GENE DUPLICATION Edited by Felix Friedberg Gene Duplication Edited by Felix Friedberg Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2011 InTech All chapters are Open Access articles distributed under the Creative Commons Non Commercial Share Alike Attribution 3.0 license, which permits to copy, distribute, transmit, and adapt the work in any medium, so long as the original work is properly cited. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published articles. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Martina Blecic Technical Editor Teodora Smiljanic Cover Designer Jan Hyrat Image Copyright Booka, 2011. Used under license from Shutterstock.com First published September, 2011 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechweb.org Gene Duplication, Edited by Felix Friedberg p. cm. ISBN 978-953-307-387-3 free online editions of InTech Books and Journals can be found at www.intechopen.com Contents Preface IX Part 1 General Aspects 1 Chapter 1 A Theoretical Scheme of the Large-Scale Evolution by Generating New Genes from Gene Duplication 3 Jinya Otsuka Chapter 2 Duplicated Gene Evolution Following Whole-Genome Duplication in Teleost Fish 27 Baocheng Guo, Andreas Wagner and Shunping He Chapter 3 Detection and Analysis of Functional Specialization in Duplicated Genes 37 Owen Z. Woody and Brendan J. McConkey Chapter 4 Predicting Tandemly Arrayed Gene Duplicates with WebScipio 59 Klas Hatje and Martin Kollmar Chapter 5 The LRR and TM Containing Multi-Domain Proteins in Arabidopsis 77 Felix Friedberg Chapter 6 Partial Gene Duplication and the Formation of Novel Genes 95 Macarena Toll-Riera, Steve Laurie, Núria Radó-Trilla and M.Mar Albà Part 2 A Look at Some Gene Families 111 Chapter 7 Immunoglobulin Polygeny: An Evolutionary Perspective 113 J. E. Butler, Xiu-Zhu Sun and Nancy Wertz VI Contents Chapter 8 Gene Duplication in Insecticide Resistance 141 Si Hyeock Lee and Deok Ho Kwon Chapter 9 Gene Duplication and the Origin of Translation Factors 151 Galina Zhouravleva and Stanislav Bondarev Chapter 10 Analysis of Duplicate Gene Families in Microbial Genomes and Application to the Study of Gene Duplication in M. tuberculosis 173 Venu Vuppu and Nicola Mulder Chapter 11 The Evolutionary History of CBF Transcription Factors: Gene Duplication of CCAAT – Binding Factors NF-Y in Plants 197 Alexandro Cagliari, Andreia Carina Turchetto-Zolet, Felipe dos Santos Maraschin, Guilherme Loss, Rogério Margis and Marcia Margis-Pinheiro Part 3 Examining Bundles of Genes 223 Chapter 12 L- Myo-Inositol 1-Phosphate Synthase (MIPS) in Chickpea: Gene Duplication and Functional Divergence 225 Manoj Majee and Harmeet Kaur Chapter 13 On the Specialization History of the ADP-Dependent Sugar Kinase Family 237 Felipe Merino and Victoria Guixé Chapter 14 Duplication of Coagulation Factor Genes and Evolution of Snake Venom Prothrombin Activators 257 Shiyang Kwong and R. Manjunatha Kini Chapter 15 A Puroindoline Mutigene Family Exhibits Sequence Diversity in Wheat and is Associated with Yield-Related Traits 279 Feng Chen, Fuyan Zhang, Craig F. Morris and Dangqun Cui Chapter 16 Evolution of GPI-Aspartyl Proteinases (Yapsines) of Candida spp 289 Berenice Parra-Ortega, Lourdes Villa-Tanaca and César Hernández-Rodríguez Chapter 17 Clues to Evolution of the SERA Multigene Family in the Genus Plasmodium 315 Nobuko Arisue, Nirianne M. Q. Palacpac, Kazuyuki Tanabe and Toshihiro Horii Contents VII Chapter 18 Molecular Evolution of Juvenile Hormone Signaling 333 Aaron A. Baumann and Thomas G. Wilson Chapter 19 Gene Duplication and Subsequent Differentiation of Esterases in Cactophilic Drosophila Species 353 Rogério P. Mateus, Luciana P. B. Machado and Carlos R. Ceron Chapter 20 SNCA Gene Multiplication: A Model Mechanism of Parkinson Disease 373 Kenya Nishioka, Owen A. Ross and Nobutaka Hattori Chapter 21 Bucentaur (Bcnt) Gene Family: Gene Duplication and Retrotransposon Insertion 383 Shintaro Iwashita and Naoki Osada Preface The book Gene Duplication consists of 21 chapters divided in 3 parts: General Aspects, A Look at Some Gene Families and Examining Bundles of Genes. The importance of the study of Gene Duplication stems from the realization that the dynamic process of duplication is the “sine qua non” underlying the evolution of all living matter. Genes may be altered before or after the duplication process thereby undergoing neofunctionalization, thus creating in time new organisms which populate the Earth. Osaka (Chapter I) suggests that similarities in amino acid sequences exhibited by paralogous proteins prove that evolution proceeds via in toto gene duplication. If the ancestral and the newly created gene perform the same function, the new gene would be labeled a subfunctional gene. It should be added that such a duplicated gene encoding an identical product might also be engaged by different cellular regulatory signals (e.g. methylation of nucleotide sites) which in turn, could hamper the expression of such a duplicated gene. (See e.g. Woody et al. Chapter 3). If this duplicated gene subsequently undergoes mutations that allow a function for the new gene that is different from the parent gene (neofunctionalization) that would represent a far more positive evolutionary event. The first three chapters in this book focus on such in toto gene duplications whereby in evolutionary time neofunctionalization could have taken hold. There are also several specific cicumscribed examples given in this book. (See e.g. Majee&Kaur, Chapter 12). Undoubtedly, duplication contributes substantially to the formation of new genes. But there is a caveat: In time, the majority of duplicated genes mutates into oblivion. In recent years, however, attention has been paid to another possible path for creating a new gene: The formation of the chimeric gene, a gene immediately ready for a new function. Such a gene might result from altering the position of spliced introns, or more likely from retropositioning of a new encoding domain into the gene: I.e. partial gene duplications and combination. It is obvious that such processes are particularly suited for the creation of genes encoding multi-domain proteins and that they may accelerate considerably the natural process of neofunctionalization. (See Hatje et al.Chapter 4; Friedberg, Chapter 5; Toll-Riera et al. Chapter 6 and Iwashita et al. Chapter 21). Retrotransposons are capable of promoting such segmental duplications. X Preface ”Retroduplication” contributes significantly to the formation of new genes. These genes, in turn may also be duplicated and eventually be erased into oblivion by mutations. Prof. Felix Friedberg Howard University Medical School, Washington DC, USA [...]... Large-Scale Evolution by Generating New Genes from Gene Duplication 19 6 Conclusions and discussion The variants, which experienced gene duplication, first decline to be minor members in a population by the load of carrying extra gene( s), but some of them revives as a new style of organisms by the generation of new gene( s) from the counterpart of duplicated genes After the new gene( s) appear, the new... Evolution by Generating New Genes from Gene Duplication 23 same sequence length of gene duplication, therefore, the reduction factor may take a smaller value in animals than in lower eukaryotes and prokaryotes Thus, the fraction of variants carrying the ‘hidden genes’ generated from gene duplication may be high enough to hybridize between them in higher eukaryotes, especially in animals Such ‘hidden genes’... respectively, in terms of the set of variables characterizing an organism in section 2 8 Gene Duplication When a biologically meaningful character is newly exhibited by two new genes generated from different origins of gene duplication, the variant, which experienced gene duplication i, must successively experience further gene duplication j in the other part of the genome to exhibit such a new character The... such satellite variants, the variant arising from the gene duplication is especially notable in the sense that it has the potential to generate a new gene from the counterpart of duplicated genes If the probability of generating a new gene I from the duplicated part in xi is denoted by qxI,xi, a new style of the organism carrying the new gene I is generated from the original style of an organism with... descendant received three new genes The descendant received three new genes I, J and K can be produced from the conjugation of variants, one carrying one new gene I and another carrying two new genes J and K Two cases are considerable for this production A Theoretical Scheme of the Large-Scale Evolution by Generating New Genes from Gene Duplication 11 One is the case that the new gene I is encoded on the... Evolution by Generating New Genes from Gene Duplication 13 reduction factor s for some values of n in Fig 2 The probability Pc2n is present in the same range of reduction factor as the probability Pmn is present and the probability Pc2n+1 is present in the same range of reduction factor as the probability Pmn+1 is This indicates that the larger size of new genes not generated from the successive gene duplication. .. as Eq (10) of the monoploid organism in the case when the gene duplication hardly changes the death rate, i e., D(xi) ≈ D(xopt) Denoting the probability of generating a new gene I from the gene duplicated part i by q(xI ← xi), the probability Pd1(xI,xo ← xo,xo) that a new style of the organism (xI, xo) carrying the new gene I heterogeneously is generated from the original style of an organism (xo, xo)... decreased by the lowering of the biological activity of the variant (xi, xo) Second, the further gene duplication to produce two or more new genes is hardly expected in the homologous chromosomes (xi, xo), because the fraction 16 Gene Duplication of such variants experienced successive gene duplication becomes much lower, not only due to the severer lowering of biological activity but also by the severer... organism carrying n kinds of new genes heterogeneously is generated with the probability Pdn Although it is laborious to follow this process completely, the essence of this process can be elucidated by investigating the ratio of children that receive these new genes homogeneously and heterogeneously from the mating between the organisms each carrying n kinds of new genes heterogeneously If the chromosomes... xi ) (16) where qxIJ,xIj is the probability of generating the new gene J from the duplicated part in j This procedure can be easily extended to the general case of successively generating three or more new genes Before describing the result of the general case, the expression of probabilities (11) and (16) will be simplified by assuming that the gene duplication only reduces the self-reproducing rate . GENE DUPLICATION Edited by Felix Friedberg Gene Duplication Edited by Felix Friedberg Published by InTech. 2. Gene Duplication 8 When a biologically meaningful character is newly exhibited by two new genes generated from different origins of gene duplication,