 0.97 0.99 0.980.890.87 Other 0.86 0.9 0.98 1 1 0.870.870.99 0.89 0.92 0.94 0.95 0.95 0.97 0.98 1 0.91 1 0.96 0.91 0.97 1 1 0.99 1 0.890.88 0.980.96 1 0.93 1 0.97 0.99 0.910.96 class I-III CPD photolyase 0.97 0.85 0.91 0.970.96 0.89 0.96 0.97 0.97 0.94 viruses C 1 0.89 1 1 0.9 1 1 0.97 1 0.95 1 1 1 1 0.98 0.99 0.941 0.96 0.860.9 0.95 1 0.94 0.96 0.97 0.99 0.96 1 0.96 1 0.92 0.91 1 1 0.95 1 0.92 1 plant cryptochrome-like 0.99 0.98 0.91 1 0.98 0.95 0.95 0.97 0.96 0.890.88 0.98 0.85 0.97 0.990.91 0.95 1 0.94 0.93 1 1 0.94 0.86 0.99 0.91 0.99 0.98 0.97 0.961 1 0.89 0.960.98 0.99 1 0.92 0.99 0.990.99 0.87 0.91 0.89 1 plant cryptochrome 1 0.86 1 0.991 0.93 0.98 1 0.870.99 0.941 0.91 0.951 0.95 0.98 1 0.87 0.99 0.88 0.86 1 0.9 0.99 unknown 1 0.92 0.98 0.95 0.940.91 0.89 0.94 0.880.91 0.87 1 0.98 0.94 1 0.92 0.870.95 1 0.95 0.991 0.95 0.91 0.96 class II CPD-like 0.99 0.94 0.94 0.98 1 0.95 0.970.96 0.95 0.99 0.91 0.98 D1 0.92 0.98 0.96 1 0.94 1 0.93 0.99 0.88 0.940.9 0.99 0.98 0.92 1 0.93 0.99 0.9 0.9 0.99 0.93 1 0.94 0.98 1 0.99 0.99 1 0.89 1 0.97 0.87 0.96 1 D2 0.98 0.92 0.9 0.99 1 0.9 1 0.850.88 0.96 1 0.97 0.98 0.9 0.99 0.98 0.94 1 0.85 0.990.9 0.950.980.910.97 1 0.890.910.97 0.88 0.91 0.95 0.99 0.98 0.99 1 0.991 0.92 1 0.890.930.860.860.94 0.970.87 0.99 Class II CPD 0.9 0.90.960.96 0.96 1 1 1 1 0.90.940.89 1 0.98 0.950.990.94 0.940.88 0.99 1 1 0.98 0.94 0.98 0.890.92 0.98 0.940.98 0.86 0.99 0.99 0.98 0.99 0.98 0.99 0.93 1 0.920.95 1 0.97 0.990.98 0.94 0.97 0.92 1 0.93 0.89 0.96 1 0.92 0.97 0.97 Fig.