scholarly journals Subfunctionalization versus neofunctionalization after whole-genome duplication

2017 ◽  
Author(s):  
Simen R. Sandve ◽  
Rori V. Rohlfs ◽  
Torgeir R. Hvidsten
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Northern Pike ◽  
Tissue Expression ◽  
Whole Genome ◽  
Expression Divergence ◽  
Evolutionary Mechanisms ◽  
Spotted Gar ◽  
Duplication Events ◽  
Evolutionary Fate

The question of what is the predominant evolutionary fate of genes after duplication events has been hotly debated for decades1,2. Two recently published articles in Nature (Lien et al.3) and Nature Genetics (Braasch et al.4) investigated the regulatory fate of gene duplicates after the salmonid-specific (Ss4R) and teleost specific (Ts3R) whole genome duplication (WGD) events, respectively. Both studies relied on tissue expression atlases for estimating regulatory divergence and used closely related unduplicated sister taxa (i.e. Northern pike and the spotted gar, respectively) as proxies for the ancestral expression state. Surprisingly, the two studies reach very different conclusions about the evolutionary mechanisms impacting gene expression after WGD. Braasch et al.4 concluded that the expression divergence was consistent with partitioning of tissue regulation between duplicates (subfunctionalization), while Lien et al.3 concluded that most divergence in tissue regulation were consistent with one copy maintaining ancestral tissue regulation while the other having diverged (in line with neofunctionalization). Here we show that this striking discrepancy in the conclusions of the two studies is a consequence of the data analysis approaches used, and is not related to underlying differences in the data.

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 Artificial whole genome duplication in paleopolyploid sturgeons yields highest documented chromosome number in vertebrates

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ievgen Lebeda ◽  
Petr Ráb ◽  
Zuzana Majtánová ◽  
Martin Flajšhans
Keyword(s):  
Chromosome Numbers ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Mitotic Division ◽  
Chromosome Count ◽  
Whole Genome ◽  
Acipenser Baerii ◽  
Ploidy Levels ◽  
Duplication Events ◽  
C Value

AbstractCritically endangered sturgeons, having undergone three whole genome duplication events, represent an exceptional example of ploidy plasticity in vertebrates. Three extant ploidy groups, combined with autopolyploidization, interspecific hybridization and the fertility of hybrids are important issues in sturgeon conservation and aquaculture. Here we demonstrate that the sturgeon genome can undergo numerous alterations of ploidy without severe physiological consequences, producing progeny with a range of ploidy levels and extremely high chromosome numbers. Artificial suppression of the first mitotic division alone, or in combination with suppression of the second meiotic division of functionally tetraploid zygotes (4n, C-value = 4.15) of Siberian sturgeon Acipenser baerii and Russian sturgeon A. gueldenstaedtii resulted in progeny of various ploidy levels—diploid/hexaploid (2n/6n) mosaics, hexaploid, octoploid juveniles (8n), and dodecaploid (12n) larvae. Counts between 477 to 520 chromosomes in octoploid juveniles of both sturgeons confirmed the modal chromosome numbers of parental species had been doubled. This exceeds the highest previously documented chromosome count among vertebrates 2n ~ 446 in the cyprinid fish Ptychobarbus dipogon.

scholarly journals Phylogeny and multiple independent whole‐genome duplication events in the Brassicales

2020 ◽  
Vol 107 (8) ◽  
pp. 1148-1164
Author(s):  
Makenzie E. Mabry ◽  
Julia M. Brose ◽  
Paul D. Blischak ◽  
Brittany Sutherland ◽  
Wade T. Dismukes ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Duplication Events

scholarly journals A comparative phylogenetic approach for dating whole genome duplication events

2004 ◽  
Vol 20 (2) ◽  
pp. 180-185 ◽  
Author(s):  
B. A. Chapman ◽  
J. E. Bowers ◽  
S. R. Schulze ◽  
A. H. Paterson
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Duplication Events

scholarly journals Fate of MHCII in salmonids following 4WGD

2020 ◽  
Author(s):  
Unni Grimholt ◽  
Morten Lukacs
Keyword(s):  
Mhc Class Ii ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Northern Pike ◽  
Class Ii ◽  
Whole Genome ◽  
Clear Cut ◽  
Mhc Genes ◽  
Histocompatibility Complex ◽  
Peptide Loading

AbstractMajor histocompatibility complex (MHC) genes are key players in the adaptive immunity providing a defense against invading pathogens. Although the basic structures are similar when comparing mammalian and teleost MHC class II (MHCII) molecules, there are also clear-cut differences. Based on structural requirements, the teleosts non-classical MHCII molecules do not comply with a function similar to the human HLA-DM and HLA-DO, i.e., assisting in peptide loading and editing of classical MHCII molecules. We have previously studied the evolution of teleost class II genes identifying various lineages and tracing their phylogenetic occurrence back to ancient ray-finned fishes. We found no syntenic MHCII regions shared between cyprinids, salmonids, and neoteleosts, suggesting regional instabilities. Salmonids have experienced a unique whole genome duplication 94 million years ago, providing them with the opportunity to experiment with gene duplicates. Many salmonid genomes have recently become available, and here we set out to investigate how MHCII has evolved in salmonids using Northern pike as a diploid sister phyla, that split from the salmonid lineage prior to the fourth whole genome duplication (4WGD) event. We identified 120 MHCII genes in pike and salmonids, ranging from 11 to 20 genes per species analyzed where DB-group genes had the most expansions. Comparing the MHC of Northern pike with that of Atlantic salmon and other salmonids species provides a tale of gene loss, translocations, and genome rearrangements.

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