Towards a More Nuanced Understanding of the Relationship between Sex-Biased Gene Expression and Rates of Protein-Coding Sequence Evolution

Selective transcription of individual protein coding genes does not occur in trypanosomes and the cellular copy number of each mRNA must be determined post-transcriptionally. Here, we provide evidence that codon choice directs the levels of constitutively expressed mRNAs. First, a novel codon usage metric, the gene expression codon adaptation index (geCAI), was developed that maximised the relationship between codon choice and the measured abundance for a transcriptome. Second, geCAI predictions of mRNA levels were tested using differently coded GFP transgenes and were successful over a 25-fold range, similar to the variation in endogenous mRNAs. Third, translation was necessary for the accelerated mRNA turnover resulting from codon choice. Thus, in trypanosomes, the information determining the levels of most mRNAs resides in the open reading frame and translation is required to access this information.

Download Full-text

Genomic footprints of repeated evolution of CAM photosynthesis in tillandsioid bromeliads

10.1101/495812 ◽

2018 ◽

Cited By ~ 2

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.

Download Full-text

Common Features in lncRNA Annotation and Classification: A Survey

Non-Coding RNA ◽

10.3390/ncrna7040077 ◽

2021 ◽

Vol 7 (4) ◽

pp. 77

Author(s):

Christopher Klapproth ◽

Rituparno Sen ◽

Peter F. Stadler ◽

Sven Findeiß ◽

Jörg Fallmann

Keyword(s):

Gene Expression ◽

Disease Progression ◽

In Silico ◽

Therapeutic Targets ◽

Untranslated Regions ◽

Protein Coding ◽

Coding Sequence ◽

Common Features ◽

Research Gap ◽

Non Coding Rnas

Long non-coding RNAs (lncRNAs) are widely recognized as important regulators of gene expression. Their molecular functions range from miRNA sponging to chromatin-associated mechanisms, leading to effects in disease progression and establishing them as diagnostic and therapeutic targets. Still, only a few representatives of this diverse class of RNAs are well studied, while the vast majority is poorly described beyond the existence of their transcripts. In this review we survey common in silico approaches for lncRNA annotation. We focus on the well-established sets of features used for classification and discuss their specific advantages and weaknesses. While the available tools perform very well for the task of distinguishing coding sequence from other RNAs, we find that current methods are not well suited to distinguish lncRNAs or parts thereof from other non-protein-coding input sequences. We conclude that the distinction of lncRNAs from intronic sequences and untranslated regions of coding mRNAs remains a pressing research gap.

Download Full-text

Sexual selection drives evolution and rapid turnover of male gene expression

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1501339112 ◽

2015 ◽

Vol 112 (14) ◽

pp. 4393-4398 ◽

Cited By ~ 107

Author(s):

Peter W. Harrison ◽

Alison E. Wright ◽

Fabian Zimmer ◽

Rebecca Dean ◽

Stephen H. Montgomery ◽

...

Keyword(s):

Gene Expression ◽

Sexual Selection ◽

Full Range ◽

Sex Bias ◽

Clear Understanding ◽

Sequence Evolution ◽

Ancestral Reconstruction ◽

Coding Sequence ◽

Rapid Turnover ◽

Relative Contribution

The profound and pervasive differences in gene expression observed between males and females, and the unique evolutionary properties of these genes in many species, have led to the widespread assumption that they are the product of sexual selection and sexual conflict. However, we still lack a clear understanding of the connection between sexual selection and transcriptional dimorphism, often termed sex-biased gene expression. Moreover, the relative contribution of sexual selection vs. drift in shaping broad patterns of expression, divergence, and polymorphism remains unknown. To assess the role of sexual selection in shaping these patterns, we assembled transcriptomes from an avian clade representing the full range of sexual dimorphism and sexual selection. We use these species to test the links between sexual selection and sex-biased gene expression evolution in a comparative framework. Through ancestral reconstruction of sex bias, we demonstrate a rapid turnover of sex bias across this clade driven by sexual selection and show it to be primarily the result of expression changes in males. We use phylogenetically controlled comparative methods to demonstrate that phenotypic measures of sexual selection predict the proportion of male-biased but not female-biased gene expression. Although male-biased genes show elevated rates of coding sequence evolution, consistent with previous reports in a range of taxa, there is no association between sexual selection and rates of coding sequence evolution, suggesting that expression changes may be more important than coding sequence in sexual selection. Taken together, our results highlight the power of sexual selection to act on gene expression differences and shape genome evolution.

Download Full-text