Abstract
Circadian rhythms are biological rhythms with a period of approximately 24 h. While canonical circadian clock genes and their regulatory mechanisms appear highly conserved, the evolution of clock gene families is still unclear due to several rounds of whole genome duplication in vertebrates. The spotted gar (Lepisosteus oculatus), as a non-teleost ray-finned fish, represents a fish lineage that diverged before the teleost genome duplication (TGD), providing an outgroup for exploring the evolutionary mechanisms of circadian clocks after whole-genome duplication. In this study, we interrogated the spotted gar draft genome sequences and found that spotted gar contains 26 circadian clock genes from 11 families. Phylogenetic analysis showed that 9 of these 11 spotted gar circadian clock gene families have the same number of genes as humans, while the members of the nfil3 and cry families are different between spotted gar and humans. Using phylogenetic and syntenic analyses, we found that nfil3-1 is conserved in vertebrates, while nfil3-2 and nfil3-3 are maintained in spotted gar, teleost fish, amphibians, and reptiles, but not in mammals. Following the two-round vertebrate genome duplication (VGD), spotted gar retained cry1a, cry1b, and cry2, and cry3 is retained in spotted gar, teleost fish, turtles, and birds, but not in mammals. We hypothesize that duplication of core clock genes, such as (nfil3 and cry), likely facilitated diversification of circadian regulatory mechanisms in teleost fish. We also found that the transcription factor binding element (Ahr::Arnt) is retained only in one of the per1 or per2 duplicated paralogs derived from the TGD in the teleost fish, implicating possible subfuctionalization cases. Together, these findings help decipher the repertoires of the spotted gar’s circadian system and shed light on how the vertebrate circadian clock systems have evolved.
Highlights
Circadian clocks regulate various cellular and physiological activities and processes in organisms ranging from cyanobacteria to mammals, allowing for them to adapt to the day–night cycle on Earth [1]
In a previous study, that the spotted gar genome retained most of its circadian clock genes, which are similar in copy numbers with those of humans [16]
Using zebrafish and human circadian clock genes to interrogate the spotted gar draft genome sequences, we found that spotted gar contains 26 circadian clock genes from 11 families, which are consistent with our previous report (Table 1) [16]
Summary
Circadian clocks regulate various cellular and physiological activities and processes in organisms ranging from cyanobacteria to mammals, allowing for them to adapt to the day–night cycle on Earth [1]. A circadian oscillator exhibits persistent rhythmical activity with a near 24 h periodicity under constant conditions [2]. The universal mechanisms of circadian clocks are transcriptional/translational feedback loops [3]. Daily biological rhythms are generated at the molecular level through auto-regulatory positive and negative feedback loops of the core clock genes (e.g., Clock, bmal, Period, Cryptochrome) [4,5]. CLOCK and BMAL1 form a heterodimer (CLOCK: BMAL1) and activate transcription of Period and Cryptochrome genes by binding to E-box motifs (CACGTG) in their promoter regions. PERIOD and CRYPTOCHROME form another heterodimer to repress
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