Gene Conversion in Duplicated Genes
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Genetic Effects on Microsatellite Diversity in Wild Emmer Wheat (Triticum Dicoccoides) at the Yehudiyya Microsite, Israel
Heredity (2003) 90, 150–156 & 2003 Nature Publishing Group All rights reserved 0018-067X/03 $25.00 www.nature.com/hdy Genetic effects on microsatellite diversity in wild emmer wheat (Triticum dicoccoides) at the Yehudiyya microsite, Israel Y-C Li1,3, T Fahima1,MSRo¨der2, VM Kirzhner1, A Beiles1, AB Korol1 and E Nevo1 1Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel; 2Institute for Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany This study investigated allele size constraints and clustering, diversity. Genome B appeared to have a larger average and genetic effects on microsatellite (simple sequence repeat number (ARN), but lower variance in repeat number 2 repeat, SSR) diversity at 28 loci comprising seven types of (sARN), and smaller number of alleles per locus than genome tandem repeated dinucleotide motifs in a natural population A. SSRs with compound motifs showed larger ARN than of wild emmer wheat, Triticum dicoccoides, from a shade vs those with perfect motifs. The effects of replication slippage sun microsite in Yehudiyya, northeast of the Sea of Galilee, and recombinational effects (eg, unequal crossing over) on Israel. It was found that allele distribution at SSR loci is SSR diversity varied with SSR motifs. Ecological stresses clustered and constrained with lower or higher boundary. (sun vs shade) may affect mutational mechanisms, influen- This may imply that SSR have functional significance and cing the level of SSR diversity by both processes. natural constraints. -
Capture of a Recombination Activating Sequence from Mammalian Cells
Gene Therapy (1999) 6, 1819–1825 1999 Stockton Press All rights reserved 0969-7128/99 $15.00 http://www.stockton-press.co.uk/gt Capture of a recombination activating sequence from mammalian cells P Olson and R Dornburg The Dorrance H Hamilton Laboratories, Center for Human Virology, Division of Infectious Diseases, Jefferson Medical College, Thomas Jefferson University, Jefferson Alumni Hall, 1020 Locust Street, Rm 329, Philadelphia, PA 19107, USA We have developed a genetic trap for identifying revealed a putative recombination signal (CCCACCC). sequences that promote homologous DNA recombination. When this heptamer or an abbreviated form (CCCACC) The trap employs a retroviral vector that normally disables were reinserted into the vector, they stimulated vector itself after one round of replication. Insertion of defined repair and other DNA rearrangements. Mutant forms of DNA sequences into the vector induced the repair of a 300 these oligomers (eg CCCAACC or CCWACWS) did not. base pair deletion, which restored its ability to replicate. Our data suggest that the recombination events occurred Tests of random sequence libraries made in the vector within 48 h after transfection. Keywords: recombination; retroviral vector; vector stability; gene conversion; gene therapy Introduction scripts are still made from the intact left LTR, but reverse transcription copies the deletion to both LTRs, disabling Recognition of cis-acting DNA signals occupies a central the daughter provirus.15–17 We found that the SIN vectors role in both site-specific and general recombination path- that could escape this programmed disablement did so 1–6 ways. Signals in site-specific pathways define the by recombinationally repairing the U3-deleted LTR. -
Conversion Between 100-Million-Year-Old Duplicated Genes Contributes to Rice Subspecies Divergence
Wei et al. BMC Genomics (2021) 22:460 https://doi.org/10.1186/s12864-021-07776-y RESEARCH Open Access Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence Chendan Wei1†, Zhenyi Wang1†, Jianyu Wang1†, Jia Teng1, Shaoqi Shen1, Qimeng Xiao1, Shoutong Bao1, Yishan Feng1, Yan Zhang1, Yuxian Li1, Sangrong Sun1, Yuanshuai Yue1, Chunyang Wu1, Yanli Wang1, Tianning Zhou1, Wenbo Xu1, Jigao Yu2,3, Li Wang1* and Jinpeng Wang1,2,3* Abstract Background: Duplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes. The genomes of Asian cultivated rice Oryza sativa ssp. indica (XI) and Oryza sativa ssp. japonica (GJ) have recently been updated, providing new opportunities for investigating ongoing gene conversion events and their impact on genome evolution. Results: Using comparative genomics and phylogenetic analyses, we evaluated gene conversion rates between duplicated genes produced by polyploidization 100 million years ago (mya) in GJ and XI. At least 5.19–5.77% of genes duplicated across the three rice genomes were affected by whole-gene conversion after the divergence of GJ and XI at ~ 0.4 mya, with more (7.77–9.53%) showing conversion of only portions of genes. Independently converted duplicates surviving in the genomes of different subspecies often use the same donor genes. The ongoing gene conversion frequency was higher near chromosome termini, with a single pair of homoeologous chromosomes, 11 and 12, in each rice genome being most affected. Notably, ongoing gene conversion has maintained similarity between very ancient duplicates, provided opportunities for further gene conversion, and accelerated rice divergence. -
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Copyright 0 1992 by the Genetics Society of America The Structure and Evolutionof Subtelomeric Y‘ Repeats in Saccharomyces cerevisiae Edward J.Louis’ and James E. Haber Rosenstiel Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02254-91 10 Manuscript received September 25, 199 1 Accepted for publication March 28, 1992 ABSTRACT The subtelomeric Y’ family of repeated DNA sequences in the yeast Saccharomyces cerevisiae is of unknown origin and function. Y’s vary in copy number and location among strains. Eight Y‘s, from two strains, were cloned and sequenced over the same 3.2-kb interval in order to assess the within- and between-strain variation as well as address their origin and function. One entireY’ sequence was reconstructed from two clones presented here and apreviously sequenced 833-bp region. It contains two large overlapping open reading frames (ORFs). The putative protein sequences have no strong homologies to any known proteins except for one region that has 27% identity with RNA helicases. RNA homologous to each ORF was detected. Comparison of the sequences revealed that the known long (Y’-L) and short (Y’-S) size classes, which coexist within cells, differ by several insertions and/or deletions within this region. The Y’-Ls from strain Y55 alsodiffer from those of strain YPl by several short deletions in the same region. Most of these deletions appear to have occurred between short (2-10 bp) direct repeats. The single base pair polymorphisms and the deletions are clustered in the first half of the interval compared. There is 0.30-1.13% divergence among Y’-Ls within a strain and 1.15-1.75% divergence between strains in the interval. -
A Long Polymorphic GT Microsatellite Within a Gene Promoter Mediates Non-Imprinted Allele-Specific DNA Methylation of a Cpg Island in a Goldfish Inter-Strain Hybrid
International Journal of Molecular Sciences Article A Long Polymorphic GT Microsatellite within a Gene Promoter Mediates Non-Imprinted Allele-Specific DNA Methylation of a CpG Island in a Goldfish Inter-Strain Hybrid 1,2, , 2, 2 Jianbo Zheng * y , Haomang Xu y and Huiwen Cao 1 Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China 2 College of Life Sciences, Zhejiang University, Hangzhou 310058, China * Correspondence: [email protected]; Tel.: +86-572-204-5681 These authors equally contributed to this work. y Received: 26 June 2019; Accepted: 6 August 2019; Published: 12 August 2019 Abstract: It is now widely accepted that allele-specific DNA methylation (ASM) commonly occurs at non-imprinted loci. Most of the non-imprinted ASM regions observed both within and outside of the CpG island show a strong correlation with DNA polymorphisms. However, what polymorphic cis-acting elements mediate non-imprinted ASM of the CpG island remains unclear. In this study, we investigated the impact of polymorphic GT microsatellites within the gene promoter on non-imprinted ASM of the local CpG island in goldfish. We generated various goldfish heterozygotes, in which the length of GT microsatellites or some non-repetitive sequences in the promoter of no tail alleles was different. By examining the methylation status of the downstream CpG island in these heterozygotes, we found that polymorphisms of a long GT microsatellite can lead to the ASM of the downstream CpG island during oogenesis and embryogenesis, polymorphisms of short GT microsatellites and non-repetitive sequences in the promoter exhibited no significant effect on the methylation of the CpG island. -
High-Frequency Germ Line Gene Conversion in Transgenic Mice J
MOLECULAR AND CELLULAR BIOLOGY, June 1992, p. 2545-2552 Vol. 12, No. 6 0270-7306/92/062545-08$02.00/0 Copyright ©) 1992, American Society for Microbiology High-Frequency Germ Line Gene Conversion in Transgenic Mice J. RAMANA MURTI, MICHAEL BUMBULIS, AND JOHN C. SCHIMENTI* Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 45106 Received 8 November 1991/Accepted 28 February 1992 Gene conversion is the nonreciprocal transfer of genetic information between two related genes or DNA sequences. It can influence the evolution of gene families, having the capacity to generate both diversity and homogeneity. The potential evolutionary significance of this process is directly related to its frequency in the germ line. While measurement of meiotic inter- and intrachromosomal gene conversion frequency is routine in fungal systems, it has hitherto been impractical in mammals. We have designed a system for identifying and quantitating germ line gene conversion in mice by analyzing transgenic male gametes for a contrived recombination event. Spermatids which undergo the designed intrachromosomal gene conversion produce functional 13-galactosidase (encoded by the lacZ gene), which is visualized by histochemical staining. We observed a high incidence of lacZ-positive spermatids (-2%), which were produced by a combination of meiotic and mitotic conversion events. These results demonstrate that gene conversion in mice is an active recombinational process leading to nonparental gametic haplotypes. This high frequency of intrachromosomal gene conversion seems incompatible with the evolutionary divergence of newly duplicated genes. Hence, a process may exist to uncouple gene pairs from frequent conversion-mediated homogenization. Gene (or DNA) duplication is a major molecular mecha- aptation. -
Somatic and Germinal Recombination of a Direct Repeat in Arabidopsis
Copyright 0 1992 by the Genetics Society of America Somatic and Germinal Recombination of a Direct Repeatin Arabidopsis Farhah F. Assaad' and Ethan R. Signer Department of Biology, Massachusetts Institute of Technology, Cambridge Massachusetts 02139 Manuscript received April 10, 1992 Accepted for publication June 25, 1992 ABSTRACT Homologous recombination between a pair of directly repeated transgenes was studied in Arabi- dopsis. The test construct included two different internal, non-overlapping deletion alleles of npt (neomycin phosphotransferase) flanking an activeHPT (hygromycin phosphotransferase) gene. This construct was introduced into Arabidopsis by agrobacterium-mediated transformationwith selection for resistance to hygromycin, and two independent single-insert lines were analyzed. Selection for active NPT by resistance to kanamycin gave both fully and partly (chimeric) recombinant seedlings. Rates for one transgenic line were estimatedat <2 X 10-5 events per division for germinal and>1 0-6 events per division for somatic recombination, a much smaller difference than between meiotic and mitotic recombination in yeast. Southern analysis showed that recombinants could be formed by either crossing over or gene conversion. A surprisingly high fraction (at least 2/17) of the recombi- nants, however, appeared to result from the concerted action of two or more independent simple events. Some evolutionary implicationsare discussed. ENOMES are not static but rather in constant suggested for other organisms (HILLISet al. 1991), G dynamic flux. That is especially so in plants, can either remove a mutation from a gene copy or which lack a permanent germline and instead produce conversely allow a new mutation to spread through gametes from somatic lineages. Thus changes in the the repeat population. -
ITS Non-Concerted Evolution and Rampant Hybridization in the Legume Genus Lespedeza
www.nature.com/scientificreports OPEN ITS non-concerted evolution and rampant hybridization in the legume genus Lespedeza Received: 15 August 2016 Accepted: 30 November 2016 (Fabaceae) Published: 04 January 2017 Bo Xu1, Xiao-Mao Zeng1, Xin-Fen Gao1, Dong-Pil Jin2 & Li-Bing Zhang3 The internal transcribed spacer (ITS) as one part of nuclear ribosomal DNA is one of the most extensively sequenced molecular markers in plant systematics. The ITS repeats generally exhibit high-level within-individual homogeneity, while relatively small-scale polymorphism of ITS copies within individuals has often been reported in literature. Here, we identified large-scale polymorphism of ITS copies within individuals in the legume genus Lespedeza (Fabaceae). Divergent paralogs of ITS sequences, including putative pseudogenes, recombinants, and multiple functional ITS copies were sometimes detected in the same individual. Thirty-seven ITS pseudogenes could be easily detected according to nucleotide changes in conserved 5.8S motives, the significantly lower GC contents in at least one of three regions, and the lost ability of 5.8S rDNA sequence to fold into a conserved secondary structure. The distribution patterns of the putative functional clones were highly different between the traditionally recognized two subgenera, suggesting different rates of concerted evolution in two subgenera which could be attributable to their different extents/frequencies of hybridization, confirmed by our analysis of the single-copy nuclear gene PGK. These findings have significant implications in using ITS marker for reconstructing phylogeny and studying hybridization. Concerted evolution is a form of multigene family evolution in which all the tendency of the different genes in a gene family or cluster are assumed to evolve as a unit in concert1,2. -
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http://www.diva-portal.org This is the published version of a paper published in Genome Biology and Evolution. Citation for the original published paper (version of record): Cossu, R M., Casola, C., Giacomello, S., Vidalis, A., Scofield, D G. et al. (2017) LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes Genome Biology and Evolution, 9(12): 3449-3462 https://doi.org/10.1093/gbe/evx260 Access to the published version may require subscription. N.B. When citing this work, cite the original published paper. Permanent link to this version: http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-144974 GBE LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes Rosa Maria Cossu1,2,†, Claudio Casola3,†, Stefania Giacomello4,5, Amaryllis Vidalis6,7, Douglas G. Scofield6,8,9,*, and Andrea Zuccolo1,10,* 1Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy 2Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Genova, Italy 3Department of Ecosystem Science and Management, Texas A&M University 4Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden 5Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden 6Department of Ecology and Environmental Science, Umea˚ University, Sweden 7Section of Population Epigenetics and Epigenomics, Center of Life and Food Sciences Weihenstephan, Technische Universitat€ Mu¨ nchen, Freising, Germany 8Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Sweden 9Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Sweden 10Istituto di Genomica Applicata, Udine, Italy †These authors contributed equally to this work. -
Transposable Elements in Sexual and Asexual Animals
Transposable elements in sexual and asexual animals Dissertation zur Erlangung des mathematisch-naturwissenschaftlichen Doktorgrades „Doctor rerum naturalium“ der Georg-August-Universität Göttingen im Promotionsprogramm Biologie der Georg-August University School of Science (GAUSS) vorgelegt von Diplom-Biologe J e n s B a s t aus Bad Bergzabern Göttingen, 2014 Betreuungsausschuss Prof. Dr. Stefan Scheu, Tierökologie, J.F. Blumenbach Institut PD Dr. Mark Maraun, Tierökologie, J.F. Blumenbach Institut Dr. Marina Schäfer, Tierökologie, J.F. Blumenbach Institut Mitglieder der Prüfungskommision Referent: Prof. Dr. Stefan Scheu, Tierökologie, J.F. Blumenbach Institut Korreferent: PD Dr. Mark Maraun, Tierökologie, J.F. Blumenbach Institut Weitere Mitglieder der Prüfungskommision: Prof. Dr. Elvira Hörandl, Systematische Botanik, Albrecht von Haller Institut Prof. Dr. Ernst Wimmer, Entwicklungsbiologie, J.F. Blumenbach Institut Prof. Dr. Ulrich Brose, Systemische Naturschutzbiologie, J.F. Blumenbach Institut PD Dr. Marko Rohlfs, Tierökologie, J.F. Blumenbach Institut Tag der mündlichen Prüfung: 30.01.2015 2 Wahrlich es ist nicht das Wissen, sondern das Lernen, nicht das Besitzen, sondern das Erwerben, nicht das Da-Seyn, sondern das Hinkommen, was den grössten Genuss gewährt. – Schreiben Gauss an Wolfgang Bolyai, 1808 3 Curriculum Vitae PERSONAL DETAILS NAME Jens Bast BIRTH January, 31 1983 in Bad Bergzabern NATIONALITY German EDUCATION 2011-2015 PhD thesis (biology) Georg-August University Goettingen Title: 'Transposable elements in sexual and -
The Organization and Evolution of the Responder Satellite in Species Of
Larracuente BMC Evolutionary Biology 2014, 14:233 http://www.biomedcentral.com/1471-2148/14/233 RESEARCH ARTICLE Open Access The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive Amanda M Larracuente Abstract Background: Satellite DNA can make up a substantial fraction of eukaryotic genomes and has roles in genome structure and chromosome segregation. The rapid evolution of satellite DNA can contribute to genomic instability and genetic incompatibilities between species. Despite its ubiquity and its contribution to genome evolution, we currently know little about the dynamics of satellite DNA evolution. The Responder (Rsp) satellite DNA family is found in the pericentric heterochromatin of chromosome 2 of Drosophila melanogaster. Rsp is well-known for being the target of Segregation Distorter (SD)? an autosomal meiotic drive system in D. melanogaster. I present an evolutionary genetic analysis of the Rsp family of repeats in D. melanogaster and its closely-related species in the melanogaster group (D. simulans, D. sechellia, D. mauritiana, D. erecta, and D. yakuba) using a combination of available BAC sequences, whole genome shotgun Sanger reads, Illumina short read deep sequencing, and fluorescence in situ hybridization. Results: I show that Rsp repeats have euchromatic locations throughout the D. melanogaster genome, that Rsp arrays show evidence for concerted evolution, and that Rsp repeats exist outside of D. melanogaster, in the melanogaster group. The repeats in these species are considerably diverged at the sequence level compared to D. melanogaster, and have a strikingly different genomic distribution, even between closely-related sister taxa. -
The Role of Gene Conversion Between Transposable Elements in Rewiring Regulatory Networks
GBE The Role of Gene Conversion between Transposable Elements in Rewiring Regulatory Networks Jeffrey A. Fawcett1,* and Hideki Innan2,* 1RIKEN iTHEMS, Wako, Saitama, Japan 2SOKENDAI, Hayama, Kanagawa, Japan *Corresponding authors: E-mails: [email protected]; [email protected]. Accepted: June 11, 2019 Abstract Nature has found many ways to utilize transposable elements (TEs) throughout evolution. Many molecular and cellular processes depend on DNA-binding proteins recognizing hundreds or thousands of similar DNA motifs dispersed throughout the genome that are often provided by TEs. It has been suggested that TEs play an important role in the evolution of such systems, in particular, the rewiring of gene regulatory networks. One mechanism that can further enhance the rewiring of regulatory networks is nonallelic gene conversion between copies of TEs. Here, we will first review evidence for nonallelic gene conversion in TEs. Then, we will illustrate the benefits nonallelic gene conversion provides in rewiring regulatory networks. For instance, nonallelic gene conversion between TE copies offers an alternative mechanism to spread beneficial mutations that improve the network, it allows multiple mutations to be combined and transferred together, and it allows natural selection to work efficiently in spreading beneficial mutations and removing disadvantageous mutations. Future studies examining the role of nonallelic gene conversion in the evolution of TEs should help us to better understand how TEs have contributed to evolution. Key words: transposable elements, rewiring regulatory network, gene conversion. Evolution of Regulatory Networks species. Many sets of motifs appear to be subject to a high Eukaryotic genomes contain many DNA-binding proteins birth-and-death rate, providing ample opportunities for new which bind to thousands of sites in the genome sharing a genes to be wired in to the network (fig.