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: 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 (2 papers)

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Research

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Article
Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development
Genes 2021, 12(10), 1628; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12101628 (registering DOI) - 16 Oct 2021
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?)
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Review

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Review
Gene Duplication and Gene Fusion Are Important Drivers of Tumourigenesis during Cancer Evolution
Genes 2021, 12(9), 1376; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12091376 - 31 Aug 2021
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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?)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Planned papers:

1. tentative title:

The role of length and sequence composition of random sequence peptides in affecting fitness in E. coli

Abstract:

To study the potential for a de novo evolution of genes out of random nucleotide sequences, we have expressed libraries of peptides in E. coli that were synthesized to achieve a random sequence composition. The fitness effects of the peptides were assessed via growing the cells in serial passages in competition with each other. Changes in frequency of individual cells harbouring a given peptide were monitored via sequencing. We find that a large fraction of peptides has a significant effect on the growth of the cells, either positive or negative. Interestingly, we find that the length of the predicted translation product correlates with the probability of being classified as positive or negative, with a bimodal distribution where the shortest and longest peptides tend to have more negative effects than the intermediate length peptides. We have also looked at other sequence features, such as GC content, amino acid distribution, intrinsic disorder and tendency for aggregation, but we do not find a clear dependence of these factors on the probability to become a negative or positive acting peptide. Our data confirm that the emergence of new genetic function out of random sequences is easily possible.

2. Tentative title: The multiple genomic signatures of adaptive introgression in Drosophila species

3. Tentative title: New regulatory elements and new genes

4. Tentative title:New gene origination in ciliates, particularly the Oxytricha lineage, associated with combinatorial DNA rearrangements and having

5.Tentative title: De novo genes

6.Tentative title: Zeuss gene

7.Tentative title: Gene duplication theory and/or horse genomes

8. Tentative title: New chimeric genes in Drosophila or humans

9. Tentative title: Mammalian promoters coming from TE

10: Tentative title: Mosquito intergenic sexual conflict and gene duplication

11.Tentative title: the polymorphic exon/intron structure and its functional/fitness effects in vertebrates

 

 
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