The molecular oscillators of the protochordate Botryllus schlosseri

Yotam Voskoboynik ^1,2 Aidan Glina ^1,2 Mark Kowarsky ³ Norma F Neff ⁴ Katherine J Ishizuka ^2,5 Karla J Palmeri ^2,5 Stephen R Quake ^4,6 Debashis Sahoo ^7,8 Ayelet Voskoboynik ^2,4,5 Rachel Ben-Shlomo ⁹

¹Bioinformatics and System Biology, Jacobs School of Engineering, University of California San Diego, USA
²Hopkins Marine Station, Stanford University, CA, USA, USA
³Department of Physics, Stanford University, USA
⁴Chan Zuckerberg Biohub, Chan Zuckerberg Biohub, USA
⁵Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, USA
⁶Departments of Applied Physics and Bioengineering, Stanford University, USA
⁷Department of Pediatrics, University of California San Diego, USA
⁸Department of Computer Science and Engineering, Jacob's School of Engineering,, University of California San Diego, USA
⁹Department of Biology and Environment, University of Haifa-Oranim, Israel

Urochordates are non-vertebrate members of the chordate phylum and are considered as the closest non-vertebrate living relative of vertebrates. The urochordate Botryllus schlosseri is a sessile diurnal colonial marine organism that inhabit the intertidal zone and thus may displays a tidal cycle (12.4hrs) as well as circadian cycles. We combined genome and transcriptome sequencing analyses to identify circadian clock genes, and their expression. Profound search for the Period (Per) and Cryptochrome (Cry) canonical clock genes orthologues was unsuccessful. Currently, the genome of 15 species from seven families and three orders of tunicates has been sequenced and none of them is showing either the Per or the Cry canonical circadian clock genes. Therefore, it seems that the subphylum Tunicata is missing the negative regulatory elements (genes) of the circadian oscillator.

We detected at least five different paralogous of the transcription activators clock-Bmal1 genes, six Casein Kinase I (CKI) paralogous and about 20 Rev-erba/Ror-a,b paralogous. RNA-seq analysis collected along the day indicated that two of the clock-Bmal1 transcripts showed lower level during the light phase. We also detected two CKI transcripts that oscillated along the day, in the same phase as the transcription factors. Several other transcripts expressed a ~12hr cycling of transcription and may be associated with a possible circatidal pacemaker. These include a homolog of the transcription factor clock-bmal1 and a homolog of CKI. We suggest that a tidal oscillator in B. schlosseri is operated in a comparable way to the circadian one, but using other homologs.