Gene duplication in the evolution of sex- and caste-biased gene expression

2016 ◽  
Author(s):  
Linh M Chau
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Evolution Of Sex

scholarly journals Functional Comparison of the Tup11 and Tup12 Transcriptional Corepressors in Fission Yeast

2005 ◽  
Vol 25 (2) ◽  
pp. 716-727 ◽  
Author(s):  
Fredrik Fagerström-Billai ◽  
Anthony P. H. Wright
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Fission Yeast ◽  
Budding Yeast ◽  
Functional Difference ◽  
Evolutionary Mechanism ◽  
Genome Wide ◽  
Number Of Genes ◽  
Transcriptional Corepressors ◽  
Genome Wide Gene Expression

ABSTRACT Gene duplication is considered an important evolutionary mechanism. Unlike many characterized species, the fission yeast Schizosaccharomyces pombe contains two paralogous genes, tup11 + and tup12 + , that encode transcriptional corepressors similar to the well-characterized budding yeast Tup1 protein. Previous reports have suggested that Tup11 and Tup12 proteins play redundant roles. Consistently, we show that the two Tup proteins can interact together when expressed at normal levels and that each can independently interact with the Ssn6 protein, as seen for Tup1 in budding yeast. However, tup11 − and tup12 − mutants have different phenotypes on media containing KCl and CaCl2. Consistent with the functional difference between tup11 − and tup12 − mutants, we identified a number of genes in genome-wide gene expression experiments that are differentially affected by mutations in the tup11 + and tup12 + genes. Many of these genes are differentially derepressed in tup11 − mutants and are over-represented in genes that have previously been shown to respond to a range of different stress conditions. Genes specifically derepressed in tup12 − mutants require the Ssn6 protein for their repression. As for Tup12, Ssn6 is also required for efficient adaptation to KCl- and CaCl2-mediated stress. We conclude that Tup11 and Tup12 are at least partly functionally diverged and suggest that the Tup12 and Ssn6 proteins have adopted a specific role in regulation of the stress response.

scholarly journals Evolutionary shifts in gene expression decoupled from gene duplication across functionally distinct spider silk glands

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Thomas H. Clarke ◽  
Jessica E. Garb ◽  
Robert A. Haney ◽  
R. Crystal Chaw ◽  
Cheryl Y. Hayashi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Spider Silk ◽  
Silk Glands

Mesotocin Gene Expression and Evidence of Gene Duplication in the Tammar Wallaby

1998 ◽  
Vol 839 (1 TRENDS IN COM) ◽  
pp. 447-449 ◽  
Author(s):  
LAURA J. PARRY ◽  
ROSS A.D. BATHGATE ◽  
RICHARD IVELL
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Tammar Wallaby

scholarly journals Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification

2014 ◽  
Vol 24 (7) ◽  
pp. 1115-1124 ◽  
Author(s):  
R. K. Arthur ◽  
L. Ma ◽  
M. Slattery ◽  
R. F. Spokony ◽  
A. Ostapenko ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Expression Evolution ◽  
Gene Expression Evolution

scholarly journals Male-biased gene expression resolves sexual conflict through the evolution of sex-specific genetic architecture

2018 ◽  
Vol 2 (2) ◽  
pp. 52-61 ◽  
Author(s):  
Alison E. Wright ◽  
Matteo Fumagalli ◽  
Christopher R. Cooney ◽  
Natasha I. Bloch ◽  
Filipe G. Vieira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sexual Conflict ◽  
Genetic Architecture ◽  
Evolution Of Sex

The evolution of sex-biased genes and sex-biased gene expression

2007 ◽  
Vol 8 (9) ◽  
pp. 689-698 ◽  
Author(s):  
Hans Ellegren ◽  
John Parsch
Keyword(s):  
Gene Expression ◽  
Evolution Of Sex

scholarly journals Genes relocated between Drosophila chromosome arms evolve under relaxed selective constraints relative to non-relocated genes

2017 ◽  
Author(s):  
Margaret L. I. Hart ◽  
Ban L. Vu ◽  
Quinten Bolden ◽  
Keith T. Chen ◽  
Casey L. Oakes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Population Genetics ◽  
Comparative Genomics ◽  
Gene Duplication ◽  
Male Fertility ◽  
Chromosomal Location ◽  
Single Copy ◽  
Duplicated Genes ◽  
Selective Constraints ◽  
Functional Analyses

AbstractGene duplication creates a second copy of a gene either in tandem to the ancestral locus or dispersed to another chromosomal location. When the ancestral copy of a dispersed duplicate is lost from the genome, it creates the appearance that the gene was “relocated” from the ancestral locus to the derived location. Gene relocations may be as common as canonical dispersed duplications in which both the ancestral and derived copies are retained. Relocated genes appear to be under more selective constraints than the derived copies of canonical duplications, and they are possibly as conserved as single-copy non-relocated genes. To test this hypothesis, we combined comparative genomics, population genetics, gene expression, and functional analyses to assess the selection pressures acting on relocated, duplicated, and non-relocated single-copy genes in Drosophila genomes. We find that relocated genes evolve faster than single-copy non-relocated genes, and there is no evidence that this faster evolution is driven by positive selection. In addition, relocated genes are less essential for viability and male fertility than single-copy non-relocated genes, suggesting that relocated genes evolve fast because of relaxed selective constraints. However, relocated genes evolve slower than the derived copies of canonical dispersed duplicated genes. We therefore conclude that relocated genes are under more selective constraints than canonical duplicates, but are not as conserved as single-copy non-relocated genes.

scholarly journals GENETIC AND DEVELOPMENTAL ANALYSIS OF SOME NEW COLOR MUTANTS IN THE GOLDFISH, CARASSIUS AURATUS

Genetics ◽  
1977 ◽  
Vol 86 (1) ◽  
pp. 161-174
Author(s):  
Takao Kajishima
Keyword(s):  
Gene Expression ◽  
Experimental Data ◽  
Gene Duplication ◽  
Carassius Auratus ◽  
Autosomal Gene ◽  
Crossing Experiments ◽  
Goldfish Carassius Auratus ◽  
Color Mutant ◽  
The Common ◽  
Developmental Analysis

ABSTRACT The genotypes of three color mutants in goldfish: a depigmentation character of larval melanophores, albinism and a recessive-transparent character, were analyzed by crossing experiments. The depigmentation character in the common goldfish is controlled by two dominant multiple genes, Dp 1 and Dp2, and only fish with double recessive alleles dp1dp1 dp2dp2 can retain larval melanophores throughout life. Albinism is also controlled by double autosomal genes, p and c. The genotype of an albino fish is represented by pp cc; the non-albino fish is PP CC. Fish with either a pp CC or pp Cc genotype are albino when scored at the time of melanosome differentiation in the pigment retina, but after the time of skin melanophore differentiation, they change to the nonalbino type under the control of the C gene. The recessive-transparent character is controlled by a single autosomal gene, g. The mechanisms of gene expression of these characters were proposed as a result of observation and/or experimental data on the differentiation processes of their phenotypes, and the genotypes of these color mutant goldfish were considered in relation to the "gene duplication hypothesis in the Cyprinidae."

scholarly journals Learning retention mechanisms and evolutionary parameters of duplicate genes from their expression data

2020 ◽  
Author(s):  
Michael DeGiorgio ◽  
Raquel Assis
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Statistical Learning ◽  
Gene Evolution ◽  
Functional Divergence ◽  
Duplicate Gene ◽  
Duplicate Genes ◽  
Evolutionary Mechanisms ◽  
Retention Mechanisms ◽  
Gene Copies

AbstractLearning about the roles that duplicate genes play in the origins of novel phenotypes requires an understanding of how their functions evolve. To date, only one method—CDROM—has been developed with this goal in mind. In particular, CDROM employs gene expression distances as proxies for functional divergence, and then classifies the evolutionary mechanisms retaining duplicate genes from comparisons of these distances in a decision tree framework. However, CDROM does not account for stochastic shifts in gene expression or leverage advances in contemporary statistical learning for performing classification, nor is it capable of predicting the underlying parameters of duplicate gene evolution. Thus, here we develop CLOUD, a multi-layer neural network built upon a model of gene expression evolution that can both classify duplicate gene retention mechanisms and predict their underlying evolutionary parameters. We show that not only is the CLOUD classifier substantially more powerful and accurate than CDROM, but that it also yields accurate parameter predictions, enabling a better understanding of the specific forces driving the evolution and long-term retention of duplicate genes. Further, application of the CLOUD classifier and predictor to empirical data from Drosophila recapitulates many previous findings about gene duplication in this lineage, showing that new functions often emerge rapidly and asymmetrically in younger duplicate gene copies, and that functional divergence is driven by strong natural selection. Hence, CLOUD represents the best available method for classifying retention mechanisms and predicting evolutionary parameters of duplicate genes, thereby also highlighting the utility of incorporating sophisticated statistical learning techniques to address long-standing questions about evolution after gene duplication.

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