Coevolution of Drosophila-type timeless with partner clock proteins

Drosophila-type timeless (dTIM) is an established key clock protein in fruit flies, regulating rhythmicity and light-mediated entrainment. However, as indicated by functional experiments, its contribution to the clock differs in various insects. Therefore, we conducted a comprehensive phylogenetic analysis of dTIM across animals, dated its origin, gene duplications, and losses. We identified variable and conserved protein domains and pinpointed animal lineages that underwent the biggest changes in the dTIM sequence. While dTIM modifications are only mildly affected by changes in the PER protein, even the complete loss of PER in echinoderms had no impact on dTIM. However, changes in dTIM always co-occur with the loss of CRYPTOCHROMES or JETLAG. This is exemplified by the remarkably accelerated evolution of dTIM in phylloxera and aphids. Finally, alternative d-tim splicing, characteristic of D. melanogaster temperature-dependent function, is conserved at least to some extent in Diptera, a..., Gene Identification and Data Sets
A systematic search for clock components was conducted, building on previous studies exploring the evolution, duplication, and loss of circadian clock components (Thakkar et al., 2022; Kotwica-Rolinska et al., 2022a). To identify circadian clock proteins and genes encoding dTIM, mTIM, TOF1, PERIOD, dCRY, mCRY, 6-4 Photolyase, JETLAG, and BRWD3 in Bilateria/Metazoa, GenBank (NCBI) protein and genomic databases, as well as transcriptome shotgun assemblies (TSA), were utilized. BLASTP and tBLASTn algorithms were applied with taxon-restricted searches targeting specific lineages at the levels of orders, suborders, infraorders, and, in some cases, families. In certain instances, annotated genomes or whole-genome shotgun contigs (wgs) were also examined. Protein sequences of circadian clock genes from Drosophila melanogaster, Danaus plexippus, and Pyrrhocoris apterus served as initial queries. Reciprocal and lineage-focused searches incorporated queries repre..., , # Data from: Coevolution of Drosophila-type timeless with partner clock proteins

[https://doi.org/10.5061/dryad.44j0zpcq0](https://doi.org/10.5061/dryad.44j0zpcq0)

**Description of the data and file structure**

Dataset contains sequences in the fasta format. The sequence title (after >) contain species name, higher taxon name (order and similar), accession number, and additional attributes (such as abbreviation TSA for protein seq translated from Transcriptome Sequence Assembly cDNA sequence). The data are amino acid sequences of the protein wrapped in 80-character line format.

mTIM TOF protein 112 seq.fasta

* Document with 112 protein sequences of the mammalian-type TIMELESS (mTIM)  and TOF proteins used in the phylogeentic analysis of dTIM origin

PER-390seq

* Document with 390 sequences of PER proteins used in the analysis of PER substitution rate

dTIM-454seq

* Document with 454 sequences of the Drosophila-type TIMELESS (dTIM) proteins

CRYs, Phr6-4-710seq

* Document with 71...,