Population biology of accessory gland-expressed de novo genes in Drosophila melanogaster

Genetics ◽  
2021 ◽  
Author(s):  
Julie M Cridland ◽  
Alex C Majane ◽  
Li Zhao ◽  
David J Begun
Keyword(s):  
Population Biology ◽  
De Novo ◽  
Formal Analysis ◽  
Accessory Gland ◽  
Male Reproduction ◽  
Chromosomal Distribution ◽  
De Novo Genes ◽  
De Novo Gene ◽  
Direct Cross ◽  
Analysis Of Variation

Abstract Early work on de novo gene discovery in Drosophila was consistent with the idea that many such genes have male-biased patterns of expression, including a large number expressed in the testis. However, there has been little formal analysis of variation in the abundance and properties of de novo genes expressed in different tissues. Here we investigate the population biology of recently evolved de novo genes expressed in the D. melanogaster accessory gland, a somatic male tissue that plays an important role in male and female fertility and the post mating response of females, using the same collection of inbred lines used previously to identify testis-expressed de novo genes, thus allowing for direct cross tissue comparisons of these genes in two tissues of male reproduction. Using RNA-seq data we identify candidate de novo genes located in annotated intergenic and intronic sequence and determine the properties of these genes including chromosomal location, expression, abundance, and coding capacity. Generally, we find major differences between the tissues in terms of gene abundance and expression, though other properties such as transcript length and chromosomal distribution are more similar. We also explore differences between regulatory mechanisms of de novo genes in the two tissues and how such differences may interact with selection to produce differences in D. melanogaster de novo genes expressed in the two tissues.

scholarly journals Comparative transcriptomics and ribo-seq: Looking at de novo gene emergence in Saccharomycotina

2017 ◽  
Author(s):  
William Blevins ◽  
Mar Albà ◽  
Lucas Carey
Keyword(s):  
De Novo ◽  
Ribosome Profiling ◽  
Rna Seq ◽  
De Novo Genes ◽  
De Novo Gene ◽  
Rich Media ◽  
Conserved Genes ◽  
Different Depths ◽  
Yeast Phylogeny ◽  
And Oxidative Stress

In de novo gene emergence, a segment of non-coding DNA undergoes a series of changes which enables transcription, potentially leading to a new protein that could eventually acquire a novel function. Due to their recent origins, young de novo genes have no homology with other genes. Furthermore, de novo genes may not initially be under the same selective constraints as other genes. Dozens of de novo genes have recently been identified in many diverse species; however, the mechanisms leading to their appearance are not yet well understood. To study this phenomenon, we have performed deep RNA sequencing (RNA-seq) on 11 species of yeast from the phylum of Ascomycota in both rich media and oxidative stress conditions. Furthermore, we performed ribosome profiling (Ribo-seq) experiments in both conditions with S. cerevisiae. These data have been used to classify the conservation of genes at different depths in the yeast phylogeny. Hundreds of genes in each species were novel (unannotated), and many were identified as putative de novo genes; these candidates were then tested for signals of translation using our Ribo-seq data. We show that putative de novo genes have different properties relative to phylogenetically conserved genes. This comparative phylotranscriptomic analysis advances our understanding of de novo gene origins.

scholarly journals Comparative transcriptomics and ribo-seq: Looking at de novo gene emergence in Saccharomycotina

2017 ◽  
Author(s):  
William Blevins ◽  
Mar Albà ◽  
Lucas Carey
Keyword(s):  
De Novo ◽  
Ribosome Profiling ◽  
Rna Seq ◽  
De Novo Genes ◽  
De Novo Gene ◽  
Rich Media ◽  
Conserved Genes ◽  
Different Depths ◽  
Yeast Phylogeny ◽  
And Oxidative Stress

In de novo gene emergence, a segment of non-coding DNA undergoes a series of changes which enables transcription, potentially leading to a new protein that could eventually acquire a novel function. Due to their recent origins, young de novo genes have no homology with other genes. Furthermore, de novo genes may not initially be under the same selective constraints as other genes. Dozens of de novo genes have recently been identified in many diverse species; however, the mechanisms leading to their appearance are not yet well understood. To study this phenomenon, we have performed deep RNA sequencing (RNA-seq) on 11 species of yeast from the phylum of Ascomycota in both rich media and oxidative stress conditions. Furthermore, we performed ribosome profiling (Ribo-seq) experiments in both conditions with S. cerevisiae. These data have been used to classify the conservation of genes at different depths in the yeast phylogeny. Hundreds of genes in each species were novel (unannotated), and many were identified as putative de novo genes; these candidates were then tested for signals of translation using our Ribo-seq data. We show that putative de novo genes have different properties relative to phylogenetically conserved genes. This comparative phylotranscriptomic analysis advances our understanding of de novo gene origins.

scholarly journals From de novo to ‘de nono’: most novel protein coding genes identified with phylostratigraphy represent old genes or recent duplicates

2018 ◽  
Author(s):  
Claudio Casola
Keyword(s):  
De Novo ◽  
Sequence Similarity ◽  
Gc Content ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Gene Sets ◽  
De Novo Genes ◽  
De Novo Gene ◽  
Similarity Searches ◽  
Novel Protein

AbstractThe evolution of novel protein-coding genes from noncoding regions of the genome is one of the most compelling evidence for genetic innovations in nature. One popular approach to identify de novo genes is phylostratigraphy, which consists of determining the approximate time of origin (age) of a gene based on its distribution along a species phylogeny. Several studies have revealed significant flaws in determining the age of genes, including de novo genes, using phylostratigraphy alone. However, the rate of false positives in de novo gene surveys, based on phylostratigraphy, remains unknown. Here, I re-analyze the findings from three studies, two of which identified tens to hundreds of rodent-specific de novo genes adopting a phylostratigraphy-centered approach. Most of the putative de novo genes discovered in these investigations are no longer included in recently updated mouse gene sets. Using a combination of synteny information and sequence similarity searches, I show that about 60% of the remaining 381 putative de novo genes share homology with genes from other vertebrates, originated through gene duplication, and/or share no synteny information with non-rodent mammals. These results led to an estimated rate of ∼12 de novo genes per million year in mouse. Contrary to a previous study (Wilson et al. 2017), I found no evidence supporting the preadaptation hypothesis of de novo gene formation. Nearly half of the de novo genes confirmed in this study are within older genes, indicating that co-option of preexisting regulatory regions and a higher GC content may facilitate the origin of novel genes.

scholarly journals Uncovering de novo gene birth in yeast using deep transcriptomics

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
William R. Blevins ◽  
Jorge Ruiz-Orera ◽  
Xavier Messeguer ◽  
Bernat Blasco-Moreno ◽  
José Luis Villanueva-Cañas ◽  
...  
Keyword(s):  
De Novo ◽  
Yeast Species ◽  
Large Fraction ◽  
Raw Material ◽  
Opposite Orientation ◽  
New Genes ◽  
Small Proteins ◽  
De Novo Genes ◽  
De Novo Gene ◽  
Response To Stress

AbstractDe novo gene origination has been recently established as an important mechanism for the formation of new genes. In organisms with a large genome, intergenic and intronic regions provide plenty of raw material for new transcriptional events to occur, but little is know about how de novo transcripts originate in more densely-packed genomes. Here, we identify 213 de novo originated transcripts in Saccharomyces cerevisiae using deep transcriptomics and genomic synteny information from multiple yeast species grown in two different conditions. We find that about half of the de novo transcripts are expressed from regions which already harbor other genes in the opposite orientation; these transcripts show similar expression changes in response to stress as their overlapping counterparts, and some appear to translate small proteins. Thus, a large fraction of de novo genes in yeast are likely to co-evolve with already existing genes.

scholarly journals Functional cysteine-less subunits of the transporter associated with antigen processing (TAP1 and TAP2) by de novo gene assembly

FEBS Letters ◽  
2002 ◽  
Vol 533 (1) ◽  
pp. 42-46 ◽  
Author(s):  
Susanne Heintke ◽  
Min Chen ◽  
Ulrike Ritz ◽  
Brigitte Lankat-Buttgereit ◽  
Joachim Koch ◽  
...  
Keyword(s):  
Antigen Processing ◽  
De Novo ◽  
Gene Assembly ◽  
De Novo Gene

scholarly journals De Novo Sequencing, Assembly, and Annotation of Four Threespine Stickleback Genomes Based on Microfluidic Partitioned DNA Libraries

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 426 ◽  
Author(s):  
Daniel Berner ◽  
Marius Roesti ◽  
Steven Bilobram ◽  
Simon K. Chan ◽  
Heather Kirk ◽  
...  
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Gene Annotation ◽  
Model System ◽  
Threespine Stickleback ◽  
Evolutionary Genomics ◽  
Digital Repository ◽  
High Quality ◽  
De Novo Gene ◽  
Dna Libraries

The threespine stickleback is a geographically widespread and ecologically highly diverse fish that has emerged as a powerful model system for evolutionary genomics and developmental biology. Investigations in this species currently rely on a single high-quality reference genome, but would benefit from the availability of additional, independently sequenced and assembled genomes. We present here the assembly of four new stickleback genomes, based on the sequencing of microfluidic partitioned DNA libraries. The base pair lengths of the four genomes reach 92–101% of the standard reference genome length. Together with their de novo gene annotation, these assemblies offer a resource enhancing genomic investigations in stickleback. The genomes and their annotations are available from the Dryad Digital Repository (https://doi.org/10.5061/dryad.113j3h7).

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