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The Molecular Evolution of Circadian Clock Genes in Spotted Gar (Lepisosteus oculatus)

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 spo...

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Autores principales: Sun, Yi, Liu, Chao, Huang, Moli, Huang, Jian, Liu, Changhong, Zhang, Jiguang, Postlethwait, John H., Wang, Han
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723592/
https://www.ncbi.nlm.nih.gov/pubmed/31426485
http://dx.doi.org/10.3390/genes10080622
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author Sun, Yi
Liu, Chao
Huang, Moli
Huang, Jian
Liu, Changhong
Zhang, Jiguang
Postlethwait, John H.
Wang, Han
author_facet Sun, Yi
Liu, Chao
Huang, Moli
Huang, Jian
Liu, Changhong
Zhang, Jiguang
Postlethwait, John H.
Wang, Han
author_sort Sun, Yi
collection PubMed
description 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.
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spelling pubmed-67235922019-09-10 The Molecular Evolution of Circadian Clock Genes in Spotted Gar (Lepisosteus oculatus) Sun, Yi Liu, Chao Huang, Moli Huang, Jian Liu, Changhong Zhang, Jiguang Postlethwait, John H. Wang, Han Genes (Basel) Article 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. MDPI 2019-08-17 /pmc/articles/PMC6723592/ /pubmed/31426485 http://dx.doi.org/10.3390/genes10080622 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Sun, Yi
Liu, Chao
Huang, Moli
Huang, Jian
Liu, Changhong
Zhang, Jiguang
Postlethwait, John H.
Wang, Han
The Molecular Evolution of Circadian Clock Genes in Spotted Gar (Lepisosteus oculatus)
title The Molecular Evolution of Circadian Clock Genes in Spotted Gar (Lepisosteus oculatus)
title_full The Molecular Evolution of Circadian Clock Genes in Spotted Gar (Lepisosteus oculatus)
title_fullStr The Molecular Evolution of Circadian Clock Genes in Spotted Gar (Lepisosteus oculatus)
title_full_unstemmed The Molecular Evolution of Circadian Clock Genes in Spotted Gar (Lepisosteus oculatus)
title_short The Molecular Evolution of Circadian Clock Genes in Spotted Gar (Lepisosteus oculatus)
title_sort molecular evolution of circadian clock genes in spotted gar (lepisosteus oculatus)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723592/
https://www.ncbi.nlm.nih.gov/pubmed/31426485
http://dx.doi.org/10.3390/genes10080622
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