scholarly journals Sex-biased gene expression in an hemimetabolous insect: pattern during development, extent, functions involved, rate of sequence evolution, and comparison with an holometabolous insect

2021 ◽  
Author(s):  
Nadia Aubin-Horth
Keyword(s):  
Gene Expression ◽  
Sequence Evolution ◽  
Holometabolous Insect ◽  
Hemimetabolous Insect

scholarly journals Transcriptome dynamics during metamorphosis of imaginal discs into wings and thoracic dorsum in Apis mellifera castes

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Michelle Prioli Miranda Soares ◽  
Daniel Guariz Pinheiro ◽  
Flávia Cristina de Paula Freitas ◽  
Zilá Luz Paulino Simões ◽  
Márcia Maria Gentile Bitondi
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Imaginal Discs ◽  
Rna Seq ◽  
Transition Analysis ◽  
Holometabolous Insect ◽  
Complex Anatomy ◽  
Gene Expression Dynamics ◽  
Wing Discs ◽  
Developmental Phases

Abstract Background Much of the complex anatomy of a holometabolous insect is built from disc-shaped epithelial structures found inside the larva, i.e., the imaginal discs, which undergo a rapid differentiation during metamorphosis. Imaginal discs-derived structures, like wings, are built through the action of genes under precise regulation. Results We analyzed 30 honeybee transcriptomes in the search for the gene expression needed for wings and thoracic dorsum construction from the larval wing discs primordia. Analyses were carried out before, during, and after the metamorphic molt and using worker and queen castes. Our RNA-seq libraries revealed 13,202 genes, representing 86.2% of the honeybee annotated genes. Gene Ontology analysis revealed functional terms that were caste-specific or shared by workers and queens. Genes expressed in wing discs and descendant structures showed differential expression profiles dynamics in premetamorphic, metamorphic and postmetamorphic developmental phases, and also between castes. At the metamorphic molt, when ecdysteroids peak, the wing buds of workers showed maximal gene upregulation comparatively to queens, thus underscoring differences in gene expression between castes at the height of the larval-pupal transition. Analysis of small RNA libraries of wing buds allowed us to build miRNA-mRNA interaction networks to predict the regulation of genes expressed during wing discs development. Conclusion Together, these data reveal gene expression dynamics leading to wings and thoracic dorsum formation from the wing discs, besides highlighting caste-specific differences during wing discs metamorphosis.

scholarly journals Modeling gene expression evolution with EvoGeneX uncovers differences in evolution of species, organs and sexes

2020 ◽  
Author(s):  
Soumitra Pal ◽  
Brian Oliver ◽  
Teresa M. Przytycka
Keyword(s):  
Gene Expression ◽  
Evolutionary Dynamics ◽  
Computational Method ◽  
Specific Gene ◽  
Species Variation ◽  
Evolutionary Divergence ◽  
Sequence Evolution ◽  
Study Gene Expression ◽  
Expression Evolution ◽  
Gene Expression Evolution

AbstractWhile DNA sequence evolution has been well studied, the expression of genes is also subject to evolution. Yet the evolution of gene expression is currently not well understood. In recent years, new tissue/organ specific gene expression datasets spanning several organisms across the tree of life, have become available providing the opportunity to study gene expression evolution in more detail. However, while a theoretical model to study evolution of continuous traits exist, in practice computational methods often cannot distinguish, with confidence, between alternative evolutionary scenarios. This lack of power has been attributed to the modest number of species with available expression data.To solve this challenge, we introduce EvoGeneX, a computationally efficient method to uncover the mode of gene expression evolution based on the Ornstein-Uhlenbeck process. Importantly, EvoGeneX in addition to modelling expression variations between species, models within species variation. To estimate the within species variation, EvoGeneX formally incorporates the data from biological replicates as a part of the mathematical model. We show that by modelling the within species diversity EvoGeneX significantly outperforms the currently available computational method. In addition, to facilitate comparative analysis of gene expression evolution, we introduce a new approach to measure the dynamics of evolutionary divergence of a group of genes.We used EvoGeneX to analyse the evolution of expression across different organs, species and sexes of the Drosophila genus. Our analysis revealed differences in the evolutionary dynamics of male and female gonads, and uncovered examples of adaptive evolution of genes expressed in the head and in the thorax.

scholarly journals An Overexpression Experiment Does Not Support the Hypothesis That Avoidance of Toxicity Determines the Rate of Protein Evolution

2020 ◽  
Vol 12 (5) ◽  
pp. 589-596
Author(s):  
Magdalena K Biesiadecka ◽  
Piotr Sliwa ◽  
Katarzyna Tomala ◽  
Ryszard Korona
Keyword(s):  
Gene Expression ◽  
Protein Evolution ◽  
Present Experiment ◽  
Structural Instability ◽  
Its Sequence ◽  
Sequence Evolution ◽  
Relative Toxicity ◽  
Considerable Decrease ◽  
Conserved Sequence ◽  
Yeast Genes

Abstract The misfolding avoidance hypothesis postulates that sequence mutations render proteins cytotoxic and therefore the higher the gene expression, the stronger the operation of selection against substitutions. This translates into prediction that relative toxicity of extant proteins is higher for those evolving faster. In the present experiment, we selected pairs of yeast genes which were paralogous but evolving at different rates. We expressed them artificially to high levels. We expected that toxicity would be higher for ones bearing more mutations, especially that overcrowding should rather exacerbate than reverse the already existing differences in misfolding rates. We did find that the applied mode of overexpression caused a considerable decrease in fitness and that the decrease was proportional to the amount of excessive protein. However, it was not higher for proteins which are normally expressed at lower levels (and have less conserved sequence). This result was obtained consistently, regardless whether the rate of growth or ability to compete in common cultures was used as a proxy for fitness. In additional experiments, we applied factors that reduce accuracy of translation or enhance structural instability of proteins. It did not change a consistent pattern of independence between the fitness cost caused by overexpression of a protein and the rate of its sequence evolution.

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 Rapid regulatory evolution of a nonrecombining autosome linked to divergent behavioral phenotypes

2018 ◽  
Vol 115 (11) ◽  
pp. 2794-2799 ◽  
Author(s):  
Dan Sun ◽  
Iksoo Huh ◽  
Wendy M. Zinzow-Kramer ◽  
Donna L. Maney ◽  
Soojin V. Yi
Keyword(s):  
Gene Expression ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Large Scale ◽  
Parental Behavior ◽  
Phenotypic Traits ◽  
Sequence Evolution ◽  
Expression Divergence ◽  
Evolutionary Mechanisms ◽  
Behavioral Phenotypes

In the white-throated sparrow (Zonotrichia albicollis), the second chromosome bears a striking resemblance to sex chromosomes. First, within each breeding pair of birds, one bird is homozygous for the standard arrangement of the chromosome (ZAL2/ZAL2) and its mate is heterozygous for a different version (ZAL2/ZAL2m). Second, recombination is profoundly suppressed between the two versions, leading to genetic differentiation between them. Third, the ZAL2mversion is linked with phenotypic traits, such as bright plumage, high aggression, and low parental behavior, which are usually associated with males. These similarities to sex chromosomes suggest that the evolutionary mechanisms that shape sex chromosomes, in particular genetic degeneration of the heterogametic version due to the suppression of recombination, are likely important in this system as well. Here, we investigated patterns of protein sequence evolution and gene expression evolution between the ZAL2 and ZAL2mchromosomes by whole-genome sequencing and transcriptome analyses. Patterns of protein evolution exhibited only weak signals of genetic degeneration, and few genes harbored signatures of positive selection. We found substantial evidence of transcriptome evolution, such as significant expression divergence between ZAL2 and ZAL2malleles and signatures of dosage compensation for highly expressed genes. These results suggest that, early in the evolution of heteromorphic chromosomes, gene expression divergence and dosage compensation can prevail before large-scale genetic degeneration. Our results show further that suppression of recombination between heteromorphic chromosomes can lead to the evolution of alternative (sex-like) behavioral phenotypes before substantial genetic degeneration.

scholarly journals Genomic footprints of repeated evolution of CAM photosynthesis in tillandsioid bromeliads

2018 ◽  
Author(s):  
Marylaure De La Harpe ◽  
Margot Paris ◽  
Jaqueline Hess ◽  
Michael H. J. Barfuss ◽  
Martha L. Serrano-Serrano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Carbohydrate Metabolism ◽  
Adaptive Radiation ◽  
Sequence Evolution ◽  
Protein Coding ◽  
Gene Duplication And Loss ◽  
Repeated Evolution ◽  
Differential Gene ◽  
Pleiotropic Regulators ◽  
Cam Photosynthesis

The adaptive radiation of Bromeliaceae (pineapple family) is one of the most diverse among Neotropical flowering plants. Diversification in this group was facilitated by several ‘key innovations’ including the transition from C3 to CAM photosynthesis. We used a phylogenomic approach complemented by differential gene expression (RNA-seq) and targeted metabolite profiling to address the patterns and mechanisms of C3/CAM evolution in the extremely species-rich bromeliad genus Tillandsia and related taxa. Evolutionary analyses at a range of different levels (selection on protein-coding genes, gene duplication and loss, regulatory evolution) revealed three common themes driving the evolution of CAM: response to heat and drought, alterations to basic carbohydrate metabolism, and regulation of organic acid storage. At the level of genes and their products, CAM/C3 shifts were accompanied by gene expansion of a circadian regulator, re-programming of ABA-related gene expression, and adaptive sequence evolution of an enolase, effectively linking carbohydrate metabolism to ABA-mediated stress response. These changes include several pleiotropic regulators, which facilitated the evolution of correlated adaptive traits during a textbook adaptive radiation.

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