The grayling genome reveals selection on gene expression regulation after whole genome duplication

Varadharajan, Srinidhi; Sandve, Simen Rød; Tørresen, Ole K.; Lien, Sigbjørn; Vøllestad, Leif Asbjørn; Jentoft, Sissel; Nederbragt, Alexander J.; Jakobsen, Kjetill S.

doi:10.1101/153270

Cited by 15 publications

(27 citation statements)

References 77 publications

(100 reference statements)

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“…The more general pattern of over-retention of duplicate genes functioning in the nervous system has been previously reported with both with respect to the TGD [97] and for other vertebrate WGDs [76,98,99]. Roux, Liu and Robinson-Rechavi argue that purifying selection opposing the appearance of sequence variants of duplicate genes expressed in neural tissues has the indirect effect of preventing the loss of the duplicates themselves [76].…”

Section: Plos Onementioning

confidence: 68%

The lasting after-effects of an ancient polyploidy on the genomes of teleosts

Conant

2020

PLoS ONE

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The ancestor of most teleost fishes underwent a whole-genome duplication event three hundred million years ago. Despite its antiquity, the effects of this event are evident both in the structure of teleost genomes and in how the surviving duplicated genes still operate to drive form and function. I inferred a set of shared syntenic regions that survive from the teleost genome duplication (TGD) using eight teleost genomes and the outgroup gar genome (which lacks the TGD). I then phylogenetically modeled the TGD's resolution via shared and independent gene losses and applied a new simulation-based statistical test for the presence of bias toward the preservation of genes from one parental subgenome. On the basis of that test, I argue that the TGD was likely an allopolyploidy. I find that duplicate genes surviving from this duplication in zebrafish are less likely to function in early embryo development than are genes that have returned to single copy at some point in this species' history. The tissues these ohnologs are expressed in, as well as their biological functions, lend support to recent suggestions that the TGD was the source of a morphological innovation in the structure of the teleost retina. Surviving duplicates also appear less likely to be essential than singletons, despite the fact that their single-copy orthologs in mouse are no less essential than other genes.

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Section: Plos Onementioning

confidence: 68%

The lasting after-effects of an ancient polyploidy on the genomes of teleosts

Conant

2020

PLoS ONE

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“…Rainbow trout proteins were obtained from an assembly and annotation of the genome (Berthelot et al., ). Grayling proteins were obtained from an assembly and annotation of the genome (Varadharajan et al., ). The coho salmon transcriptome (Kim, Leong, Koop, & Devlin, ) was obtained from NCBI (GDQG00000000.1).…”

Section: Methodsmentioning

confidence: 99%

Life‐stage‐associated remodelling of lipid metabolism regulation in Atlantic salmon

et al. 2018

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Atlantic salmon migrates from rivers to sea to feed, grow and develop gonads before returning to spawn in freshwater. The transition to marine habitats is associated with dramatic changes in the environment, including water salinity, exposure to pathogens and shift in dietary lipid availability. Many changes in physiology and metabolism occur across this life-stage transition, but little is known about the molecular nature of these changes. Here, we use a long-term feeding experiment to study transcriptional regulation of lipid metabolism in Atlantic salmon gut and liver in both fresh- and saltwater. We find that lipid metabolism becomes significantly less plastic to differences in dietary lipid composition when salmon transitions to saltwater and experiences increased dietary lipid availability. Expression of genes in liver relating to lipogenesis and lipid transport decreases overall and becomes less responsive to diet, while genes for lipid uptake in gut become more highly expressed. Finally, analyses of evolutionary consequences of the salmonid-specific whole-genome duplication on lipid metabolism reveal several pathways with significantly different (p < .05) duplicate retention or duplicate regulatory conservation. We also find a limited number of cases where the whole-genome duplication has resulted in an increased gene dosage. In conclusion, we find variable and pathway-specific effects of the salmonid genome duplication on lipid metabolism genes. A clear life-stage-associated shift in lipid metabolism regulation is evident, and we hypothesize this to be, at least partly, driven by nondietary factors such as the preparatory remodelling of gene regulation and physiology prior to sea migration.

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“…), European grayling ( Thymallus thymallus ; Varadharajan et al . ) and Arctic charr ( Salvelinus alpinus ; Christensen et al . ), or are available yet currently unpublished, including for coho salmon ( Oncorhynchus kisutch ; NCBI accession no.…”

Section: State Of the Art And Perspectivesmentioning

confidence: 99%

Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding

Houston

Macqueen

2018

Animal Genetics

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Summary Atlantic salmon ( Salmo salar L.) is among the most iconic and economically important fish species and was the first member of Salmonidae to have a high‐quality reference genome assembly published. Advances in genomics have become increasingly central to the genetic improvement of farmed Atlantic salmon as well as conservation of wild salmon stocks. The salmon genome has also been pivotal in shaping our understanding of the evolutionary and functional consequences arising from an ancestral whole‐genome duplication event characterising all Salmonidae members. Here, we provide a review of the current status of Atlantic salmon genetics and genomics, focussed on progress made from genome‐wide research aimed at improving aquaculture production and enhancing understanding of salmonid ecology, physiology and evolution. We present our views on the future direction of salmon genomics, including the role of emerging technologies (e.g. genome editing) in elucidating genetic features that underpin functional variation in traits of commercial and evolutionary importance.

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The grayling genome reveals selection on gene expression regulation after whole genome duplication

Cited by 15 publications

References 77 publications

The lasting after-effects of an ancient polyploidy on the genomes of teleosts

The lasting after-effects of an ancient polyploidy on the genomes of teleosts

Life‐stage‐associated remodelling of lipid metabolism regulation in Atlantic salmon

Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding

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