scholarly journals The high turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

2018 ◽  
Author(s):  
Éléonore Durand ◽  
Isabelle Gagnon-Arsenault ◽  
Johan Hallin ◽  
Isabelle Hatin ◽  
Alexandre K Dubé ◽  
...  
Keyword(s):  
Time Scales ◽  
De Novo ◽  
Raw Material ◽  
Translation Efficiency ◽  
Evolutionary Time ◽  
Individual Genome ◽  
High Turnover ◽  
Wild Yeast ◽  
Intergenic Sequences ◽  
Rate Of Emergence

AbstractLittle is known about the rate of emergence of genes de novo, how they spread in populations and what their initial properties are. We examined wild yeast (Saccharomyces paradoxus) populations to characterize the diversity and turnover of intergenic ORFs over short evolutionary time-scales. With ~34,000 intergenic ORFs per individual genome for a total of ~64,000 orthogroups identified, we found de novo ORF formation to have a lower estimated turnover rate than gene duplication. Hundreds of intergenic ORFs show translation signatures similar to canonical genes. However, they have lower translation efficiency, which could reflect a mechanism to reduce their production cost or simply a lack of optimization. We experimentally confirmed the translation of many of these ORFs in laboratory conditions using a reporter assay. Translated intergenic ORFs tend to display low expression levels with sequence properties that generally are close to expectations based on intergenic sequences. However, some of the very recent translated intergenic ORFs, which appeared less than 110 Kya ago, already show gene- like characteristics, suggesting that the raw material for functional innovations could appear over short evolutionary time-scales.

scholarly journals Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Rafik Neme ◽  
Diethard Tautz
Keyword(s):  
De Novo ◽  
Gene Evolution ◽  
Large Fraction ◽  
Phylogenetic Distance ◽  
Evolutionary Time ◽  
High Turnover ◽  
Entire Genome ◽  
De Novo Gene ◽  
Phylogenetic Level ◽  
Transcriptome Coverage

Deep sequencing analyses have shown that a large fraction of genomes is transcribed, but the significance of this transcription is much debated. Here, we characterize the phylogenetic turnover of poly-adenylated transcripts in a comprehensive sampling of taxa of the mouse (genus Mus), spanning a phylogenetic distance of 10 Myr. Using deep RNA sequencing we find that at a given sequencing depth transcriptome coverage becomes saturated within a taxon, but keeps extending when compared between taxa, even at this very shallow phylogenetic level. Our data show a high turnover of transcriptional states between taxa and that no major transcript-free islands exist across evolutionary time. This suggests that the entire genome can be transcribed into poly-adenylated RNA when viewed at an evolutionary time scale. We conclude that any part of the non-coding genome can potentially become subject to evolutionary functionalization via de novo gene evolution within relatively short evolutionary time spans.

scholarly journals Distinct PKC-mediated posttranscriptional events set cytokine production kinetics in CD8+ T cells

2017 ◽  
Vol 114 (36) ◽  
pp. 9677-9682 ◽  
Author(s):  
Fiamma Salerno ◽  
Nahuel A. Paolini ◽  
Regina Stark ◽  
Marieke von Lindern ◽  
Monika C. Wolkers
Keyword(s):  
T Cells ◽  
Mrna Stability ◽  
Cytokine Production ◽  
De Novo ◽  
Translation Efficiency ◽  
Mrna Stabilization ◽  
Relative Contribution ◽  
Production Kinetics ◽  
Tnf Α ◽  
Ifn Γ

Effective T cell responses against invading pathogens require the concerted production of three key cytokines: TNF-α, IFN-γ, and IL-2. The cytokines functionally synergize, but their production kinetics widely differ. How the differential timing of expression is regulated remains, however, poorly understood. We compared the relative contribution of transcription, mRNA stability, and translation efficiency on cytokine production in murine effector and memory CD8+ T cells. We show that the immediate and ample production of TNF-α is primarily mediated by translation of preformed mRNA through protein kinase C (PKC)-induced recruitment of mRNA to polyribosomes. Also, the initial production of IFN-γ uses translation of preformed mRNA. However, the magnitude and subsequent expression of IFN-γ, and of IL-2, depends on calcium-induced de novo transcription and PKC-dependent mRNA stabilization. In conclusion, PKC signaling modulates translation efficiency and mRNA stability in a transcript-specific manner. These cytokine-specific regulatory mechanisms guarantee that T cells produce ample amounts of cytokines shortly upon activation and for a limited time.

scholarly journals RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Krisztian Buza ◽  
Bartek Wilczynski ◽  
Norbert Dojer
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Real Data ◽  
Reference Sequence ◽  
Individual Genome ◽  
Single Experiment ◽  
Sequencing Technologies ◽  
Sequencing Cost ◽  
The Individual ◽  
Assembly Software

Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of the species. However, in most typical protocols, this information is disregarded and the reference genome is used.Results. We provide a new approach that allows researchers to reconstruct genomes very closely related to the reference genome (e.g., mutants of the same species) directly from the reads used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. In this way, it can very quickly, and at no additional sequencing cost, generate new, modified reference sequence that is closer to the actual sequenced genome and has a full coverage. In this paper, we describe our approach and test its implementation called RECORD. We evaluate RECORD on both simulated and real data. We made our software publicly available on sourceforge.Conclusion. Our tests show that on closely related sequences RECORD outperforms more general assisted-assembly software.

Milankovitch cycles and their effects on species in ecological and evolutionary time

Paleobiology ◽  
1990 ◽  
Vol 16 (1) ◽  
pp. 11-21 ◽  
Author(s):  
K. D. Bennett
Keyword(s):  
Time Scales ◽  
Climatic Changes ◽  
Milankovitch Cycles ◽  
Mass Extinctions ◽  
Geological Time ◽  
Evolutionary Time ◽  
Abiotic Environment ◽  
Earth History ◽  
Microevolutionary Change ◽  
Second Tier

The Quaternary ice ages were paced by astronomical cycles with periodicities of 20–100 k.y. (Milankovitch cycles). These cycles have been present throughout earth history. The Quaternary fossil record, marine and terrestrial, near to and remote from centers of glaciation, shows that communities of plants and animals are temporary, lasting only a few thousand years at the most. Response of populations to the climatic changes of Quaternary Milankovitch cycles can be taken as typical of the way populations have behaved throughout earth history. Milankovitch cycles thus force an instability of climate and other aspects of the biotic and abiotic environment on time scales much less than typical species durations (1–30 m.y.). Any microevolutionary change that accumulates on a time scale of thousands of years is likely to be lost as communities are reorganized following climatic changes. A four-tier hierarchy of time scales for evolutionary processes can be constructed as follows: ecological time (thousands of years), Milankovitch cycles (20–100 k.y.), geological time (millions of years), mass extinctions (approximately 26 m.y.). “Ecological time” and “geological time” are defined temporally as the intervals between events of the second and fourth tiers, respectively. Gould's (1985) “paradox of the first tier” can be resolved, at least in part, through the undoing of Darwinian natural selection at the first tier by Milankovitch cycles at the second tier.

scholarly journals The life cycle of Drosophila orphan genes

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Nicola Palmieri ◽  
Carolin Kosiol ◽  
Christian Schlötterer
Keyword(s):  
Life Cycle ◽  
Time Scales ◽  
High Rate ◽  
Sequence Evolution ◽  
Functional Requirements ◽  
Evolutionary Time ◽  
Orphan Genes ◽  
Functional Conservation ◽  
Close Relatives ◽  
Obscura Group

Orphans are genes restricted to a single phylogenetic lineage and emerge at high rates. While this predicts an accumulation of genes, the gene number has remained remarkably constant through evolution. This paradox has not yet been resolved. Because orphan genes have been mainly analyzed over long evolutionary time scales, orphan loss has remained unexplored. Here we study the patterns of orphan turnover among close relatives in the Drosophila obscura group. We show that orphans are not only emerging at a high rate, but that they are also rapidly lost. Interestingly, recently emerged orphans are more likely to be lost than older ones. Furthermore, highly expressed orphans with a strong male-bias are more likely to be retained. Since both lost and retained orphans show similar evolutionary signatures of functional conservation, we propose that orphan loss is not driven by high rates of sequence evolution, but reflects lineage-specific functional requirements.

scholarly journals Extinction in complex communities as driven by adaptive dynamics

2021 ◽  
Author(s):  
Vu Nguyen ◽  
Dervis Vural
Keyword(s):  
Time Scales ◽  
Computer Simulations ◽  
Analytical Solutions ◽  
Adaptive Dynamics ◽  
Mathematical Framework ◽  
Evolutionary Time ◽  
Community Interactions ◽  
Fitness Functions ◽  
Evolutionary Changes

In a complex community, species continuously adapt to each other. On rare occasions, the adaptation of a species can lead to the extinction of others, and even its own. ``Adaptive dynamics'' is the standard mathematical framework to describe evolutionary changes in community interactions, and in particular, predict adaptation driven extinction. Unfortunately, most authors implement the equations of adaptive dynamics through computer simulations, that require assuming a large number of questionable parameters and fitness functions. In this study we present analytical solutions to adaptive dynamics equations, thereby clarifying how outcomes depend on any computational input. We develop general formulas that predict equilibrium abundances over evolutionary time scales. Additionally, we predict which species will go extinct next, and when this will happen.

scholarly journals An Improved Human smORF Annnotation Workflow Combining De Novo Transcriptome Assembly and Ribo-Seq

2019 ◽  
Author(s):  
Thomas F. Martinez ◽  
Qian Chu ◽  
Cynthia Donaldson ◽  
Dan Tan ◽  
Maxim N. Shokhirev ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Human Leukocyte ◽  
Open Reading Frames ◽  
Translation Efficiency ◽  
Proteomics Data ◽  
Protein Coding ◽  
Leukocyte Antigen ◽  
Human Genes ◽  
Small Open Reading Frames

Protein-coding small open reading frames (smORFs) are emerging as an important class of genes, however, the coding capacity of smORFs in the human genome is unclear. By integrating de novo transcriptome assembly and Ribo-Seq, we confidently annotate thousands of novel translated smORFs in three human cell lines. We find that smORF translation prediction is noisier than for annotated coding sequences, underscoring the importance of analyzing multiple experiments and footprinting conditions. These smORFs are located within non-coding and antisense transcripts, the UTRs of mRNAs, and unannotated transcripts. Analysis of RNA levels and translation efficiency during cellular stress identifies regulated smORFs, providing an approach to select smORFs for further investigation. Sequence conservation and signatures of positive selection indicate that encoded microproteins are likely functional. Additionally, proteomics data from enriched human leukocyte antigen complexes validates the translation of hundreds of smORFs and positions them as a source of novel antigens. Thus, smORFs represent a significant number of important, yet unexplored human genes.

scholarly journals Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

2019 ◽  
Vol 29 (6) ◽  
pp. 932-943 ◽  
Author(s):  
Éléonore Durand ◽  
Isabelle Gagnon-Arsenault ◽  
Johan Hallin ◽  
Isabelle Hatin ◽  
Alexandre K. Dubé ◽  
...  
Keyword(s):  
De Novo ◽  
Wild Yeast ◽  
De Novo Gene

scholarly journals Evolution and Diversity of Inherited Spiroplasma Symbionts in Myrmica Ants

2017 ◽  
Vol 84 (4) ◽  
Author(s):  
Matthew J. Ballinger ◽  
Logan D. Moore ◽  
Steve J. Perlman
Keyword(s):  
Time Scales ◽  
Genome Sequencing ◽  
Host Species ◽  
Species Interactions ◽  
Bacterial Symbiont ◽  
Evolutionary Time ◽  
Content Type ◽  
Myrmica Ants ◽  
Microbial Symbionts ◽  
Nutrient Provisioning

ABSTRACT Microbial partners play important roles in the biology and ecology of animals. In insects, maternally transmitted symbionts are especially common and can have host effects ranging from reproductive manipulation to nutrient provisioning and defense against natural enemies. In this study, we report a genus-wide association of Myrmica ants with the inherited bacterial symbiont Spiroplasma . We screen Myrmica ants collected from the wild, including the invasive European fire ant, Myrmica rubra , and find an extraordinarily high prevalence of this symbiont—8 of 9 species, 42 of 43 colonies, and 250 of 276 individual workers harbored Spiroplasma —only one host species was uninfected. In our screens, each host species carried a distinct Spiroplasma strain, and none were infected with more than one strain. All symbionts belong to the citri clade, allied most closely with pathogenic strains of Spiroplasma infecting corn crops and honeybees, and there is strong evidence of host-symbiont persistence across evolutionary time scales. Genome sequencing of two Spiroplasma symbionts revealed candidate genes that may play a part in the symbiosis, a nutrient transporter absent from other Spiroplasma strains, and a ribosome-inactivating protein previously implicated in parasite defense. These results together suggest long-term, likely mutualistic, relationships atypical of Spiroplasma -insect associations with potential significance for broad ecological interactions with Myrmica . IMPORTANCE Animal-associated microbial symbionts can dramatically affect the biology of their hosts. The identification and characterization of these intimate partnerships remain an essential component of describing and predicting species interactions, especially for invasive host species. Ants perform crucial ecological functions as ecosystem engineers, scavengers, and predators, and ants in the genus Myrmica can be aggressive resource competitors and reach high densities in their native and invaded habitats. In this study, a novel symbiosis is identified between Myrmica ants and the facultative bacterial symbiont Spiroplasma . Broad host distribution, high frequencies of infection, and host-symbiont codivergence over evolutionary time scales, an uncommon feature of Spiroplasma associations, suggest an important likely mutualistic interaction. Genome sequencing identified highly divergent gene candidates that may contribute to Spiroplasma 's role as a possible defensive or nutritional partner in Myrmica .

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