scholarly journals The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication

2018 ◽  
Vol 10 (10) ◽  
pp. 2785-2800 ◽  
Author(s):  
Srinidhi Varadharajan ◽  
Simen R Sandve ◽  
Gareth B Gillard ◽  
Ole K Tørresen ◽  
Teshome D Mulugeta ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gene Expression Regulation ◽  
Expression Regulation ◽  
Whole Genome

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

2017 ◽  
Author(s):  
Srinidhi Varadharajan ◽  
Simen R. Sandve ◽  
Gareth B. Gillard ◽  
Ole K. Tørresen ◽  
Teshome D. Mulugeta ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Draft Genome ◽  
Tissue Expression ◽  
Expression Regulation ◽  
Niche Shift ◽  
Whole Genome ◽  
Expression Divergence ◽  
European Grayling

AbstractWhole genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates. One such event occurred in the salmonid family ~80 million years ago (Ss4R) giving rise to a plethora of structural and regulatory duplicate-driven divergence, making salmonids an exemplary system to investigate the evolutionary consequences of WGD. Here, we present a draft genome assembly of European grayling (Thymallus thymallus) and use this in a comparative framework to study evolution of gene regulation following WGD. Among the Ss4R duplicates identified in European grayling and Atlantic salmon (Salmo salar), one third reflect non-neutral tissue expression evolution, with strong purifying selection, maintained over ~50 million years. Of these, the majority reflect conserved tissue regulation under strong selective constraints related to brain and neural-related functions, as well as higher-order protein-protein interactions. A small subset of the duplicates has evolved tissue regulatory expression divergence in a common ancestor, which have been subsequently conserved in both lineages, suggestive of adaptive divergence following WGD. These candidates for adaptive tissue expression divergence have elevated rates of protein coding- and promoter-sequence evolution and are enriched for immune- and lipid metabolism ontology terms. Lastly, lineage-specific duplicate divergence points towards underlying differences in adaptive pressures on expression regulation in the non-anadromous grayling versus the anadromous Atlantic salmon.Our findings enhance our understanding of the role of WGD in genome evolution and highlights cases of regulatory divergence of Ss4R duplicates, possibly related to a niche shift in early salmonid evolution.

scholarly journals A high‐quality walnut genome assembly reveals extensive gene expression divergences after whole‐genome duplication

2020 ◽  
Vol 18 (9) ◽  
pp. 1848-1850 ◽  
Author(s):  
Junpei Zhang ◽  
Wenting Zhang ◽  
Feiyang Ji ◽  
Jie Qiu ◽  
Xiaobo Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Assembly ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
High Quality

scholarly journals Diversified regulation of circadian clock gene expression following whole genome duplication

PLoS Genetics ◽  
2020 ◽  
Vol 16 (10) ◽  
pp. e1009097
Author(s):  
Alexander C. West ◽  
Marianne Iversen ◽  
Even H. Jørgensen ◽  
Simen R. Sandve ◽  
David G. Hazlerigg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Whole Genome Duplication ◽  
Clock Gene ◽  
Genome Duplication ◽  
Whole Genome ◽  
Circadian Clock Gene ◽  
Clock Gene Expression

scholarly journals Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome

2017 ◽  
Vol 328 (7) ◽  
pp. 709-721 ◽  
Author(s):  
Jeremy Pasquier ◽  
Ingo Braasch ◽  
Peter Batzel ◽  
Cedric Cabau ◽  
Jérome Montfort ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Spotted Gar

scholarly journals Characterization of intermediate-sized insertions using whole genome sequencing data and analysis of their functional impacts on gene expression

2021 ◽  
Author(s):  
Saeideh Ashouri ◽  
Jing Hao Wong ◽  
Hidewaki Nakagawa ◽  
Mihoko Shimada ◽  
Katsushi Tokunaga ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Gene Expression Regulation ◽  
Regulatory Elements ◽  
Expression Regulation ◽  
Ctcf Binding ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data

Abstract Intermediate-sized insertions are one of the structural variants contributing to genome diversity. However, due to technical difficulties in identifying them, their importance in disease pathogenicity and gene expression regulation remains unclear. We used whole-genome sequencing data of 174 Japanese samples to characterize intermediate-sized insertions using a highly-accurate insertion calling method (IMSindel software and joint-call recovery) and obtained a catalogue of 4,254 insertions. We constructed an imputation panel comprising of insertions and SNVs from all samples, and conducted imputation of intermediate-sized insertions for 82 publicly-available Japanese samples. Imputation accuracy, evaluated using Nanopore long-read sequencing data, was 97%. Subsequent eQTL analysis predicted 128 (~ 3.0%) insertions as causative for gene expression level changes. Enrichment analysis of causal insertions for genome regulatory elements showed significant associations with CTCF-binding sites, super-enhancers, and promoters. Among 17 causal insertions found in the same causal set with GWAS hits, there were insertions associated with changes in expression of cancer-related genes such as BRCA1, ZNF222, and ABCB10. Analysis of insertions sequences revealed that 461 insertions were short tandem duplications frequently found in early replicating regions of genome. Furthermore, comparison of functional importance of intermediate-sized insertions with that of intermediate-sized deletions detected in the same sample set in our previous study showed that insertions were more frequent in genic regions, and proportion of functional candidates was smaller in insertions. Here, we characterize a high-confidence set of intermediate-sized insertions and indicate their importance in gene expression regulation. Our results emphasize the importance of considering intermediate-sized insertions in trait association studies.

scholarly journals Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Le Zhang ◽  
Jingtian Zhao ◽  
Hao Bi ◽  
Xiangyu Yang ◽  
Zhiyang Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Populus Euphratica ◽  
Epigenetic Modifications ◽  
Chromatin Organization ◽  
Whole Genome ◽  
Duplicated Genes

AbstractThe nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged ~14 Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.

scholarly journals Diversified regulation of circadian clock gene expression following whole genome duplication

2020 ◽  
Author(s):  
Alexander C. West ◽  
Marianne Iversen ◽  
Even H. Jørgensen ◽  
Simen R. Sandve ◽  
David G. Hazlerigg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Genome Duplication ◽  
Clock Gene ◽  
Genome Duplication ◽  
Clock Genes ◽  
Expression Patterns ◽  
Whole Genome ◽  
Functional Diversification ◽  
Clock Gene Expression ◽  
Multiple Copies

AbstractAcross taxa, circadian control of physiology and behavior arises from cell-autonomous oscillations in gene expression, governed by a networks of so-called ‘clock genes’, collectively forming transcription-translation feedback loops. In modern vertebrates, these networks contain multiple copies of clock gene family members, which arose through whole genome duplication (WGD) events during evolutionary history. It remains unclear to what extent multiple copies of clock gene family members are functionally redundant or have allowed for functional diversification. We addressed this problem through an analysis of clock gene expression in the Atlantic salmon, a representative of the salmonids, a group which has undergone at least 4 rounds of WGD since the base of the vertebrate lineage, giving an unusually large complement of clock genes. By comparing expression patterns across multiple tissues, and during development, we present evidence for gene- and tissue-specific divergence in expression patterns, consistent with functional diversification of clock gene duplicates. In contrast to mammals, we found no evidence for coupling between cortisol and circadian gene expression, but cortisol mediated non-circadian regulated expression of a subset of clock genes in the salmon gill was evident. This regulation is linked to changes in gill function necessary for the transition from fresh- to sea-water in anadromous fish. Overall, this analysis emphasises the potential for a richly diversified clock gene network to serve a mixture of circadian and non-circadian functions in vertebrate groups with complex genomes.Author SummaryThe generation of daily (circadian) rhythms in behaviour and physiology depends on the activities of networks of so-called clock genes. In vertebrates, these have become highly complex due to a process known as whole genome duplication, which has occurred repeatedly during evolutionary history, giving rise to additional copies of key elements of the clock gene network. It remains unclear whether this results in functional redundancy, or whether it has permitted new roles for clock genes to emerge. Here, based on studies in the Atlantic salmon, a species with an unusually large complement of clock genes, we present evidence in favour of the latter scenario. We observe marked tissue-specific, and developmentally-dependent differences in the expression patterns of duplicated copies of key clock genes, and we identify a subset of clock genes whose expression is associated with the physiological preparation to migrate to sea, but is independent of circadian regulation. Associated with this, cortisol secretion is uncoupled from circadian organisation, contrasting with the situation in mammals. Our results indicate that whole genome duplication has permitted clock genes to diversify into non-circadian functions, and raise interesting questions about the ubiquity of mammal-like coupling between circadian and endocrine function.

scholarly journals Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Jeremy Pasquier ◽  
Cédric Cabau ◽  
Thaovi Nguyen ◽  
Elodie Jouanno ◽  
Dany Severac ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gene Evolution ◽  
Whole Genome

scholarly journals Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure

2017 ◽  
Vol 7 (7) ◽  
pp. 2015-2022 ◽  
Author(s):  
Sunita Sinha ◽  
Stephane Flibotte ◽  
Mauricio Neira ◽  
Sean Formby ◽  
Ana Plemenitaš ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Molecule ◽  
Chromatin Structure ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Extreme Environments ◽  
Cell Physiology ◽  
Whole Genome ◽  
Entire Genome ◽  
Hortaea Werneckii

Abstract Extremophilic organisms demonstrate the flexibility and adaptability of basic biological processes by highlighting how cell physiology adapts to environmental extremes. Few eukaryotic extremophiles have been well studied and only a small number are amenable to laboratory cultivation and manipulation. A detailed characterization of the genome architecture of such organisms is important to illuminate how they adapt to environmental stresses. One excellent example of a fungal extremophile is the halophile Hortaea werneckii (Pezizomycotina, Dothideomycetes, Capnodiales), a yeast-like fungus able to thrive at near-saturating concentrations of sodium chloride and which is also tolerant to both UV irradiation and desiccation. Given its unique lifestyle and its remarkably recent whole genome duplication, H. werneckii provides opportunities for testing the role of genome duplications and adaptability to extreme environments. We previously assembled the genome of H. werneckii using short-read sequencing technology and found a remarkable degree of gene duplication. Technology limitations, however, precluded high-confidence annotation of the entire genome. We therefore revisited the H. wernickii genome using long-read, single-molecule sequencing and provide an improved genome assembly which, combined with transcriptome and nucleosome analysis, provides a useful resource for fungal halophile genomics. Remarkably, the ∼50 Mb H. wernickii genome contains 15,974 genes of which 95% (7608) are duplicates formed by a recent whole genome duplication (WGD), with an average of 5% protein sequence divergence between them. We found that the WGD is extraordinarily recent, and compared to Saccharomyces cerevisiae, the majority of the genome’s ohnologs have not diverged at the level of gene expression of chromatin structure.

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