scholarly journals The effects of sex-biased gene expression and X-linkage on rates of adaptive protein sequence evolution in Drosophila

2015 ◽  
Vol 11 (4) ◽  
pp. 20150117 ◽  
Author(s):  
Victoria Ávila ◽  
José L. Campos ◽  
Brian Charlesworth
Keyword(s):  
Gene Expression ◽  
Adaptive Evolution ◽  
Genetic Recombination ◽  
Strong Association ◽  
Sequence Evolution ◽  
Female Fitness ◽  
Synonymous Mutations ◽  
X Linkage ◽  
Different Levels ◽  
Protein Sequence Evolution

A faster rate of adaptive evolution of X-linked genes compared with autosomal genes may be caused by the fixation of new recessive or partially recessive advantageous mutations (the Faster-X effect). This effect is expected to be largest for mutations that affect only male fitness and absent for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using genes with different levels of sex-biased expression and by estimating the extent of adaptive evolution of non-synonymous mutations from polymorphism and divergence data. We detected both a Faster-X effect and an effect of male-biased gene expression. There was no evidence for a strong association between the two effects—modest levels of male-biased gene expression increased the rate of adaptive evolution on both the autosomes and the X chromosome, but a Faster-X effect occurred for both unbiased genes and female-biased genes. The rate of genetic recombination did not influence the magnitude of the Faster-X effect, ruling out the possibility that it reflects less Hill–Robertson interference for X-linked genes.

scholarly journals Adaptive evolution of transcription factor binding affinities

2017 ◽  
Author(s):  
Jungeui Hong ◽  
Nathan Brandt ◽  
Ally Yang ◽  
Tim Hughes ◽  
David Gresham
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Dna Binding ◽  
Adaptive Evolution ◽  
Consensus Sequence ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Missense Mutations ◽  
Binding Affinities ◽  
Synonymous Mutations

Understanding the molecular basis of gene expression evolution is a central problem in evolutionary biology. However, connecting changes in gene expression to increased fitness, and identifying the functional basis of those changes, remains challenging. To study adaptive evolution of gene expression in real time, we performed long term experimental evolution (LTEE) of Saccharomyces cerevisiae (budding yeast) in ammonium-limited chemostats. Following several hundred generations of continuous selection we found significant divergence of nitrogen-responsive gene expression in lineages with increased fitness. In multiple independent lineages we found repeated selection for non-synonymous mutations in the zinc finger DNA binding domain of the activating transcription factor (TF), GAT1, that operates within incoherent feedforward loops to control expression of the nitrogen catabolite repression (NCR) regulon. Missense mutations in the DNA binding domain of GAT1 reduce its binding affinity for the GATAA consensus sequence in a promoter-specific manner, resulting in increased expression of ammonium permease genes via both direct and indirect effects, thereby conferring increased fitness. We find that altered transcriptional output of the NCR regulon results in antagonistic pleiotropy in alternate environments and that the DNA binding domain of GAT1 is subject to purifying selection in natural populations. Our study shows that adaptive evolution of gene expression can entail tuning expression output by quantitative changes in TF binding affinities while maintaining the overall topology of a gene regulatory network.

scholarly journals The Effects of Sex-Biased Gene Expression and X-Linkage on Rates of Sequence Evolution in Drosophila

2017 ◽  
Vol 35 (3) ◽  
pp. 655-665 ◽  
Author(s):  
José Luis Campos ◽  
Keira J A Johnston ◽  
Brian Charlesworth
Keyword(s):  
Gene Expression ◽  
Sequence Evolution ◽  
X Linkage

scholarly journals Sex-biased genes expressed in the cricket brain evolve rapidly

2020 ◽  
Author(s):  
Carrie A. Whittle ◽  
Arpita Kulkarni ◽  
Cassandra G. Extavour
Keyword(s):  
Gene Expression ◽  
Sexual Selection ◽  
Positive Selection ◽  
Protein Sequence ◽  
Seminal Fluid ◽  
Sequence Evolution ◽  
Evolutionary Trend ◽  
A Genome ◽  
The Brain ◽  
Protein Sequence Evolution

AbstractBackgroundSex-biased gene expression, particularly male-biased expression in the gonad, has often been linked to rapid protein sequence evolution (dN/dS) in animals. This evolutionary trend may arise from one or both of sexual selection pressures during mating or low pleiotropy. In insects, research on sex-biased transcription and dN/dS remains largely focused on a few holometabolous species, with variable findings on male and female gonadal effects. The brain is central to the mating process, and provides neurological foundation for mating behaviors, such as courtship, intrasex competition and mate choice. However, there is a striking paucity of research on sex-biased expression of genes in the brain and the rate of protein sequence evolution in such genes.ResultsHere, we studied sex-biased gene expression in a hemimetabolous insect, the cricket Gryllus bimaculatus. We generated novel RNA-seq data for two sexual tissue types, the gonad and somatic reproductive system, and for two core components of the nervous system, the brain and ventral nerve cord. From a genome-wide analysis of genes expressed in these tissues, we report the accelerated evolution of testis-biased genes and seminal fluid proteins (SFPs) genes, as compared to ovary-biased and unbiased genes in this cricket model, which includes an elevated frequency of positive selection events. With respect to the brain, while sex-biased brain genes were much less common than for the gonads, they exhibited exceptionally rapid evolution, an effect that was stronger for the female than for the male brain. Certain sex-biased brain genes were predicted to be involved in mating or sex-related functions, which we suggest may cause exposure to sexual selection. Moreover, the sex-biased brain genes exhibited remarkably low cross-tissue expression breadth, or pleiotropy. We speculate that this feature may permit relaxed purifying selection, and allow the freedom for adaptive protein functional changes in these brain-expressed genes.ConclusionsOur results demonstrate that sex-biased expression in the male gonad, and sex-biased gene expression in the brain, especially the female brain, are associated with rapid protein sequence evolution in a cricket model system. We discuss the results with respect to our findings on pleiotropy and positive selection, and consider the potential role of the dynamic mating biology of this cricket model in shaping these patterns.

scholarly journals Roles of Solvent Accessibility and Gene Expression in Modeling Protein Sequence Evolution

2015 ◽  
Vol 11 ◽  
pp. EBO.S22911 ◽  
Author(s):  
Kuangyu Wang ◽  
Shuhui Yu ◽  
Xiang Ji ◽  
Clemens Lakner ◽  
Alexander Griffing ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Sequence ◽  
Solvent Accessibility ◽  
Sequence Evolution ◽  
Protein Sequence Evolution

scholarly journals Gene body methylation mediates epigenetic inheritance of plant traits

2021 ◽  
Author(s):  
Zaigham Shahzad ◽  
Jonathan D. Moore ◽  
Daniel Zilberman
Keyword(s):  
Gene Expression ◽  
Flowering Time ◽  
Cytosine Methylation ◽  
Plant Traits ◽  
Phenotypic Diversity ◽  
Strong Association ◽  
Epigenetic Inheritance ◽  
Evolutionary Significance ◽  
Gene Body ◽  
Gene Body Methylation

AbstractCytosine methylation is an epigenetically heritable DNA modification common in plant and animal genes, but the functional and evolutionary significance of gene body methylation (gbM) has remained enigmatic. Here we show that gbM enhances gene expression in Arabidopsis thaliana. We also demonstrate that natural gbM variation influences drought and heat tolerance and flowering time by modulating gene expression, including that of Flowering Locus C (FLC). Notably, epigenetic variation accounts for as much trait heritability in natural populations as DNA sequence polymorphism. Furthermore, we identify gbM variation in numerous genes associated with environmental variables, including a strong association between flowering time, spring atmospheric NO2 – a by-product of fossil fuel burning – and FLC epialleles. Our study demonstrates that gbM is an important modulator of gene expression, and its natural variation fundamentally shapes phenotypic diversity in plant populations. Thus, gbM provides an epigenetic basis for adaptive evolution independent of genetic polymorphism.

scholarly journals Genomic structural and transcriptional variation of Oryctes rhinoceros nudivirus (OrNV) in Coconut Rhinoceros Beetle

2020 ◽  
Author(s):  
Kayvan Etebari ◽  
Rhys Parry ◽  
Marie Joy B. Beltran ◽  
Michael J. Furlong
Keyword(s):  
Gene Expression ◽  
Solomon Islands ◽  
Dna Helicase ◽  
The Philippines ◽  
Comparative Genomic ◽  
Viral Gene ◽  
Geographic Population ◽  
Oryctes Rhinoceros ◽  
Synonymous Mutations ◽  
Rhinoceros Beetle

AbstractOryctes rhinoceros nudivirus (OrNV) is a large circular double-stranded DNA virus which has been used as a biological control agent to suppress Coconut Rhinoceros Beetle (Oryctes rhinoceros) in Southeast Asia and the Pacific Islands. Recently a new wave of O. rhinoceros incursions in Oceania in previously non-infested areas is thought to be related to the presence of low virulence isolates of OrNV or virus tolerant haplotypes of beetles. In this study, chronically infected O. rhinoceros adults were field collected from the Philippines, Fiji, Papua New Guinea and the Solomon Islands. We extracted total RNA from these samples to investigate the global viral gene expression profiles and comparative genomic analysis of structural variations between the four different populations. Maximum likelihood phylogenic analysis indicated that OrNV strains from the Solomon Islands and the Philippines are closely related to while OrNV strains from PNG and Fiji formed a distinct adjacent clade. We detected several polymorphic sites with a frequency higher than 35% in 892 positions of the viral genome. The highest number of structural variants, including single nucleotide variants (SNV), insertion, deletion and non-synonymous mutations, were found in strains from Fiji and PNG when compared to complete recently sequenced Solomon Islands OrNV reference genome. Non-synonymous mutations were detected in several hypothetical proteins, and 15 nudivirus core genes such as OrNV_gp034 (DNA Helicase), lef-8, lef-4 and vp91. For examination of the global gene expression profile of OrNV in chronically infected populations, we found limited evidence of variation between geographic populations. Only a few genes such as OrNV_gp01 (DNA polymerase B), OrNV_gp022 and OrNV_gp107 (Pif-3) were differentially expressed among different strains. Additionally, small RNA sequencing from the Solomon Islands population suggests that OrNV is targeted by the host RNA interference (RNAi) response with abundant 21nt small RNAs. Additionally, we identified a highly abundant putative 22 nt miRNA from the 3’ of a pre-miRNA-like hairpin originating from OrNV-gp-098. These findings provide valuable resources for future studies to improve our understanding of the OrNV genetic variation. Some of these structural changes are specific to the geographic population and could be related to particular phenotypic characteristics of the strain, such as viral pathogenicity or transmissibility, and this requires further investigation.

Expression of ERG11 and efflux pump genes CDR1, CDR2 and SNQ2 in voriconazole susceptible and resistant Candida glabrata strains

2019 ◽  
Vol 58 (1) ◽  
pp. 30-38
Author(s):  
Patricia Navarro-Rodríguez ◽  
Adela Martin-Vicente ◽  
Loida López-Fernández ◽  
Josep Guarro ◽  
Javier Capilla
Keyword(s):  
Gene Expression ◽  
Candida Glabrata ◽  
Efflux Pump ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Clear Correlation ◽  
Synonymous Mutations ◽  
First Time

AbstractCandida glabrata causes difficult to treat invasive candidiasis due to its antifungal resistance, mainly to azoles. The aim of the present work was to study the role of the genes ERG11, CDR1, CDR2, and SNQ2 on the resistance to voriconazole (VRC) in a set of C. glabrata strains with known in vitro and in vivo susceptibility to this drug. Eighteen clinical isolates of C. glabrata were exposed in vitro to VRC, and the expression of the cited genes was quantified by real time quantitative polymerase chain reaction (q-PCR). In addition, the ERG11 gene was amplified and sequenced to detect possible mutations. Ten synonymous mutations were found in 15 strains, two of them being reported for the first time; however, no amino acid changes were detected. ERG11 and CDR1 were the most expressed genes in all the strains tested, while the expression of CDR2 and SNQ2 was modest. Our results show that gene expression does not directly correlate with the VRC MIC. In addition, the expression profiles of ERG11 and efflux pump genes did not change consistently after exposure to VRC. Although individual analysis did not result in a clear correlation between MIC and gene expression, we did observe an increase in ERG11 and CDR1 expression in resistant strains. It is of interest that considering both in vitro and in vivo results, the slight increase in such gene expression correlates with the observed resistance to VRC.

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