The circadian clock controls behavior and metabolism in various organisms. However, the exact timing and strength of rhythmic phenotypes can vary significantly between individuals of the same species. This is highly relevant for rhythmically complex marine environments where organismal rhythmic diversity likely permits the occupation of different microenvironments. When investigating circadian locomotor behavior of Platynereis dumerilii, a model system for marine molecular chronobiology, we found strain-specific, high variability between individual worms. The individual patterns were maintained for several weeks. A diel head transcriptome comparison of behaviorally rhythmic versus arrhythmic wildtype worms showed that 24h cycling of core circadian clock transcripts is identical between both behavioral phenotypes. While behaviorally arrhythmic worms showed a similar total number of cycling transcripts compared to their behaviorally rhythmic counterparts, the annotation categories of their transcripts, however, differed substantially. Consistent with their locomotor phenotype, behaviorally rhythmic worms exhibit an enrichment of cycling transcripts related to neuronal/behavioral processes. In contrast, behaviorally arrhythmic worms showed significantly increased diel cycling for metabolism- and physiology-related transcripts. The prominent role of the neuropeptide pigment-dispersing factor (PDF) in Drosophila circadian behavior prompted us to test for a possible functional involvement of Platynereis pdf. Differing from its role in Drosophila, loss of pdf impacts overall activity levels, but shows only indirect effects on rhythmicity. Our results show that individuals arrhythmic in a given process can show increased rhythmicity in others. Across the Platynereis population, rhythmic phenotypes exist as a continuum, with no distinct ‘boundaries’ between rhythmicity and arrhythmicity. We suggest that such diel rhythm breadth is an important biodiversity resource enabling the species to quickly adapt to heterogeneous or changing marine environments. In times of massive sequencing, our work also emphasizes the importance of time series and functional tests.

Here we described the data provided in addition to the publication 'Molecular circadian rhythms are robust in marine annelids lacking rhythmic behavior' (doi: 10.1371/journal.pbio.3002572). For further details on how the data was generated, please consult the original publication.

Reference transcriptome description:
The reference transcriptome used for read mapping was created from samples of regenerated Platynereis dumerilii tail pieces (newly grown blastema + adjacent old segment) collected at different stages of regeneration (0, 1, 2, 3 and 5) staged according to Planques et al. 2019 [1]. Per regeneration stage, 3 replicates were collected (n=15 samples total). After library preparation with poly-A enrichment, samples were sequenced on an Illumina NovaSeq System (S1 flow cell, 100bp paired-end reads). The sequencing produced ~141 million reads (after standard quality control) that were assembled into a de novo transcriptome of 364,574 transcripts incl. isoforms (GC content: 39.65%, median/mean transcript length: 356bp/810.65bp). The transcriptome is provided in FASTA-format with all 364,574 transcripts listed.

Trimmed/filtered reads of samples from rhythmic vs. arrhythmic phenotype transcriptome comparison:
Samples of phenotypically rhythmic or arrhythmic worms collected over the 24 hour cycle were sequenced as paired-end reads on a Illumina NextSeq550 System (see methods of associated paper for details). For each sample (n=36 total), reads after trimming/filtering are provided as compressed fastq-files. The naming is based on the phenotype (R, A), sampling time point (ZT00, ZT04, ZT08, ZT12, ZT16, ZT20), replicate (1, 2, 3), and an indicator for forward/reverse reads (1, 2). For example, the file ‘R_ZT08_1_2.trim.fastq.gz’ contains the trimmed/filtered reverse reads of replicate 1 collected at time point ZT08 from rhythmic worms. Furthermore, a FastQC quality report is provided for each file.

Python code for binary behavior reproducibility analysis:
The presented code was used to determine the reproducibility of diel/circadian worm locomotor behavior as described in tzhe publication.

R-script for GO-term analysis incl. associated files:
The R-script was used to determine the enrichment of biological processes based on the trascriptome expression data. The file includes the R-script as well as the other files mentioned in the script and needed to re-create the analysis.

References:
[1] Planques, A., Malem, J., Parapar, J., Vervoort, M., and Gazave, E. (2019). Morphological, cellular and molecular characterization of posterior regeneration in the marine annelid Platynereis dumerilii. Dev. Biol. 445, 189–210. doi:10.1016/j.ydbio.2018.11.004

[2] Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021;38: 4647–4654. doi:10.1093/molbev/msab199