scholarly journals Entire genome transcription across evolutionary time exposes non-coding DNA to de novo gene emergence

2015 ◽  
Author(s):  
Rafik Neme ◽  
Diethard Tautz
Keyword(s):  
De Novo ◽  
Gene Evolution ◽  
Sequencing Analysis ◽  
Phylogenetic Distance ◽  
Evolutionary Time ◽  
Entire Genome ◽  
De Novo Gene ◽  
Mammalian Genomes ◽  
Genome Transcription ◽  
Deep Sequencing Analysis

Even in the best studied Mammalian genomes, less than 5% of the total genome length is annotated as exonic. However, deep sequencing analysis in humans has shown that around 40% of the genome may be covered by poly-adenylated non-coding transcripts occurring at low levels. Their functional significance is unclear, and there has been a dispute whether they should be considered as noise of the transcriptional machinery. We propose that if such transcripts show some evolutionary stability they will serve as substrates for de novo gene evolution, i.e. gene emergence out of non-coding DNA. Here, we characterize the phylogenetic turnover of low-level poly-adenylated transcripts in a comprehensive sampling of populations, sub-species and species of the genus Mus, spanning a phylogenetic distance of about 10 Myr. We find evidence for more evolutionary stable gains of transcription than losses among closely related taxa, balanced by a loss of older transcripts across the whole phylogeny. We show that adding taxa increases the genomic transcript coverage and that no major transcript-free islands exist over time. This suggests that the entire genome can be transcribed into poly-adenylated RNA when viewed at an evolutionary time scale. Thus, any part of the "non-coding" genome can become subject to evolutionary functionalization via de novo gene evolution.

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 De novo whole-genome assembly in interspecific hybrid table grape, ‘Shine Muscat’

2019 ◽  
Author(s):  
Kenta Shirasawa ◽  
Akifumi Azuma ◽  
Fumiya Taniguchi ◽  
Toshiya Yamamoto ◽  
Akihiko Sato ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Genome Structure ◽  
Table Grape ◽  
Sequencing Analysis ◽  
Entire Genome ◽  
Table Grapes ◽  
Eukaryotic Genes

AbstractThis study presents the first genome sequence of an interspecific grape hybrid, ‘Shine Muscat’ (Vitis labruscana × V. vinifera), an elite table grape cultivar bred in Japan. The complexity of the genome structure, arising from the interspecific hybridization, necessitated the use of a sophisticated genome assembly pipeline with short-read genome sequence data. The resultant genome assemblies consisted of two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a “haploid” genome. The unphased sequences spanned 490.1 Mb in length, 99.4% of the estimated genome size, with 8,696 scaffold sequences with an N50 length of 13.2 Mb. The phased sequences had 15,650 scaffolds spanning 1.0 Gb with N50 of 4.2 Mb. The two sequences comprised 94.7% and 96.3% of the core eukaryotic genes, indicating that the entire genome of ‘Shine Muscat’ was represented. Examination of genome structures revealed possible genome rearrangements between the genomes of ‘Shine Muscat’ and a V. vinifera line. Furthermore, full-length transcriptome sequencing analysis revealed 13,947 gene loci on the ‘Shine Muscat’ genome, from which 26,199 transcript isoforms were transcribed. These genome resources provide new insights that could help cultivation and breeding strategies produce more high-quality table grapes such as ‘Shine Muscat’.

scholarly journals Translation of neutrally evolving peptides provides a basis for de novo gene evolution

2018 ◽  
Vol 2 (5) ◽  
pp. 890-896 ◽  
Author(s):  
Jorge Ruiz-Orera ◽  
Pol Verdaguer-Grau ◽  
José Luis Villanueva-Cañas ◽  
Xavier Messeguer ◽  
M. Mar Albà
Keyword(s):  
De Novo ◽  
Gene Evolution ◽  
De Novo Gene

scholarly journals Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids

2019 ◽  
Vol 116 (10) ◽  
pp. 4400-4405 ◽  
Author(s):  
Xuan Zhuang ◽  
Chun Yang ◽  
Katherine R. Murphy ◽  
C.-H. Christina Cheng
Keyword(s):  
Molecular Mechanism ◽  
Evolutionary Biology ◽  
De Novo ◽  
Gene Evolution ◽  
Regulatory Element ◽  
Evolutionary Process ◽  
Transcriptional Initiation ◽  
Translocation Event ◽  
Antifreeze Glycoprotein ◽  
De Novo Gene

A fundamental question in evolutionary biology is how genetic novelty arises. De novo gene birth is a recently recognized mechanism, but the evolutionary process and function of putative de novo genes remain largely obscure. With a clear life-saving function, the diverse antifreeze proteins of polar fishes are exemplary adaptive innovations and models for investigating new gene evolution. Here, we report clear evidence and a detailed molecular mechanism for the de novo formation of the northern gadid (codfish) antifreeze glycoprotein (AFGP) gene from a minimal noncoding sequence. We constructed genomic DNA libraries for AFGP-bearing and AFGP-lacking species across the gadid phylogeny and performed fine-scale comparative analyses of theAFGPgenomic loci and homologs. We identified the noncoding founder region and a nine-nucleotide (9-nt) element therein that supplied the codons for one Thr-Ala-Ala unit from which the extant repetitive AFGP-coding sequence (cds) arose through tandem duplications. The latent signal peptide (SP)-coding exons were fortuitous noncoding DNA sequence immediately upstream of the 9-nt element, which, when spliced, supplied a typical secretory signal. Through a 1-nt frameshift mutation, these two parts formed a single read-through open reading frame (ORF). It became functionalized when a putative translocation event conferred the essentialcispromoter for transcriptional initiation. We experimentally proved that all genic components of the extant gadidAFGPoriginated from entirely nongenic DNA. The gadidAFGPevolutionary process also represents a rare example of the proto-ORF model of de novo gene birth where a fully formed ORF existed before the regulatory element to activate transcription was acquired.

scholarly journals The Discovery of De Novo Gene Evolution

2014 ◽  
Vol 57 (1) ◽  
pp. 149-161 ◽  
Author(s):  
Diethard Tautz
Keyword(s):  
De Novo ◽  
Gene Evolution ◽  
De Novo Gene

scholarly journals The ancient Salicoid genome duplication event: A platform for reconstruction of de Novo gene evolution in Populus trichocarpa

2021 ◽  
Author(s):  
Timothy B Yates ◽  
Kai Feng ◽  
Jin Zhang ◽  
Vasanth Singan ◽  
Sara S Jawdy ◽  
...  
Keyword(s):  
Genome Duplication ◽  
De Novo ◽  
Gene Evolution ◽  
Populus Trichocarpa ◽  
Duplication Event ◽  
Functional Enrichment ◽  
Orphan Genes ◽  
Genome Duplication Event ◽  
Orphan Gene ◽  
De Novo Gene

Abstract Orphan genes are characteristic genomic features that have no detectable homology to genes in any other species and represent an important attribute of genome evolution as sources of novel genetic functions. Here, we identified 445 genes specific to Populus trichocarpa. Of these, we performed deeper reconstruction of 13 orphan genes to provide evidence of de novo gene evolution. Populus and its sister genera Salix are particularly well suited for the study of orphan gene evolution because of the Salicoid whole-genome duplication event (WGD) which resulted in highly syntenic sister chromosomal segments across the Salicaceae. We leveraged this genomic feature to reconstruct de novo gene evolution from inter-genera, inter-species, and intra-genomic perspectives by comparing the syntenic regions within the P. trichocarpa reference, then P. deltoides, and finally Salix purpurea. Furthermore, we demonstrated that 86.5% of the putative orphan genes had evidence of transcription. Additionally, we also utilized the Populus genome-wide association mapping panel (GWAS), a collection of 1,084 undomesticated P. trichocarpa genotypes to further determine putative regulatory networks of orphan genes using expression quantitative trait loci (eQTL) mapping. Functional enrichment of these eQTL subnetworks identified common biological themes associated with orphan genes such as response to stress and defense response. We also identify a putative cis-element for a de novo gene and leverage conserved synteny to describe evolution of a putative transcription factor binding site. Overall, 45% of orphan genes were captured in trans-eQTL networks.

scholarly journals Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila

2019 ◽  
Author(s):  
Evan Witt ◽  
Sigi Benjamin ◽  
Nicolas Svetec ◽  
Li Zhao
Keyword(s):  
Single Cell ◽  
De Novo ◽  
Gene Evolution ◽  
Expression Patterns ◽  
Reproductive Function ◽  
Cell Types ◽  
Mutational Bias ◽  
Evolutionary Innovation ◽  
New Genes ◽  
De Novo Gene

SummaryThe testis is a peculiar tissue in many respects. It shows patterns of rapid gene evolution and provides a hotspot for the origination of genetic novelties such as de novo genes, duplications and mutations. To investigate the expression patterns of genetic novelties across cell types, we performed single-cell RNA-sequencing of adult Drosophila testis. We found that new genes were expressed in various cell types, the patterns of which may be influenced by their mode of origination. In particular, lineage-specific de novo genes are commonly expressed in early spermatocytes, while young duplicated genes are often bimodally expressed. Analysis of germline substitutions suggests that spermatogenesis is a highly reparative process, with the mutational load of germ cells decreasing as spermatogenesis progresses. By elucidating the distribution of genetic novelties across spermatogenesis, this study provides a deeper understanding of how the testis maintains its core reproductive function while being a hotbed of evolutionary innovation.

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