DOI: 10.5061/dryad.31zcrjdnq
title: Data from: Molecular circadian rhythms are robust in marine annelids lacking rhythmic behavior

description: 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.
description: Here we described
 the data provided in addition to the publication
 '<strong>Molecular circadian rhythms are robust in marine
 annelids lacking rhythmic behavior</strong>' (doi:
 10.1371/journal.pbio.3002572). For further details on how the data was
 generated, please consult the original publication.
 <strong>Reference transcriptome
 description:</strong><br>The reference transcriptome used for
 read mapping was created from samples of regenerated <em>Platynereis
 dumerilii</em> tail pieces (newly grown blastema + adjacent old
 segment) collected at different stages of regeneration (0, 1, 2, 3 and 5)
 staged according to Planques <em>et al.</em> 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.<br><br><strong>Trimmed/filtered reads
 of samples from rhythmic vs. arrhythmic phenotype transcriptome
 comparison:</strong><br>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.<br><br><strong>Python code for binary behavior
 reproducibility analysis:</strong><br>The presented code was
 used to determine the reproducibility of diel/circadian worm locomotor
 behavior as described in tzhe
 publication.<br><br><strong>R-script for GO-term
 analysis incl. associated files:</strong><br>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:<br>[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
description: # Data from: Molecular circadian rhythms are robust in marine annelids
 lacking rhythmic behavior 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). BUSCO analysis showed that 98.9% of near-universal
 single-copy orthologs were included [2] 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 24h 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. Dryad references: 1\.
    Planques A, Malem J, Parapar J, Vervoort M, Gazave E. Morphological,
 cellular and molecular characterization of posterior regeneration in the
 marine annelid *Platynereis dumerilii*. Dev Biol. 2019;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