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GENE DUPLICATION
Edited by Felix Friedberg
Gene Duplication
Edited by Felix Friedberg
Published by InTech
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Technical Editor Teodora Smiljanic
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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
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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,
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