Abstract

To better understand the complexity of clock genes in salmonids, a taxon with an additional whole genome duplication, an analysis was performed to identify and classify gene family members (clock, arntl, period, cryptochrome, nr1d, ror, and csnk1). The majority of clock genes, in zebrafish and Northern pike, appeared to be duplicated. In comparison to the 29 clock genes described in zebrafish, 48 clock genes were discovered in salmonid species. There was also evidence of species-specific reciprocal gene losses conserved to the Oncorhynchus sister clade. From the six period genes identified three were highly significantly rhythmic, and circadian in their expression patterns (per1a.1, per1a.2, per1b) and two was significantly rhythmically expressed (per2a, per2b). The transcriptomic study of juvenile Atlantic salmon (parr) brain tissues confirmed gene identification and revealed that there were 2,864 rhythmically expressed genes (p < 0.001), including 1,215 genes with a circadian expression pattern, of which 11 were clock genes. The majority of circadian expressed genes peaked 2 h before and after daylight. These findings provide a foundation for further research into the function of clock genes circadian rhythmicity and the role of an enriched number of clock genes relating to seasonal driven life history in salmonids.

Highlights

  • Putative core clock gene sequences were identified for several salmonid species (S. alpinus, O. mykiss, O. kisutch, and O. tshawytscha) through a combination of literature searches, BLASTp and BLASTn searches of published salmonid genomes identified as part of the Functional Annotation of All Salmonid Genomes (FAASG) initiative (Amaral and Johnston, 2012)

  • The coding sequence (CDS) of variants sharing LOC ID were aligned to the CDS of D. rerio reference genes

  • Variants with the highest percentage identity compared to the reference for each locus were selected, leaving a total of 48 core clock genes identified in the S. salar across the 7 gene families explored (Table 1 and Supplementary Table 2)

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Summary

Introduction

The importance of biological time keeping is apparent across all organisms, from bacteria to humans (Wulund and Reddy, 2015) These time-dependent adaptations can last seconds or minutes and recur throughout the day (ultradian) or endure days or months (infradian). Allelic diversity and variation in length polymorphism of the clock PolyQ domain was reported in four Pacific salmon species (chinook, chum, coho, and pink) with overlapping geographical ranges and diversity in spawning times.

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