Special Issue "Gene Conversion in Duplicated Genes"

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics".

Deadline for manuscript submissions: closed (30 November 2010)

Special Issue Editor

Guest Editor
Dr. Hideki Innan

Graduate University for Advanced Studies Hayama, Kanagawa 240-0193, Japan
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Fax: +81-46-858-1544

Special Issue Information

Dear Colleagues,

Gene conversion is a nonreciprocal recombination process that occurs not only between orthologous regions (allelic gene conversion) but also between paralogous regions (non-allelic or interlocus gene conversion) and this special issue concerns the latter. Growing evidence shows that gene conversion between duplicated genes (or regions) is common and plays significant roles in the early stages of gene duplicates. This special issue aims at covering a wide range of topics about gene conversion between duplicates, from basic molecular biology on the mechanisms to evolutionary genetics and genomics. We welcome reviews and original papers on any kind of topic related to gene conversion.

Dr. Hideki Innan
Guest Editor

Keywords

  • non-allelic gene conversion
  • gene duplication
  • mechanism
  • evolution
  • disease

Published Papers (11 papers)

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Editorial

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Open AccessEditorial Special Issue: Gene Conversion in Duplicated Genes
Genes 2011, 2(2), 394-396; doi:10.3390/genes2020394
Received: 13 June 2011 / Accepted: 17 June 2011 / Published: 17 June 2011
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Abstract
Gene conversion is an outcome of recombination, causing non-reciprocal transfer of a DNA fragment. Several decades later than the discovery of crossing over, gene conversion was first recognized in fungi when non-Mendelian allelic distortion was observed. Gene conversion occurs when a double-strand break
[...] Read more.
Gene conversion is an outcome of recombination, causing non-reciprocal transfer of a DNA fragment. Several decades later than the discovery of crossing over, gene conversion was first recognized in fungi when non-Mendelian allelic distortion was observed. Gene conversion occurs when a double-strand break is repaired by using homologous sequences in the genome. In meiosis, there is a strong preference to use the orthologous region (allelic gene conversion), which causes non-Mendelian allelic distortion, but paralogous or duplicated regions can also be used for the repair (inter-locus gene conversion, also referred to as non-allelic and ectopic gene conversion). The focus of this special issue is the latter, interlocus gene conversion; the rate is lower than allelic gene conversion but it has more impact on phenotype because more drastic changes in DNA sequence are involved. [...] Full article
(This article belongs to the Special Issue Gene Conversion in Duplicated Genes)

Research

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Open AccessArticle The Rate and Tract Length of Gene Conversion between Duplicated Genes
Genes 2011, 2(2), 313-331; doi:10.3390/genes2020313
Received: 17 February 2011 / Revised: 11 March 2011 / Accepted: 17 March 2011 / Published: 25 March 2011
Cited by 11 | PDF Full-text (642 KB) | HTML Full-text | XML Full-text
Abstract
Interlocus gene conversion occurs such that a certain length of DNA fragment is non-reciprocally transferred (copied and pasted) between paralogous regions. To understand the rate and tract length of gene conversion, there are two major approaches. One is based on mutation-accumulation experiments, and
[...] Read more.
Interlocus gene conversion occurs such that a certain length of DNA fragment is non-reciprocally transferred (copied and pasted) between paralogous regions. To understand the rate and tract length of gene conversion, there are two major approaches. One is based on mutation-accumulation experiments, and the other uses natural DNA sequence variation. In this review, we overview the two major approaches and discuss their advantages and disadvantages. In addition, to demonstrate the importance of statistical analysis of empirical and evolutionary data for estimating tract length, we apply a maximum likelihood method to several data sets. Full article
(This article belongs to the Special Issue Gene Conversion in Duplicated Genes)
Open AccessArticle Neutral and Non-Neutral Evolution of Duplicated Genes with Gene Conversion
Genes 2011, 2(1), 191-209; doi:10.3390/genes2010191
Received: 30 December 2010 / Revised: 20 January 2011 / Accepted: 12 February 2011 / Published: 18 February 2011
Cited by 13 | PDF Full-text (550 KB) | HTML Full-text | XML Full-text
Abstract
Gene conversion is one of the major mutational mechanisms involved in the DNA sequence evolution of duplicated genes. It contributes to create unique patters of DNA polymorphism within species and divergence between species. A typical pattern is so-called concerted evolution, in which the
[...] Read more.
Gene conversion is one of the major mutational mechanisms involved in the DNA sequence evolution of duplicated genes. It contributes to create unique patters of DNA polymorphism within species and divergence between species. A typical pattern is so-called concerted evolution, in which the divergence between duplicates is maintained low for a long time because of frequent exchanges of DNA fragments. In addition, gene conversion affects the DNA evolution of duplicates in various ways especially when selection operates. Here, we review theoretical models to understand the evolution of duplicates in both neutral and non-neutral cases. We also explain how these theories contribute to interpreting real polymorphism and divergence data by using some intriguing examples. Full article
(This article belongs to the Special Issue Gene Conversion in Duplicated Genes)

Review

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Open AccessReview Enlightenment of Yeast Mitochondrial Homoplasmy: Diversified Roles of Gene Conversion
Genes 2011, 2(1), 169-190; doi:10.3390/genes2010169
Received: 13 January 2011 / Revised: 18 January 2011 / Accepted: 25 January 2011 / Published: 14 February 2011
Cited by 7 | PDF Full-text (554 KB) | HTML Full-text | XML Full-text
Abstract
Mitochondria have their own genomic DNA. Unlike the nuclear genome, each cell contains hundreds to thousands of copies of mitochondrial DNA (mtDNA). The copies of mtDNA tend to have heterogeneous sequences, due to the high frequency of mutagenesis, but are quickly homogenized within
[...] Read more.
Mitochondria have their own genomic DNA. Unlike the nuclear genome, each cell contains hundreds to thousands of copies of mitochondrial DNA (mtDNA). The copies of mtDNA tend to have heterogeneous sequences, due to the high frequency of mutagenesis, but are quickly homogenized within a cell (“homoplasmy”) during vegetative cell growth or through a few sexual generations. Heteroplasmy is strongly associated with mitochondrial diseases, diabetes and aging. Recent studies revealed that the yeast cell has the machinery to homogenize mtDNA, using a common DNA processing pathway with gene conversion; i.e., both genetic events are initiated by a double-stranded break, which is processed into 3' single-stranded tails. One of the tails is base-paired with the complementary sequence of the recipient double-stranded DNA to form a D-loop (homologous pairing), in which repair DNA synthesis is initiated to restore the sequence lost by the breakage. Gene conversion generates sequence diversity, depending on the divergence between the donor and recipient sequences, especially when it occurs among a number of copies of a DNA sequence family with some sequence variations, such as in immunoglobulin diversification in chicken. MtDNA can be regarded as a sequence family, in which the members tend to be diversified by a high frequency of spontaneous mutagenesis. Thus, it would be interesting to determine why and how double-stranded breakage and D-loop formation induce sequence homogenization in mitochondria and sequence diversification in nuclear DNA. We will review the mechanisms and roles of mtDNA homoplasmy, in contrast to nuclear gene conversion, which diversifies gene and genome sequences, to provide clues toward understanding how the common DNA processing pathway results in such divergent outcomes. Full article
(This article belongs to the Special Issue Gene Conversion in Duplicated Genes)
Open AccessReview Gene Duplication and Ectopic Gene Conversion in Drosophila
Genes 2011, 2(1), 131-151; doi:10.3390/genes2010131
Received: 24 December 2010 / Revised: 26 January 2011 / Accepted: 27 February 2011 / Published: 11 February 2011
Cited by 3 | PDF Full-text (337 KB) | HTML Full-text | XML Full-text
Abstract
The evolutionary impact of gene duplication events has been a theme of Drosophila genetics dating back to the Morgan School. While considerable attention has been placed on the genetic novelties that duplicates are capable of introducing, and the role that positive selection plays
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The evolutionary impact of gene duplication events has been a theme of Drosophila genetics dating back to the Morgan School. While considerable attention has been placed on the genetic novelties that duplicates are capable of introducing, and the role that positive selection plays in their early stages of duplicate evolution, much less attention has been given to the potential consequences of ectopic (non-allelic) gene conversion on these evolutionary processes. In this paper we consider the historical origins of ectopic gene conversion models and present a synthesis of the current Drosophila data in light of several primary questions in the field. Full article
(This article belongs to the Special Issue Gene Conversion in Duplicated Genes)
Open AccessReview Gene Conversion in Angiosperm Genomes with an Emphasis on Genes Duplicated by Polyploidization
Genes 2011, 2(1), 1-20; doi:10.3390/genes2010001
Received: 26 November 2010 / Revised: 6 December 2010 / Accepted: 6 January 2011 / Published: 10 January 2011
Cited by 15 | PDF Full-text (492 KB) | HTML Full-text | XML Full-text
Abstract
Angiosperm genomes differ from those of mammals by extensive and recursive polyploidizations. The resulting gene duplication provides opportunities both for genetic innovation, and for concerted evolution. Though most genes may escape conversion by their homologs, concerted evolution of duplicated genes can last for
[...] Read more.
Angiosperm genomes differ from those of mammals by extensive and recursive polyploidizations. The resulting gene duplication provides opportunities both for genetic innovation, and for concerted evolution. Though most genes may escape conversion by their homologs, concerted evolution of duplicated genes can last for millions of years or longer after their origin. Indeed, paralogous genes on two rice chromosomes duplicated an estimated 60–70 million years ago have experienced gene conversion in the past 400,000 years. Gene conversion preserves similarity of paralogous genes, but appears to accelerate their divergence from orthologous genes in other species. The mutagenic nature of recombination coupled with the buffering effect provided by gene redundancy, may facilitate the evolution of novel alleles that confer functional innovations while insulating biological fitness of affected plants. A mixed evolutionary model, characterized by a primary birth-and-death process and occasional homoeologous recombination and gene conversion, may best explain the evolution of multigene families. Full article
(This article belongs to the Special Issue Gene Conversion in Duplicated Genes)
Figures

Open AccessReview Genetic Diversification by Somatic Gene Conversion
Genes 2011, 2(1), 48-58; doi:10.3390/genes2010048
Received: 21 October 2010 / Revised: 14 December 2010 / Accepted: 15 December 2010 / Published: 10 January 2011
Cited by 4 | PDF Full-text (355 KB) | HTML Full-text | XML Full-text
Abstract
Gene conversion is a type of homologous recombination that leads to transfer of genetic information among homologous DNA sequences. It can be categorized into two classes: homogenizing and diversifying gene conversions. The former class results in neutralization and homogenization of any sequence variation
[...] Read more.
Gene conversion is a type of homologous recombination that leads to transfer of genetic information among homologous DNA sequences. It can be categorized into two classes: homogenizing and diversifying gene conversions. The former class results in neutralization and homogenization of any sequence variation among repetitive DNA sequences, and thus is important for concerted evolution. On the other hand, the latter functions to increase genetic diversity at the recombination-recipient loci. Thus, these two types of gene conversion play opposite roles in genome dynamics. Diversifying gene conversion is observed in the immunoglobulin (Ig) loci of chicken, rabbit, and other animals, and directs the diversification of Ig variable segments and acquisition of functional Ig repertoires. This type of gene conversion is initiated by the biased occurrence of recombination initiation events (e.g., DNA single- or double-strand breaks) on the recipient DNA site followed by unidirectional homologous recombination from multiple template sequences. Transcription and DNA accessibility is also important in the regulation of biased recombination initiation. In this review, we will discuss the biological significance and possible mechanisms of diversifying gene conversion in somatic cells of eukaryotes. Full article
(This article belongs to the Special Issue Gene Conversion in Duplicated Genes)
Open AccessReview Gene Conversion in Human Genetic Disease
Genes 2010, 1(3), 550-563; doi:10.3390/genes1030550
Received: 15 October 2010 / Revised: 12 November 2010 / Accepted: 17 November 2010 / Published: 22 December 2010
Cited by 8 | PDF Full-text (320 KB) | HTML Full-text | XML Full-text
Abstract
Gene conversion is a specific type of homologous recombination that involves the unidirectional transfer of genetic material from a ‘donor’ sequence to a highly homologous ‘acceptor’. We have recently reviewed the molecular mechanisms underlying gene conversion, explored the key part that this process
[...] Read more.
Gene conversion is a specific type of homologous recombination that involves the unidirectional transfer of genetic material from a ‘donor’ sequence to a highly homologous ‘acceptor’. We have recently reviewed the molecular mechanisms underlying gene conversion, explored the key part that this process has played in fashioning extant human genes, and performed a meta-analysis of gene-conversion events known to have caused human genetic disease. Here we shall briefly summarize some of the latest developments in the study of pathogenic gene conversion events, including (i) the emerging idea of minimal efficient sequence homology (MESH) for homologous recombination, (ii) the local DNA sequence features that appear to predispose to gene conversion, (iii) a mechanistic comparison of gene conversion and transient hypermutability, and (iv) recently reported examples of pathogenic gene conversion events. Full article
(This article belongs to the Special Issue Gene Conversion in Duplicated Genes)
Open AccessReview Genomic and Population-Level Effects of Gene Conversion in Caenorhabditis Paralogs
Genes 2010, 1(3), 452-468; doi:10.3390/genes1030452
Received: 25 October 2010 / Revised: 22 November 2010 / Accepted: 6 December 2010 / Published: 9 December 2010
Cited by 7 | PDF Full-text (270 KB) | HTML Full-text | XML Full-text
Abstract
Interlocus gene conversion, the nonreciprocal exchange of genetic material between genes, is facilitated by high levels of sequence identity between DNA sequences and has the dual effect of homogenizing intergenic sequences while increasing intragenic variation. Gene conversion can have important consequences for the
[...] Read more.
Interlocus gene conversion, the nonreciprocal exchange of genetic material between genes, is facilitated by high levels of sequence identity between DNA sequences and has the dual effect of homogenizing intergenic sequences while increasing intragenic variation. Gene conversion can have important consequences for the evolution of paralogs subsequent to gene duplication, as well as result in misinterpretations regarding their evolution. We review the current state of research on gene conversion in paralogs within Caenorhabditis elegans and its congeneric species, including the relative rates of gene conversion, the range of observable conversion tracts, the genomic variables that strongly influence the frequency of gene conversion and its contribution to concerted evolution of multigene families. Additionally, we discuss recent studies that examine the phenotypic and population-genetic effects of interlocus gene conversion between the sex-determination locus fog-2 and its paralog ftr-1 in natural and experimental populations of C. elegans. In light of the limitations of gene conversion detection methods that rely solely on the statistical distribution of identical nucleotides between paralogs, we suggest that analyses of gene conversion in C. elegans take advantage of mutation accumulation experiments and sequencing projects of related Caenorhabditis species. Full article
(This article belongs to the Special Issue Gene Conversion in Duplicated Genes)
Open AccessReview Mechanisms of Ectopic Gene Conversion
Genes 2010, 1(3), 427-439; doi:10.3390/genes1030427
Received: 27 September 2010 / Revised: 12 November 2010 / Accepted: 16 November 2010 / Published: 29 November 2010
Cited by 9 | PDF Full-text (310 KB) | HTML Full-text | XML Full-text
Abstract
Gene conversion (conversion), the unidirectional transfer of DNA sequence information, occurs as a byproduct of recombinational repair of broken or damaged DNA molecules. Whereas excision repair processes replace damaged DNA by copying the complementary sequence from the undamaged strand of duplex DNA, recombinational
[...] Read more.
Gene conversion (conversion), the unidirectional transfer of DNA sequence information, occurs as a byproduct of recombinational repair of broken or damaged DNA molecules. Whereas excision repair processes replace damaged DNA by copying the complementary sequence from the undamaged strand of duplex DNA, recombinational mechanisms copy similar sequence, usually in another molecule, to replace the damaged sequence. In mitotic cells the other molecule is usually a sister chromatid, and the repair does not lead to genetic change. Less often a homologous chromosome or homologous sequence in an ectopic position is used. Conversion results from repair in two ways. First, if there was a double-strand gap at the site of a break, homologous sequence will be used as the template for synthesis to fill the gap, thus transferring sequence information in both strands. Second, recombinational repair uses complementary base pairing, and the heteroduplex molecule so formed is a source of conversion, both as heteroduplex and when donor (undamaged template) information is retained after correction of mismatched bases in heteroduplex. There are mechanisms that favour the use of sister molecules that must fail before ectopic homology can be used. Meiotic recombination events lead to the formation of crossovers required in meiosis for orderly segregation of pairs of homologous chromosomes. These events result from recombinational repair of programmed double-strand breaks, but in contrast with mitotic recombination, meiotic recombinational events occur predominantly between homologous chromosomes, so that transfer of sequence differences by conversion is very frequent. Transient recombination events that do not form crossovers form both between homologous chromosomes and between regions of ectopic homology, and leave their mark in the occurrence of frequent non-crossover conversion, including ectopic conversion. Full article
(This article belongs to the Special Issue Gene Conversion in Duplicated Genes)
Open AccessReview Gene Conversion and Evolution of Gene Families: An Overview
Genes 2010, 1(3), 349-356; doi:10.3390/genes1030349
Received: 16 August 2010 / Revised: 27 September 2010 / Accepted: 28 September 2010 / Published: 30 September 2010
Cited by 16 | PDF Full-text (45 KB) | HTML Full-text | XML Full-text
Abstract
The importance of gene conversion for the evolution of gene families is reviewed. Four problems concerning gene conversion, i.e., concerted evolution, generation of useful variation, deleterious effects, and relation to neofunctionalization, are discussed by surveying reported examples of evolving gene families. Emphasis
[...] Read more.
The importance of gene conversion for the evolution of gene families is reviewed. Four problems concerning gene conversion, i.e., concerted evolution, generation of useful variation, deleterious effects, and relation to neofunctionalization, are discussed by surveying reported examples of evolving gene families. Emphasis is given toward understanding interactive effects of gene conversion and natural selection. Full article
(This article belongs to the Special Issue Gene Conversion in Duplicated Genes)

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.

 

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