scholarly journals A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster

2021 ◽  
Author(s):  
Emily L. Rivard ◽  
Andrew G. Ludwig ◽  
Prajal H. Patel ◽  
Anna Grandchamp ◽  
Sarah E. Arnold ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Male Fertility ◽  
De Novo ◽  
Developmental Process ◽  
Chromatin Condensation ◽  
Protein Coding ◽  
Non Coding Rna ◽  
De Novo Genes ◽  
History Of ◽  
Redundant Role

Comparative genomics has enabled the identification of genes that potentially evolved de novo from non-coding sequences. Many such genes are expressed in male reproductive tissues, but their functions remain poorly understood. To address this, we conducted a functional genetic screen of over 40 putative de novo genes with testis-enriched expression in Drosophila melanogaster and identified one gene, atlas, required for male fertility. Detailed genetic and cytological analyses show that atlas is required for proper chromatin condensation during the final stages of spermatogenesis. Atlas protein is expressed in spermatid nuclei and facilitates the transition from histone- to protamine-based chromatin packaging. Complementary evolutionary analyses revealed the complex evolutionary history of atlas. The protein-coding portion of the gene likely arose at the base of the Drosophila genus on the X chromosome but was unlikely to be essential, as it was then lost in several independent lineages. Within the last ~15 million years, however, the gene moved to an autosome, where it fused with a conserved non-coding RNA and evolved a non-redundant role in male fertility. Altogether, this study provides insight into the integration of novel genes into biological processes, the links between genomic innovation and functional evolution, and the genetic control of a fundamental developmental process, gametogenesis.

scholarly journals A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster

PLoS Genetics ◽  
2021 ◽  
Vol 17 (9) ◽  
pp. e1009787
Author(s):  
Emily L. Rivard ◽  
Andrew G. Ludwig ◽  
Prajal H. Patel ◽  
Anna Grandchamp ◽  
Sarah E. Arnold ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Male Fertility ◽  
De Novo ◽  
Developmental Process ◽  
Chromatin Condensation ◽  
Protein Coding ◽  
Non Coding Rna ◽  
History Of ◽  
Redundant Role ◽  
Insight Into

Comparative genomics has enabled the identification of genes that potentially evolved de novo from non-coding sequences. Many such genes are expressed in male reproductive tissues, but their functions remain poorly understood. To address this, we conducted a functional genetic screen of over 40 putative de novo genes with testis-enriched expression in Drosophila melanogaster and identified one gene, atlas, required for male fertility. Detailed genetic and cytological analyses showed that atlas is required for proper chromatin condensation during the final stages of spermatogenesis. Atlas protein is expressed in spermatid nuclei and facilitates the transition from histone- to protamine-based chromatin packaging. Complementary evolutionary analyses revealed the complex evolutionary history of atlas. The protein-coding portion of the gene likely arose at the base of the Drosophila genus on the X chromosome but was unlikely to be essential, as it was then lost in several independent lineages. Within the last ~15 million years, however, the gene moved to an autosome, where it fused with a conserved non-coding RNA and evolved a non-redundant role in male fertility. Altogether, this study provides insight into the integration of novel genes into biological processes, the links between genomic innovation and functional evolution, and the genetic control of a fundamental developmental process, gametogenesis.

scholarly journals Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence

2020 ◽  
Vol 12 (8) ◽  
pp. 1355-1366
Author(s):  
Karina Zile ◽  
Christophe Dessimoz ◽  
Yannick Wurm ◽  
Joanna Masel
Keyword(s):  
Drosophila Melanogaster ◽  
De Novo ◽  
Experimental Studies ◽  
High Confidence ◽  
Protein Coding ◽  
Noncoding Sequences ◽  
De Novo Genes ◽  
Intergenic Sequences ◽  
Drosophila Melanogaster Subgroup ◽  
Reading Frames

Abstract Taxonomically restricted genes (TRGs) are genes that are present only in one clade. Protein-coding TRGs may evolve de novo from previously noncoding sequences: functional ncRNA, introns, or alternative reading frames of older protein-coding genes, or intergenic sequences. A major challenge in studying de novo genes is the need to avoid both false-positives (nonfunctional open reading frames and/or functional genes that did not arise de novo) and false-negatives. Here, we search conservatively for high-confidence TRGs as the most promising candidates for experimental studies, ensuring functionality through conservation across at least two species, and ensuring de novo status through examination of homologous noncoding sequences. Our pipeline also avoids ascertainment biases associated with preconceptions of how de novo genes are born. We identify one TRG family that evolved de novo in the Drosophila melanogaster subgroup. This TRG family contains single-copy genes in Drosophila simulans and Drosophila sechellia. It originated in an intron of a well-established gene, sharing that intron with another well-established gene upstream. These TRGs contain an intron that predates their open reading frame. These genes have not been previously reported as de novo originated, and to our knowledge, they are the best Drosophila candidates identified so far for experimental studies aimed at elucidating the properties of de novo genes.

scholarly journals A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila

2020 ◽  
Vol 88 (4) ◽  
pp. 382-398 ◽  
Author(s):  
Brennen Heames ◽  
Jonathan Schmitz ◽  
Erich Bornberg-Bauer
Keyword(s):  
De Novo ◽  
Protein Coding ◽  
De Novo Genes

scholarly journals NOVEL INTRONIC NON-CODING RNAS CONTRIBUTE TO MAINTENANCE OF PHENOTYPE IN SACCHAROMYCES CEREVISIAE

2015 ◽  
Author(s):  
Katarzyna B Hooks ◽  
Samina Naseeb ◽  
Sam Griffiths-Jones ◽  
Daniela Delneri
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Structure ◽  
Structure Prediction ◽  
De Novo ◽  
Intron Retention ◽  
Intron Loss ◽  
Common Belief ◽  
Rna Structures ◽  
Protein Coding ◽  
Non Coding Rna

The Saccharomyces cerevisiae genome has undergone extensive intron loss during its evolutionary history. It has been suggested that the few remaining introns (in only 5% of protein-coding genes) are retained because of their impact on function under stress conditions. Here, we explore the possibility that novel non-coding RNA structures (ncRNAs) are embedded within intronic sequences and are contributing to phenotype and intron retention in yeast. We employed de novo RNA structure prediction tools to screen intronic sequences in S. cerevisiae and 36 other fungi. We identified and validated 19 new intronic RNAs via RNAseq and RT-PCR. Contrary to common belief that excised introns are rapidly degraded, we found that, in six cases, the excised introns were maintained intact in the cells. In other two cases we showed that the ncRNAs were further processed from their introns. RNAseq analysis confirmed higher expression of introns in the ribosomial protein genes containing predicted RNA structures. We deleted the novel intronic RNA structure within the GLC7 intron and showed that this predicted ncRNA, rather than the intron itself, is responsible for the cell???s ability to respond to salt stress. We also showed a direct association between the presence of the intronic ncRNA and GLC7 expression. Overall, these data support the notion that some introns may have been maintained in the genome because they harbour functional ncRNAs.

scholarly journals Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae

Plants ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 737 ◽  
Author(s):  
Abdullah ◽  
Claudia L. Henriquez ◽  
Furrukh Mehmood ◽  
Iram Shahzadi ◽  
Zain Ali ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Trna Genes ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
History Of ◽  
And Bisexual ◽  
Contraction And Expansion

The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17–18 genes are duplicated in the inverted repeat (IR) regions, comprising 6–7 protein-coding (including trans-splicing gene rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in S. bogneri, including ycf2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.

scholarly journals Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

Science ◽  
2014 ◽  
Vol 343 (6172) ◽  
pp. 769-772 ◽  
Author(s):  
L. Zhao ◽  
P. Saelao ◽  
C. D. Jones ◽  
D. J. Begun
Keyword(s):  
Drosophila Melanogaster ◽  
De Novo ◽  
De Novo Genes

scholarly journals Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mingzheng Duan ◽  
Haiying Bao ◽  
Tolgor Bau
Keyword(s):  
Life History ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Gene Families ◽  
Single Copy ◽  
Mushroom Species ◽  
Protein Coding ◽  
Homologous Genes ◽  
Metabolic Genes ◽  
History Of

AbstractIn this study, we report a de novo assembly of the first high-quality genome for a wild mushroom species Leucocalocybe mongolica (LM). We performed high-throughput transcriptome sequencing to analyze the genetic basis for the life history of LM. Our results show that the genome size of LM is 46.0 Mb, including 26 contigs with a contig N50 size of 3.6 Mb. In total, we predicted 11,599 protein-coding genes, of which 65.7% (7630) could be aligned with high confidence to annotated homologous genes in other species. We performed phylogenetic analyses using genes form 3269 single-copy gene families and showed support for distinguishing LM from the genus Tricholoma (L.) P.Kumm., in which it is sometimes circumscribed. We believe that one reason for limited wild occurrences of LM may be the loss of key metabolic genes, especially carbohydrate-active enzymes (CAZymes), based on comparisons with other closely related species. The results of our transcriptome analyses between vegetative (mycelia) and reproductive (fruiting bodies) organs indicated that changes in gene expression among some key CAZyme genes may help to determine the switch from asexual to sexual reproduction. Taken together, our genomic and transcriptome data for LM comprise a valuable resource for both understanding the evolutionary and life history of this species.

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.

The origins and evolutionary history of human non-coding RNA regulatory networks

2017 ◽  
Vol 15 (02) ◽  
pp. 1750005 ◽  
Author(s):  
Masih Sherafatian ◽  
Seyed Javad Mowla
Keyword(s):  
Cell Cycle ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Evolutionary History ◽  
Regulatory Function ◽  
Protein Coding ◽  
Evolutionary Pattern ◽  
Non Coding Rna ◽  
History Of ◽  
Non Coding Rnas

The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3′-UTR and lesser known 5′-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3′ and 5′ UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.

scholarly journals Evolution of the rapidly mutating human salivary agglutinin gene (DMBT1) and population subsistence strategy

2015 ◽  
Vol 112 (16) ◽  
pp. 5105-5110 ◽  
Author(s):  
Shamik Polley ◽  
Sandra Louzada ◽  
Diego Forni ◽  
Manuela Sironi ◽  
Theodosius Balaskas ◽  
...  
Keyword(s):  
Mutation Rate ◽  
De Novo ◽  
Scavenger Receptor ◽  
Dietary Change ◽  
De Novo Mutation ◽  
Protein Coding ◽  
History Of Agriculture ◽  
Oral Bacterium ◽  
Number Variation ◽  
History Of

The dietary change resulting from the domestication of plant and animal species and development of agriculture at different locations across the world was one of the most significant changes in human evolution. An increase in dietary carbohydrates caused an increase in dental caries following the development of agriculture, mediated by the cariogenic oral bacteriumStreptococcus mutans. Salivary agglutinin [SAG, encoded by the deleted in malignant brain tumors 1 (DMBT1) gene] is an innate immune receptor glycoprotein that binds a variety of bacteria and viruses, and mediates attachment ofS. mutansto hydroxyapatite on the surface of the tooth. In this study we show that multiallelic copy number variation (CNV) withinDMBT1is extensive across all populations and is predicted to result in between 7–20 scavenger–receptor cysteine-rich (SRCR) domains within each SAG molecule. Direct observation of de novo mutation in multigeneration families suggests these CNVs have a very high mutation rate for a protein-coding locus, with a mutation rate of up to 5% per gamete. Given that the SRCR domains bindS. mutansand hydroxyapatite in the tooth, we investigated the association of sequence diversity at the SAG-binding gene ofS. mutans, andDMBT1CNV. Furthermore, we show thatDMBT1CNV is also associated with a history of agriculture across global populations, suggesting that dietary change as a result of agriculture has shaped the pattern of CNV atDMBT1, and that theDMBT1-S. mutansinteraction is a promising model of host-pathogen-culture coevolution in humans.

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