The Effects of Trans Modifiers and Tandem Duplications on Meiotic Recombination in Maize Marna D
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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. -
Biology Dictionary English - Khmer
vcnanuRkm CIvviTüa Gg;eKøs-Exµr Biology Dictionary English - Khmer saklviTüal½yPUminÞPñMeBj ed)a:tWm:g; CIvviTüa e)aHBum<elIkTI 3 ¬EksMrYl¦ 2003 Preface to the Third Edition (Revised) This dictionary is the work of many teachers and some students in the Biology department of The Royal University of Phnom Penh. It has developed over the last three years in response to the need of Biology students to learn Biology from English text books. We have also tried to anticipate the future needs of Biology students and teachers in Cambodia. If they want to join the global scientific community; read scientific journals, listen to international media, attend international conferences or study outside Cambodia, then they will probably need to communicate in English. Therefore, the main aim of this book is to help Cambodian students and teachers at the university level to understand Biology in English. All languages evolve. In the past the main influence on Khmer language was French. Nowadays, it is increasingly English. Some technical terms have already been absorbed from French and have become Khmer. Nowadays new technical terms are usually created in English and are used around the world. Language is also created by those who use it and only exists when it is used. Therefore, common usage has also influenced our translation. We have tried to respond to these various influences when preparing this dictionary, so that it represents many different opinions - old and new, Francophile, Anglophile and Khmer. But there will always be some disagreement about the translation of some terms. This is normal and occurs in all languages. -
A Field Guide to Eukaryotic Transposable Elements
GE54CH23_Feschotte ARjats.cls September 12, 2020 7:34 Annual Review of Genetics A Field Guide to Eukaryotic Transposable Elements Jonathan N. Wells and Cédric Feschotte Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850; email: [email protected], [email protected] Annu. Rev. Genet. 2020. 54:23.1–23.23 Keywords The Annual Review of Genetics is online at transposons, retrotransposons, transposition mechanisms, transposable genet.annualreviews.org element origins, genome evolution https://doi.org/10.1146/annurev-genet-040620- 022145 Abstract Annu. Rev. Genet. 2020.54. Downloaded from www.annualreviews.org Access provided by Cornell University on 09/26/20. For personal use only. Copyright © 2020 by Annual Reviews. Transposable elements (TEs) are mobile DNA sequences that propagate All rights reserved within genomes. Through diverse invasion strategies, TEs have come to oc- cupy a substantial fraction of nearly all eukaryotic genomes, and they rep- resent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic be- havior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species. 23.1 Review in Advance first posted on , September 21, 2020. -
Tandemly Arrayed Genes in Vertebrate Genomes
Tandemly Arrayed Genes in Vertebrate Genomes Deng Pan1 and Liqing Zhang2∗ 1Department of Computer Science, Virginia Tech, 2050 Torgerson Hall, Blacksburg, VA 24061-0106, USA 2Program in Genetics, Bioinformatics, and Computational Biology ∗To whom correspondence should be addressed; E-mail: [email protected] July 9, 2008 Abstract Tandemly arrayed genes (TAGs) are duplicated genes that are linked as neighbors on a chromosome, many of which have important physio- logical and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72-94%) have parallel tran- scription orientation (i.e. are encoded on the same strand), in contrast to the genome, which has about 50% of its genes in parallel transcrip- tion orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our re- cent finding that tandem duplication played a more important role than retroposition in large families, this fact suggests that among all types of duplication mechanisms, tandem duplication is the predominant mecha- nism of duplication, especially in large families. Species-specific tandem arrays (SSTAs) are identified and results of statistical tests suggest that natural selection played a role in maintaining some of the SSTAs. Our 1 work will provide more insight into the evolutionary history of TAGs in vertebrates. 2 1 Introduction Although the importance of duplicated genes in providing raw materials for genetic innovation has been recognized since the 1930s and is highlighted in Ohno’s book Evolution by gene duplication (Ohno, 1970), it is only recently that the availability of numerous genomic sequences has made it possible to quantitatively estimate how many genes in a genome are generated by gene duplication. -
Evolution of Orthologous Tandemly Arrayed Gene Clusters
Tremblay Savard et al. BMC Bioinformatics 2011, 12(Suppl 9):S2 http://www.biomedcentral.com/1471-2105/12/S9/S2 PROCEEDINGS Open Access Evolution of orthologous tandemly arrayed gene clusters Olivier Tremblay Savard1*, Denis Bertrand2*, Nadia El-Mabrouk1* From Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Com- parative Genomics Galway, Ireland. 8-10 October 2011 Abstract Background: Tandemly Arrayed Gene (TAG) clusters are groups of paralogous genes that are found adjacent on a chromosome. TAGs represent an important repertoire of genes in eukaryotes. In addition to tandem duplication events, TAG clusters are affected during their evolution by other mechanisms, such as inversion and deletion events, that affect the order and orientation of genes. The DILTAG algorithm developed in [1] makes it possible to infer a set of optimal evolutionary histories explaining the evolution of a single TAG cluster, from an ancestral single gene, through tandem duplications (simple or multiple, direct or inverted), deletions and inversion events. Results: We present a general methodology, which is an extension of DILTAG, for the study of the evolutionary history of a set of orthologous TAG clusters in multiple species. In addition to the speciation events reflected by the phylogenetic tree of the considered species, the evolutionary events that are taken into account are simple or multiple tandem duplications, direct or inverted, simple or multiple deletions, and inversions. We analysed the performance of our algorithm on simulated data sets and we applied it to the protocadherin gene clusters of human, chimpanzee, mouse and rat. Conclusions: Our results obtained on simulated data sets showed a good performance in inferring the total number and size distribution of duplication events. -
Correlated Variation and Population Differentiation in Satellite DNA Abundance Among Lines of Drosophila Melanogaster
Correlated variation and population differentiation in satellite DNA abundance among lines of Drosophila melanogaster Kevin H.-C. Wei, Jennifer K. Grenier, Daniel A. Barbash, and Andrew G. Clark1 Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703 Contributed by Andrew G. Clark, November 18, 2014 (sent for review October 1, 2014; reviewed by Giovanni Bosco and Keith A. Maggert) Tandemly repeating satellite DNA elements in heterochromatin repeats of simple sequences (≤10 bp); the most abundant include occupy a substantial portion of many eukaryotic genomes. Al- AAGAG (aka GAGA-satellite), AACATAGAAT (aka 2L3L), though often characterized as genomic parasites deleterious to and AATAT (11, 14, 15). In comparison, the genome of its sister the host, they also can be crucial for essential processes such as species Drosophila simulans,fromwhichD. melanogaster di- chromosome segregation. Adding to their interest, satellite DNA verged ∼2.5 mya, is estimated to have only 5% satellite DNA, elements evolve at high rates; among Drosophila, closely related more than 10-fold less AAGAG, and little to no AACATA- species often differ drastically in both the types and abundances GAAT (16). For further contrast, nearly 50% of the Drosophila of satellite repeats. However, due to technical challenges, the evo- virilis and less than 0.5% of Drosophila erecta genomes are sat- lutionary mechanisms driving this rapid turnover remain unclear. ellite DNA (16, 17). Strikingly, such rapid changes in genomes have been implicated in postzygotic isolation of species in the Here we characterize natural variation in simple-sequence repeats – of 2–10 bp from inbred Drosophila melanogaster lines derived form of hybrid incompatibility in several species of flies (18 20), from multiple populations, using a method we developed called demonstrating the critical role satellite DNA has on the evolu- k-Seek that analyzes unassembled Illumina sequence reads. -
Genome Analysis of Protozoan Parasites: Proceedings of a Workshop Held at ILRAD, Nairobi, Kenya, 11–13 November 1992, Ed
G E N O M E A N A L Y S I S OF PROTOZOAN PARASITES PROCEEDINGS OF A WORKSHOP HELD AT ILRAD NAIROBI, KENYA 11–13 NOVEMBER 1992 Edited by S.P. Morzaria THE INTERNATIONAL LABORATORY FOR RESEARCH ON ANIMAL DISEASES BOX 30709 • NAIROBI • KENYA The International Laboratory for Research on Animal Diseases (ILRAD) was established in 1973 with a global mandate to develop effective control measures for livestock diseases that seriously limit world food production. ILRAD’s research program focuses on animal trypanosomiasis and tick-borne diseases, particularly theileriosis (East Coast fever). ILRAD is one of 18 centres in a worldwide agricultural research network sponsored by the Consultative Group on International Agricultural Research. In 1992 ILRAD received funding from the United Nations Development Programme, the World Bank and the governments of Australia, Belgium, Canada, Denmark, Finland, France, Germany, Italy, Japan, the Netherlands, Norway, Sweden, Switzerland, the United Kingdom and the United States of America. Production Editor: Peter Werehire This publication was typeset on a microcomputer and the final pages produced on a laser printer at ILRAD, P.O. Box 30709, Nairobi, Kenya, telephone 254 (2) 632311, fax 254 (2) 631499, e-mail BT GOLD TYMNET CGI017. Colour separations for cover were done by PrePress Productions, P.O. Box 41921, Nairobi, Kenya. Printed by English Press Ltd., P.O. Box 30127, Nairobi, Kenya. Copyright © 1993 by the International Laboratory for Research on Animal Diseases. ISBN 92-9055-296-4 The correct citation for this book is Genome Analysis of Protozoan Parasites: Proceedings of a Workshop Held at ILRAD, Nairobi, Kenya, 11–13 November 1992, ed. -
Molecular Biology and Applied Genetics
MOLECULAR BIOLOGY AND APPLIED GENETICS FOR Medical Laboratory Technology Students Upgraded Lecture Note Series Mohammed Awole Adem Jimma University MOLECULAR BIOLOGY AND APPLIED GENETICS For Medical Laboratory Technician Students Lecture Note Series Mohammed Awole Adem Upgraded - 2006 In collaboration with The Carter Center (EPHTI) and The Federal Democratic Republic of Ethiopia Ministry of Education and Ministry of Health Jimma University PREFACE The problem faced today in the learning and teaching of Applied Genetics and Molecular Biology for laboratory technologists in universities, colleges andhealth institutions primarily from the unavailability of textbooks that focus on the needs of Ethiopian students. This lecture note has been prepared with the primary aim of alleviating the problems encountered in the teaching of Medical Applied Genetics and Molecular Biology course and in minimizing discrepancies prevailing among the different teaching and training health institutions. It can also be used in teaching any introductory course on medical Applied Genetics and Molecular Biology and as a reference material. This lecture note is specifically designed for medical laboratory technologists, and includes only those areas of molecular cell biology and Applied Genetics relevant to degree-level understanding of modern laboratory technology. Since genetics is prerequisite course to molecular biology, the lecture note starts with Genetics i followed by Molecular Biology. It provides students with molecular background to enable them to understand and critically analyze recent advances in laboratory sciences. Finally, it contains a glossary, which summarizes important terminologies used in the text. Each chapter begins by specific learning objectives and at the end of each chapter review questions are also included. -
First Efficient CRISPR-Cas9-Mediated Genome Editing in Leishmania Parasites
First efficient CRISPR-Cas9-mediated genome editing in Leishmania parasites. Lauriane Sollelis, Mehdi Ghorbal, Cameron Ross Macpherson, Rafael Miyazawa Martins, Nada Kuk, Lucien Crobu, Patrick Bastien, Artur Scherf, Jose-Juan Lopez-Rubio, Yvon Sterkers To cite this version: Lauriane Sollelis, Mehdi Ghorbal, Cameron Ross Macpherson, Rafael Miyazawa Martins, Nada Kuk, et al.. First efficient CRISPR-Cas9-mediated genome editing in Leishmania parasites.. Cellular Mi- crobiology, Wiley, 2015, 17 (10), pp.1405-1412. 10.1111/cmi.12456. hal-01992713 HAL Id: hal-01992713 https://hal.umontpellier.fr/hal-01992713 Submitted on 2 Mar 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. First efficient CRISPR-Cas9-mediated genome editing in Leishmania parasites Lauriane Sollelis1,2, Mehdi Ghorbal1,2, Cameron Ross MacPherson3, Rafael Miyazawa Martins3, Nada Kuk1, Lucien Crobu2, Patrick Bastien1,2,4, Artur Scherf3, Jose-Juan Lopez- Rubio1,2 and Yvon Sterkers1,2,4# Running title: CRISPR-Cas9 for genome editing in Leishmania 1 University of Montpellier, Faculty of Medicine, Laboratory of Parasitology-Mycology, 2 CNRS 5290 - IRD 224 – University of Montpellier (UMR "MiVEGEC"), 3 Institut Pasteur - INSERM U1201 - CNRS ERL9195, "Biology of Host-Parasite Interactions" Unit, Paris, France, 4 CHRU (Centre Hospitalier Universitaire de Montpellier), Department of Parasitology-Mycology, Montpellier, France #To whom correspondence should be addressed. -
The Importance of Genetic Redundancy in Evolution
TREE 2688 No. of Pages 14 Trends in Ecology & Evolution Review The Importance of Genetic Redundancy in Evolution Áki J. Láruson,1,3,*,@ Sam Yeaman,2,@ and Katie E. Lotterhos1,3,@ Genetic redundancy has been defined in many different ways at different levels Highlights of biological organization. Here, we briefly review the general concept of redun- The use of the term ‘genetic redundancy’ dancy and focus on the evolutionary importance of redundancy in terms of the has changed over the past 100 years. number of genotypes that give rise to the same phenotype. We discuss the chal- The amount of redundancy in the lenges in determining redundancy empirically, with published experimental mapping of genotype to phenotype is a examples, and demonstrate the use of the C-score metric to quantify redun- critical parameter for evolutionary out- dancy in evolution studies. We contrast the implicit assumptions of redundancy comes under a range of models. in quantitative versus population genetic models, show how this contributes to Distinguishing the conceptual terms signatures of allele frequency shifts, and highlight how the rapid accumulation ‘genotypic redundancy’ and ‘segregating of genome-wide association data provides an avenue for further understanding redundancy’ promotes clearer language the prevalence and role of redundancy in evolution. to further the study of redundancy at all levels of evolutionary biology. History of Redundancy in Evolutionary Studies Empirical determination of redundancy is Redundancy describes a situation in which there is an excess of causal components in a system, challenging, but there are approaches above the minimum needed for its proper function. Understanding how redundancy is built into which allow for the quantitative inference of redundancy. -
Recombination and the Evolution of Satellite DNA
Genet. Res., Comb. (1986), 47, pp. 167-174 With 1 text-figure Printed in Great Britain 167 Recombination and the evolution of satellite DNA WOLFGANG STEPHAN* Institute of Animal Genetics, University of Edinburgh, West Mains Road, Edinburgh EH9 3JN, U.K. (Received 11 September 1985 and in revised form 6 December 1985) Summary In eukaryotic chromosomes, large blocks of satellite DNA are associated with regions of reduced meiotic recombination. No function of highly repeated, tandemly arranged DNA sequences has been identified so far at the cellular level, though the structural properties of satellite DNA are relatively well known. In studying the joint action of meiotic recombination, genetic drift and natural selection on the copy number of a family of highly repeated DNA (HRDNA), this paper looks at the structure-function debate for satellite DNA from the standpoint of molecular population genetics. It is shown that (i) HRDNA accumulates most probably in regions of near zero crossing over (heterochromatin), and that (ii), due to random genetic drift the effect of unequal crossover on copy numbers is stronger, the smaller the population size. As a consequence, highly repeated sequences are likely to persist longest (over evolutionary times) in small populations. The results are based on a fairly general class of models of unequal crossing over and natural selection which have been treated both analytically and by computer simulation. 1. Introduction lem of the function of these DNAs has been the sub- Eukaryotic chromosomes contain nucleotide se- ject of major controversies during the past two quences of lengths from about 10 to several hundred decades. -
Applying CRISPR/Cas for Genome Engineering in Plants
Available online at www.sciencedirect.com ScienceDirect Applying CRISPR/Cas for genome engineering in plants: the best is yet to come Holger Puchta Less than 5 years ago the CRISPR/Cas nuclease was first zinc finger nucleases (ZFNs) and transcription activator- introduced into eukaryotes, shortly becoming the most efficient like effector nucleases (TALENs), which allow the tar- and widely used tool for genome engineering. For plants, geting of most genomic sites, have been developed and efforts were centred on obtaining heritable changes in most applied for a long period of time in plants (for reviews see transformable crop species by inducing mutations into open [6–8]). Although with the advent of ZFNs the basic reading frames of interest, via non-homologous end joining. problem of targeting DSBs to specific site in the genome Now it is important to take the next steps and further develop was solved, the system revealed numerous drawbacks. the technology to reach its full potential. For breeding, besides The construction of the enzymes is time consuming and using DNA-free editing and avoiding off target effects, it will be expensive and their specificity is limited, resulting in desirable to apply the system for the mutation of regulatory DSB at genomic site that very similar but nor identical elements and for more complex genome rearrangements. to the target site. Thus, unwanted secondary, ‘off-target’ Targeting enzymatic activities, like transcriptional regulators or mutations were introduced regularly. After their intro- DNA modifying enzymes, will be important for plant biology in duction TALENs outcompeted ZFNs in specificity as the future.