scholarly journals Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution

2016 ◽  
Vol 33 (5) ◽  
pp. 1245-1256 ◽  
Author(s):  
Bryan A. Moyers ◽  
Jianzhi Zhang
Keyword(s):  
Genome Evolution ◽  
De Novo ◽  
De Novo Gene

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 Software Evaluation for de novo Detection of Transposons

2021 ◽  
Author(s):  
Matias Rodriguez ◽  
Wojciech Makałowski
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
De Novo ◽  
Simulated Data ◽  
Genomic Sequences ◽  
Software Evaluation ◽  
Easy Task ◽  
Eukaryotic Genomes

AbstractTransposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance on both simulated data and well curated genomic sequences. The results will be helpful for identifying common issues associated with TE-annotation and for evaluating how comparable are the results obtained with different tools.

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).

scholarly journals De novo gene conversion in the RCA gene cluster (1q32) causes mutations in complement factor H associated with atypical hemolytic uremic syndrome

2006 ◽  
Vol 27 (3) ◽  
pp. 292-293 ◽  
Author(s):  
Stefan Heinen ◽  
Pilar Sanchez-Corral ◽  
Michael S Jackson ◽  
Lisa Strain ◽  
Judith A. Goodship ◽  
...  
Keyword(s):  
Hemolytic Uremic Syndrome ◽  
Gene Conversion ◽  
Gene Cluster ◽  
De Novo ◽  
Atypical Hemolytic Uremic Syndrome ◽  
Factor H ◽  
Complement Factor H ◽  
Complement Factor ◽  
De Novo Gene ◽  
Uremic Syndrome

scholarly journals Contribution of retrotransposition to developmental disorders

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Eugene J. Gardner ◽  
Elena Prigmore ◽  
Giuseppe Gallone ◽  
Petr Danecek ◽  
Kaitlin E. Samocha ◽  
...  
Keyword(s):  
Developmental Disorders ◽  
De Novo ◽  
Purifying Selection ◽  
Selective Constraint ◽  
Protein Coding ◽  
Genome Wide ◽  
De Novo Gene ◽  
The Impact ◽  
Transcribed Sequences

Abstract Mobile genetic Elements (MEs) are segments of DNA which can copy themselves and other transcribed sequences through the process of retrotransposition (RT). In humans several disorders have been attributed to RT, but the role of RT in severe developmental disorders (DD) has not yet been explored. Here we identify RT-derived events in 9738 exome sequenced trios with DD-affected probands. We ascertain 9 de novo MEs, 4 of which are likely causative of the patient’s symptoms (0.04%), as well as 2 de novo gene retroduplications. Beyond identifying likely diagnostic RT events, we estimate genome-wide germline ME mutation rate and selective constraint and demonstrate that coding RT events have signatures of purifying selection equivalent to those of truncating mutations. Overall, our analysis represents a comprehensive interrogation of the impact of retrotransposition on protein coding genes and a framework for future evolutionary and disease studies.

Platelet microparticles reprogram macrophage gene expression and function

2016 ◽  
Vol 115 (02) ◽  
pp. 311-323 ◽  
Author(s):  
Matthieu Rousseau ◽  
Anne-Claire Duchez ◽  
Chan Ho C. Lee ◽  
Eric Boilard ◽  
Benoit Laffont ◽  
...  
Keyword(s):  
Actinomycin D ◽  
De Novo ◽  
Phagocytic Capacity ◽  
Human Macrophages ◽  
Mrna Targets ◽  
De Novo Gene ◽  
Supplementary Material ◽  
And Function ◽  
Microarray Analyses ◽  
Platelet Microparticles

SummaryPlatelet microparticles (MPs) represent the most abundant MPs subtype in the circulation, and can mediate intercellular communication through delivery of bioactives molecules, such as cytokines, proteins, lipids and RNAs. Here, we show that platelet MPs can be internalised by primary human macrophages and deliver functional miR-126–3p. The increase in macrophage miR-126–3p levels was not prevented by actinomycin D, suggesting that it was not due to de novo gene transcription. Platelet MPs dose-dependently downregulated expression of four predicted mRNA targets of miR-126–3p, two of which were confirmed also at the protein level. The mRNA downregulatory effects of platelet MPs were abrogated by expression of a neutralising miR-126–3p sponge, implying the involvement of miR-126–3p. Transcriptome-wide, microarray analyses revealed that as many as 66 microRNAs and 653 additional RNAs were significantly and differentially expressed in macrophages upon exposure to platelet MPs. More specifically, platelet MPs induced an upregulation of 34 microRNAs and a concomitant downregulation of 367 RNAs, including mRNAs encoding for cytokines/chemokines CCL4, CSF1 and TNF. These changes were associated with reduced CCL4, CSF1 and TNF cytokine/chemokine release by macrophages, and accompanied by a marked increase in their phagocytic capacity. These findings demonstrate that platelet MPs can modify the transcriptome of macrophages, and reprogram their function towards a phagocytic phenotype.Supplementary Material to this article is available online at www.thrombosis-online.com.

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
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