Special Issue "How Do New Genes Originate and Evolve?"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (25 October 2021).

Special Issue Editors

Prof. Manyuan Long
E-Mail Website
Guest Editor
Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA
Interests: New gene evolution, including rate, pattern, molecular mechanisms, and evolutionary forces. The Long lab is exploring the evolution of gene functionality and protein diversity by de novo genes and investigating evolutionary forces that drive new gene origination, ranging from adaptive evolution to sexual selection to sexual conflict leading to functional imperfection.
Prof. Esther Betran
E-Mail Website
Guest Editor
Department of Biology, University of Texas at Arlington, Arlington, TX, USA
Interests: The general topics of interest are evolutionary genomics and molecular evolution. In particular the Betrán lab focusses on the origin of functional innovations in the genomes. This includes the study of retrogenes (i.e., gene duplicates produced by means of an mRNA intermediate) and domesticated transposable element proteins.

Special Issue Information

Dear Colleagues, 

Every species has its own distinct genetic makeup and they underlie the great diversity of molecular functions and morphologies. How new genes with functional novelties originate is a fundamental evolutionary problem, having attracted a wide range of attention from scientists to audiences outside the scientific community. With the advent of the high throughput genome sequencing, powerful gene editing and precision molecular biological analyses, the evolutionary and functional properties of new genes are being unveiled. Consequently, the study of new genes has become more accessible and feasible, not only for model species but also for non-model organisms, revealing their evolution and often functional importance. The scientific questions that are explored to understand new genes can be enounced but they are not limited to: How do new genes originate and for what functions? What evolutionary forces operate during their acquisition? Are there any patterns or rules in the molecular mechanisms responsible for the origination of new genes? What are the rates of new gene origination in different lineages? We hope to receive a diverse set of submissions that represent the diversity of life and systems where those questions are being addressed. 

Prof. Manyuan Long
Prof. Esther Betran
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • New genes 
  • Gene duplication 
  • De novo genes 
  • Origin of sex-specific genes 
  • Transposable element protein domestication 
  • Viral protein domestication 
  • Horizontal gene transfer

Published Papers (8 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

Article
The Effects of Sequence Length and Composition of Random Sequence Peptides on the Growth of E. coli Cells
Genes 2021, 12(12), 1913; https://doi.org/10.3390/genes12121913 - 28 Nov 2021
Viewed by 192
Abstract
We study the potential for the de novo evolution of genes from random nucleotide sequences using libraries of E. coli expressing random sequence peptides. We assess the effects of such peptides on cell growth by monitoring frequency changes in individual clones in a [...] Read more.
We study the potential for the de novo evolution of genes from random nucleotide sequences using libraries of E. coli expressing random sequence peptides. We assess the effects of such peptides on cell growth by monitoring frequency changes in individual clones in a complex library through four serial passages. Using a new analysis pipeline that allows the tracing of peptides of all lengths, we find that over half of the peptides have consistent effects on cell growth. Across nine different experiments, around 16% of clones increase in frequency and 36% decrease, with some variation between individual experiments. Shorter peptides (8–20 residues), are more likely to increase in frequency, longer ones are more likely to decrease. GC content, amino acid composition, intrinsic disorder, and aggregation propensity show slightly different patterns between peptide groups. Sequences that increase in frequency tend to be more disordered with lower aggregation propensity. This coincides with the observation that young genes with more disordered structures are better tolerated in genomes. Our data indicate that random sequences can be a source of evolutionary innovation, since a large fraction of them are well tolerated by the cells or can provide a growth advantage. Full article
(This article belongs to the Special Issue How Do New Genes Originate and Evolve?)
Show Figures

Figure 1

Article
Evolutionary Characterization of the Short Protein SPAAR
Genes 2021, 12(12), 1864; https://doi.org/10.3390/genes12121864 - 24 Nov 2021
Viewed by 180
Abstract
Microproteins (<100 amino acids) are receiving increasing recognition as important participants in numerous biological processes, but their evolutionary dynamics are poorly understood. SPAAR is a recently discovered microprotein that regulates muscle regeneration and angiogenesis through interactions with conserved signaling pathways. Interestingly, SPAAR does [...] Read more.
Microproteins (<100 amino acids) are receiving increasing recognition as important participants in numerous biological processes, but their evolutionary dynamics are poorly understood. SPAAR is a recently discovered microprotein that regulates muscle regeneration and angiogenesis through interactions with conserved signaling pathways. Interestingly, SPAAR does not belong to any known protein family and has known homologs exclusively among placental mammals. This lack of distant homology could be caused by challenges in homology detection of short sequences, or it could indicate a recent de novo emergence from a noncoding sequence. By integrating syntenic alignments and homology searches, we identify SPAAR orthologs in marsupials and monotremes, establishing that SPAAR has existed at least since the emergence of mammals. SPAAR shows substantial primary sequence divergence but retains a conserved protein structure. In primates, we infer two independent evolutionary events leading to the de novo origination of 5′ elongated isoforms of SPAAR from a noncoding sequence and find evidence of adaptive evolution in this extended region. Thus, SPAAR may be of ancient origin, but it appears to be experiencing continual evolutionary innovation in mammals. Full article
(This article belongs to the Special Issue How Do New Genes Originate and Evolve?)
Show Figures

Figure 1

Article
Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes
Genes 2021, 12(11), 1819; https://doi.org/10.3390/genes12111819 - 19 Nov 2021
Viewed by 350
Abstract
Origination of new genes are of inherent interest of evolutionary geneticists for decades, but few studies have addressed the general pattern in a fish lineage. Using our recent released whole genome data of flatfishes, which evolved one of the most specialized body plans [...] Read more.
Origination of new genes are of inherent interest of evolutionary geneticists for decades, but few studies have addressed the general pattern in a fish lineage. Using our recent released whole genome data of flatfishes, which evolved one of the most specialized body plans in vertebrates, we identified 1541 (6.9% of the starry flounder genes) flatfish-lineage-specific genes. The origination pattern of these flatfish new genes is largely similar to those observed in other vertebrates, as shown by the proportion of DNA-mediated duplication (1317; 85.5%), RNA-mediated duplication (retrogenes; 96; 6.2%), and de novo–origination (128; 8.3%). The emergence rate of species-specific genes is 32.1 per Mya and the whole average level rate for the flatfish-lineage-specific genes is 20.9 per Mya. A large proportion (31.4%) of these new genes have been subjected to selection, in contrast to the 4.0% in primates, while the old genes remain quite similar (66.4% vs. 65.0%). In addition, most of these new genes (70.8%) are found to be expressed, indicating their functionality. This study not only presents one example of systematic new gene identification in a teleost taxon based on comprehensive phylogenomic data, but also shows that new genes may play roles in body planning. Full article
(This article belongs to the Special Issue How Do New Genes Originate and Evolve?)
Show Figures

Figure 1

Article
New Genes in the Drosophila Y Chromosome: Lessons from D. willistoni
Genes 2021, 12(11), 1815; https://doi.org/10.3390/genes12111815 - 18 Nov 2021
Viewed by 251
Abstract
Y chromosomes play important roles in sex determination and male fertility. In several groups (e.g., mammals) there is strong evidence that they evolved through gene loss from a common X-Y ancestor, but in Drosophila the acquisition of new genes plays a major role. [...] Read more.
Y chromosomes play important roles in sex determination and male fertility. In several groups (e.g., mammals) there is strong evidence that they evolved through gene loss from a common X-Y ancestor, but in Drosophila the acquisition of new genes plays a major role. This conclusion came mostly from studies in two species. Here we report the identification of the 22 Y-linked genes in D. willistoni. They all fit the previously observed pattern of autosomal or X-linked testis-specific genes that duplicated to the Y. The ratio of gene gains to gene losses is ~25 in D. willistoni, confirming the prominent role of gene gains in the evolution of Drosophila Y chromosomes. We also found four large segmental duplications (ranging from 62 kb to 303 kb) from autosomal regions to the Y, containing ~58 genes. All but four of these duplicated genes became pseudogenes in the Y or disappeared. In the GK20609 gene the Y-linked copy remained functional, whereas its original autosomal copy degenerated, demonstrating how autosomal genes are transferred to the Y chromosome. Since the segmental duplication that carried GK20609 contained six other testis-specific genes, it seems that chance plays a significant role in the acquisition of new genes by the Drosophila Y chromosome. Full article
(This article belongs to the Special Issue How Do New Genes Originate and Evolve?)
Show Figures

Figure 1

Article
On the Origin and Evolution of Drosophila New Genes during Spermatogenesis
Genes 2021, 12(11), 1796; https://doi.org/10.3390/genes12111796 - 15 Nov 2021
Viewed by 568
Abstract
The origin of functional new genes is a basic biological process that has significant contribution to organismal diversity. Previous studies in both Drosophila and mammals showed that new genes tend to be expressed in testes and avoid the X chromosome, presumably because of [...] Read more.
The origin of functional new genes is a basic biological process that has significant contribution to organismal diversity. Previous studies in both Drosophila and mammals showed that new genes tend to be expressed in testes and avoid the X chromosome, presumably because of meiotic sex chromosome inactivation (MSCI). Here, we analyze the published single-cell transcriptome data of Drosophila adult testis and find an enrichment of male germline mitotic genes, but an underrepresentation of meiotic genes on the X chromosome. This can be attributed to an excess of autosomal meiotic genes that were derived from their X-linked mitotic progenitors, which provides direct cell-level evidence for MSCI in Drosophila. We reveal that new genes, particularly those produced by retrotransposition, tend to exhibit an expression shift toward late spermatogenesis compared with their parental copies, probably due to the more intensive sperm competition or sexual conflict. Our results dissect the complex factors including age, the origination mechanisms and the chromosomal locations that influence the new gene origination and evolution in testes, and identify new gene cases that show divergent cell-level expression patterns from their progenitors for future functional studies. Full article
(This article belongs to the Special Issue How Do New Genes Originate and Evolve?)
Show Figures

Figure 1

Article
Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes
Genes 2021, 12(11), 1777; https://doi.org/10.3390/genes12111777 - 09 Nov 2021
Viewed by 259
Abstract
The de novo birth of functional genes from non-coding DNA as an important contributor to new gene formation is increasingly supported by evidence from diverse eukaryotic lineages. However, many uncertainties remain, including how the incipient de novo genes would continue to evolve and [...] Read more.
The de novo birth of functional genes from non-coding DNA as an important contributor to new gene formation is increasingly supported by evidence from diverse eukaryotic lineages. However, many uncertainties remain, including how the incipient de novo genes would continue to evolve and the molecular mechanisms underlying their evolutionary trajectory. Here we address these questions by investigating evolutionary history of the de novo antifreeze glycoprotein (AFGP) gene and gene family in gadid (codfish) lineages. We examined AFGP phenotype on a phylogenetic framework encompassing a broad sampling of gadids from freezing and non-freezing habitats. In three select species representing different AFGP-bearing clades, we analyzed all AFGP gene family members and the broader scale AFGP genomic regions in detail. Codon usage analyses suggest that motif duplication produced the intragenic AFGP tripeptide coding repeats, and rapid sequence divergence post-duplication stabilized the recombination-prone long repetitive coding region. Genomic loci analyses support AFGP originated once from a single ancestral genomic origin, and shed light on how the de novo gene proliferated into a gene family. Results also show the processes of gene duplication and gene loss are distinctive in separate clades, and both genotype and phenotype are commensurate with differential local selective pressures. Full article
(This article belongs to the Special Issue How Do New Genes Originate and Evolve?)
Show Figures

Figure 1

Article
Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development
Genes 2021, 12(10), 1628; https://doi.org/10.3390/genes12101628 - 16 Oct 2021
Viewed by 386
Abstract
Gene duplications generate new genes that can contribute to expression changes and the evolution of new functions. Genomes often consist of gene families that undergo expansions, some of which occur in specific lineages that reflect recent adaptive diversification. In this study, lineage-specific genes [...] Read more.
Gene duplications generate new genes that can contribute to expression changes and the evolution of new functions. Genomes often consist of gene families that undergo expansions, some of which occur in specific lineages that reflect recent adaptive diversification. In this study, lineage-specific genes and gene family expansions were studied across five dictyostelid species to determine when and how they are expressed during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression (predominant expression in one developmental stage) in each species and at most developmental time points, suggesting independent functional innovations of new genes throughout the phylogeny. Biased duplicate genes had greater expression divergence than their orthologs and paralogs, consistent with subfunctionalization or neofunctionalization. Lineage-specific expansions in particular had biased genes with both molecular signals of positive selection and high expression, suggesting adaptive genetic and transcriptional diversification following duplication. Our results present insights into the potential contributions of lineage-specific genes and families in generating species-specific phenotypes during multicellular development in dictyostelids. Full article
(This article belongs to the Special Issue How Do New Genes Originate and Evolve?)
Show Figures

Figure 1

Review

Jump to: Research

Review
Gene Duplication and Gene Fusion Are Important Drivers of Tumourigenesis during Cancer Evolution
Genes 2021, 12(9), 1376; https://doi.org/10.3390/genes12091376 - 31 Aug 2021
Viewed by 567
Abstract
Chromosomal rearrangement and genome instability are common features of cancer cells in human. Consequently, gene duplication and gene fusion events are frequently observed in human malignancies and many of the products of these events are pathogenic, representing significant drivers of tumourigenesis and cancer [...] Read more.
Chromosomal rearrangement and genome instability are common features of cancer cells in human. Consequently, gene duplication and gene fusion events are frequently observed in human malignancies and many of the products of these events are pathogenic, representing significant drivers of tumourigenesis and cancer evolution. In certain subsets of cancers duplicated and fused genes appear to be essential for initiation of tumour formation, and some even have the capability of transforming normal cells, highlighting the importance of understanding the events that result in their formation. The mechanisms that drive gene duplication and fusion are unregulated in cancer and they facilitate rapid evolution by selective forces akin to Darwinian survival of the fittest on a cellular level. In this review, we examine current knowledge of the landscape and prevalence of gene duplication and gene fusion in human cancers. Full article
(This article belongs to the Special Issue How Do New Genes Originate and Evolve?)
Show Figures

Figure 1

Back to TopTop