Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling
Abstract Background Clock family genes encode transcription factors that regulate clock-controlled genes and thus regulate many physiological mechanisms/processes in a circadian fashion. Clock1 duplicates and copies of Clock3 and NPAS2-like genes were partially characterized (genomic sequencing) and...
Published in: | BMC Research Notes |
---|---|
Main Authors: | , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
BMC
2010
|
Subjects: | |
Online Access: | https://doi.org/10.1186/1756-0500-3-215 https://doaj.org/article/4967bff5b5594bd3a6f20d659a60383d |
id |
ftdoajarticles:oai:doaj.org/article:4967bff5b5594bd3a6f20d659a60383d |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:4967bff5b5594bd3a6f20d659a60383d 2023-05-15T14:30:13+02:00 Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling Ferguson Moira M Moghadam Hooman K Paibomesai Marion I Danzmann Roy G 2010-07-01T00:00:00Z https://doi.org/10.1186/1756-0500-3-215 https://doaj.org/article/4967bff5b5594bd3a6f20d659a60383d EN eng BMC http://www.biomedcentral.com/1756-0500/3/215 https://doaj.org/toc/1756-0500 doi:10.1186/1756-0500-3-215 1756-0500 https://doaj.org/article/4967bff5b5594bd3a6f20d659a60383d BMC Research Notes, Vol 3, Iss 1, p 215 (2010) Medicine R Biology (General) QH301-705.5 Science (General) Q1-390 article 2010 ftdoajarticles https://doi.org/10.1186/1756-0500-3-215 2022-12-31T08:10:48Z Abstract Background Clock family genes encode transcription factors that regulate clock-controlled genes and thus regulate many physiological mechanisms/processes in a circadian fashion. Clock1 duplicates and copies of Clock3 and NPAS2-like genes were partially characterized (genomic sequencing) and mapped using family-based indels/SNPs in rainbow trout (RT)( Oncorhynchus mykiss ), Arctic charr (AC)( Salvelinus alpinus ), and Atlantic salmon (AS)( Salmo salar ) mapping panels. Results Clock1 duplicates mapped to linkage groups RT-8/-24, AC-16/-13 and AS-2/-18. Clock3/NPAS2-like genes mapped to RT-9/-20, AC-20/-43, and AS-5. Most of these linkage group regions containing the Clock gene duplicates were derived from the most recent 4R whole genome duplication event specific to the salmonids. These linkage groups contain quantitative trait loci (QTL) for life history and growth traits (i.e., reproduction and cell cycling). Comparative synteny analyses with other model teleost species reveal a high degree of conservation for genes in these chromosomal regions suggesting that functionally related or co-regulated genes are clustered in syntenic blocks. For example, anti-müllerian hormone (amh), regulating sexual maturation, and ornithine decarboxylase antizymes (oaz1 and oaz2), regulating cell cycling, are contained within these syntenic blocks. Conclusions Synteny analyses indicate that regions homologous to major life-history QTL regions in salmonids contain many candidate genes that are likely to influence reproduction and cell cycling. The order of these genes is highly conserved across the vertebrate species examined, and as such, these genes may make up a functional cluster of genes that are likely co-regulated. CLOCK, as a transcription factor, is found within this block and therefore has the potential to cis-regulate the processes influenced by these genes. Additionally, clock-controlled genes (CCGs) are located in other life-history QTL regions within salmonids suggesting that at least in part, ... Article in Journal/Newspaper Arctic charr Arctic Atlantic salmon Salmo salar Salvelinus alpinus Directory of Open Access Journals: DOAJ Articles Arctic BMC Research Notes 3 1 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Medicine R Biology (General) QH301-705.5 Science (General) Q1-390 |
spellingShingle |
Medicine R Biology (General) QH301-705.5 Science (General) Q1-390 Ferguson Moira M Moghadam Hooman K Paibomesai Marion I Danzmann Roy G Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling |
topic_facet |
Medicine R Biology (General) QH301-705.5 Science (General) Q1-390 |
description |
Abstract Background Clock family genes encode transcription factors that regulate clock-controlled genes and thus regulate many physiological mechanisms/processes in a circadian fashion. Clock1 duplicates and copies of Clock3 and NPAS2-like genes were partially characterized (genomic sequencing) and mapped using family-based indels/SNPs in rainbow trout (RT)( Oncorhynchus mykiss ), Arctic charr (AC)( Salvelinus alpinus ), and Atlantic salmon (AS)( Salmo salar ) mapping panels. Results Clock1 duplicates mapped to linkage groups RT-8/-24, AC-16/-13 and AS-2/-18. Clock3/NPAS2-like genes mapped to RT-9/-20, AC-20/-43, and AS-5. Most of these linkage group regions containing the Clock gene duplicates were derived from the most recent 4R whole genome duplication event specific to the salmonids. These linkage groups contain quantitative trait loci (QTL) for life history and growth traits (i.e., reproduction and cell cycling). Comparative synteny analyses with other model teleost species reveal a high degree of conservation for genes in these chromosomal regions suggesting that functionally related or co-regulated genes are clustered in syntenic blocks. For example, anti-müllerian hormone (amh), regulating sexual maturation, and ornithine decarboxylase antizymes (oaz1 and oaz2), regulating cell cycling, are contained within these syntenic blocks. Conclusions Synteny analyses indicate that regions homologous to major life-history QTL regions in salmonids contain many candidate genes that are likely to influence reproduction and cell cycling. The order of these genes is highly conserved across the vertebrate species examined, and as such, these genes may make up a functional cluster of genes that are likely co-regulated. CLOCK, as a transcription factor, is found within this block and therefore has the potential to cis-regulate the processes influenced by these genes. Additionally, clock-controlled genes (CCGs) are located in other life-history QTL regions within salmonids suggesting that at least in part, ... |
format |
Article in Journal/Newspaper |
author |
Ferguson Moira M Moghadam Hooman K Paibomesai Marion I Danzmann Roy G |
author_facet |
Ferguson Moira M Moghadam Hooman K Paibomesai Marion I Danzmann Roy G |
author_sort |
Ferguson Moira M |
title |
Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling |
title_short |
Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling |
title_full |
Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling |
title_fullStr |
Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling |
title_full_unstemmed |
Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling |
title_sort |
clock genes and their genomic distributions in three species of salmonid fishes: associations with genes regulating sexual maturation and cell cycling |
publisher |
BMC |
publishDate |
2010 |
url |
https://doi.org/10.1186/1756-0500-3-215 https://doaj.org/article/4967bff5b5594bd3a6f20d659a60383d |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic charr Arctic Atlantic salmon Salmo salar Salvelinus alpinus |
genre_facet |
Arctic charr Arctic Atlantic salmon Salmo salar Salvelinus alpinus |
op_source |
BMC Research Notes, Vol 3, Iss 1, p 215 (2010) |
op_relation |
http://www.biomedcentral.com/1756-0500/3/215 https://doaj.org/toc/1756-0500 doi:10.1186/1756-0500-3-215 1756-0500 https://doaj.org/article/4967bff5b5594bd3a6f20d659a60383d |
op_doi |
https://doi.org/10.1186/1756-0500-3-215 |
container_title |
BMC Research Notes |
container_volume |
3 |
container_issue |
1 |
_version_ |
1766304106051272704 |