DOCSLIB.ORG

Gene Duplication and Evolution

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Gene Duplication and Evolution T ECHNICAL C OMMENTS An analogy for the application of half- lives is the mortality of newborns centuries Gene Duplication and Evolution ago: At that time the infant mortality rate was Lynch and Conery (1) presented one of the in the mouse Sp100-rs family, a short lineage very high, because medical science was un- first serious efforts to study the evolutionary of Mus musculus has created at least 60 gene derdeveloped—but just because the “half- fate of gene duplication using genomic se- duplicates within 1.7 million years; other lin- life” of newborns is short, it does not follow quence data. Their analysis led to several eages such as the sibling taxa Mus caroli,a that half of all adults will die shortly. We interesting observations, particularly with re- group that diverged 2.5 million years ago, suggest that figure 2 of (1) supports a con- spect to the rate of gene duplication in eu- contain few duplicates (4). If the duplication clusion opposite to the one that Lynch and karyotic genomes and the subsequent half- rate over the time during which divergence is Conery drew: A large proportion of duplicate life of duplicates. These two parameters are observed is much lower than the recent rate genes either have evolved new functions (7) of particular importance in studying the evo- of duplication, the half-life calculated by or have been maintained by subfunctionaliza- lutionary processes of gene duplication and Lynch and Conery would represent a serious tion (8, 9) or other mechanisms. subsequent functional divergence. The most underestimate. Manyuan Long frequent class of duplications appeared to be Finally, an alternative interpretation for Department of Ecology and Evolution similar in all six species, which suggests the short half-life of duplicate genes before University of Chicago some silencing process for old duplicates. silencing may deserve consideration. Assum- 1101 East 57th Street Several additional considerations in the anal- ing that small values of S may more reliably Chicago, IL 60637, USA ysis and interpretation, however, might have reflect a short evolutionary time, the authors led to some different conclusions. chose to estimate the half-life of duplicate Kevin Thornton First, Lynch and Conery (1) used the genes only from gene pairs with S values in Committee on Genetics number of substitutions per silent site, S,to the range of 0 to 0.25. They estimated a mean University of Chicago measure the age of a duplicate-gene pair half-life of 4 million years, concluding that [figure 2 of (1)]. It is unclear, however, that “the fate awaiting most gene duplications References silent divergence is a suitable proxy for a appears to be silencing rather than preserva- 1. M. Lynch, J. S. Conery, Science 290, 1151 (2000). 2. L.-W. Zeng, J. M. Comeron, B. Chen, M. Kreitman, molecular clock involving different genes or tion,” and, hence, that “duplicate genes may Genetica 102Ð103, 369 (1998). gene duplicates. For example, Zeng et al. (2) only rarely evolve new functions.” Yet their 3. W.-H. Li, Molecular Evolution (Sinauer Associates, reported 9- to 15-fold differences in S values analysis appears to have ignored several im- Sunderland, MA, 1997). and a flat distribution of S for 24 single-copy portant features of the data [figure 2 of (1)]. 4. D. Weichenhan, B. Kunze, W. Traut, H. Winking, Cytogenet. Cell Genet. 80, 226 (1998). genes in Drosophila. Two points are impor- (i) Notwithstanding their model of “young” 5. D. A. Petrov, E. R. Lozovskaya, D. L. Hartl, Nature 384, tant in this context: (i) this large variation in duplicates, the tails of the distribution are 346 (1996). S is expected when the divergence time is long and flat, which suggests that the data are 6. G. M. Rubin et al., Science. 287, 2204 (2000). 7. W. Wang, J. Zhang, C. Alvarez, A. Llopart, M. Long, low; and (ii) the divergence time for each actually heterogeneous. (ii) The proportions Mol. Biol. Evol. 17, 1294 (2000). comparison made by Zeng et al.(2) was of the duplications that reside in the tails are 8. A. Force et al., Genetics 151, 1531 (1999). fixed. Thus, for different genes, S may vary high—85% for Drosophila melanogaster, 9. M. Lynch, A. Force, Genetics 154, 459 (2000). by more than an order of magnitude given a 66% for Caenorhabditis elegans, and 65% 21 December 2000; accepted 21 June 2001 fixed divergence time. This situation differs for Saccharomyces cerevisiae. (iii) The tails from description of divergence time using S include old and ancient duplications. The Lynch and Conery (1) have proposed a num- values from homologous genes across a heterogeneity of the age distribution in figure ber of provocative hypotheses regarding the group of organisms, in which a dependable 2of(1) suggests that the short half-life cal- evolution of duplicate genes, using data from molecular clock may exist. The same S val- culated from young duplicate-gene pairs can- nine eukaryotic species. One hypothesis is ues may represent duplicates of very different not be extended to most pairs. After all, a that the ratio of replacement (R) to silent (S ) ages, and the different S values may be from large proportion of these older duplicates nucleotide substitutions among recently du- duplicates of the same or similar ages. Thus, may be much older than 4 million years, with plicated genes is near 1.0, the neutral expec- figure 2 of (1) should be viewed with caution real ages of tens or hundreds of million years. tation. Their analysis indicates that this phase as a description of the age distribution of It is likely that these genes have been func- of relaxed selection is confined to recently gene duplications. A related issue is the reli- tional since their origin; otherwise, the dupli- duplicated gene pairs. Another hypothesis is ability of estimates of S, because many of the cate sequences would have been deleted from that many duplicate-gene pairs are short- values presented by Lynch and Conery (1) the genome (5). lived, with half-lives of 3 to 7 million years, were larger than 1. Estimates larger than 1 are In addition, the absolute number of old or depending on the organism. associated with a large variance due to satu- ancient gene duplicates is relatively large. Unfortunately, their conclusions are com- ration of substitutions and should generally For example, 40% of the approximately promised by the fact that their data, obtained be considered unreliable (3). 13,600 coding sequences in the D. melano- through GenBank taxon searches, included Second, the calculation of the half-life of gaster genome appear to have arisen by gene many redundant records. For example, 43.3% gene duplicates was based on the untested, duplication (6). Thus, some 34% of the fly of the gene pairs in their Arabidopsis data set hidden assumption that the rate of gene du- genome, or 4624 genes [40% ϫ 85% ϫ had no synonymous differences (S ϭ 0). We plication is constant over evolutionary 13,600, with the 85% from item (ii), above], randomly examined 50 of these gene pairs time—an assumption implicit in both figure 3 comprise old or ancient duplicates. It is there- and found that 86% were derived from the and equation 3 of (1). Unfortunately, there fore misleading to assert that the vast major- same genomic sequence, mostly because of are insufficient data with which to estimate ity of gene duplicates are quickly silenced, the presence of a single gene on two overlap- the variation in the rate of gene duplication even if the calculation of the half-life is ping clones. These redundant sequences were on a short time scale; nevertheless, there is correct. Rather, it appears that the accumula- used to estimate the rate at which duplicate- some evidence that the duplication rate for tion of “survivors” of the silencing process gene pairs reverted to single copies, a proce- some families may indeed not be stationary constitutes a large fraction of modern eukary- dure that tended to overestimate the rate of over a short evolutionary time. For example, otic genomes. gene loss. Such problems were not limited to www.sciencemag.org SCIENCE VOL 293 31 AUGUST 2001 1551a T ECHNICAL C OMMENTS Arabidopsis; 58.3% of human gene pairs and Liqing Zhang demographic analysis of gene duplicates 67.7% of mouse gene pairs had R ϭ S ϭ 0. Brandon S. Gaut made the hidden assumption of a constant Because Lynch and Conery recognized the Department of Ecology and rate of gene duplication over time. This as- potential problem of redundancy, human and Evolutionary Biology sumption was actually stated explicitly in (1), mouse gene pairs with S Ͻ0.01 were not used University of California, Irvine although strictly speaking we only assumed in their analyses. In many cases, however, Irvine, CA 92697, USA rate constancy over the time scale for which S Ͻ Ͻ both gene sequences from an S 0.01 pair Todd J. Vision 0.25. Long-term rate constancy was not were compared with a more distant gene USDA-ARS Center for Agricultural relevant to our birthrate estimates, which family member, which did result in the use of Bioinformatics were simply the average values that apply redundant data entries. Cornell University over the time scale required for S to reach Also problematic are the mammalian Ithaca, NY 14853, USA 0.01—perhaps the past few hundred thousand gene pairs in the 0.01 Ͻ S Ͻ0.05 class, to million years for the species analyzed. Rate which were crucial to the conclusion by References constancy is an important assumption under- Lynch and Conery (1) that selective con- 1.
Load more

Recommended publications
  • "Evolutionary Emergence of Genes Through Retrotransposition"
    Evolutionary Emergence of Advanced article Genes Through Article Contents . Introduction Retrotransposition . Gene Alteration Following Retrotransposon Insertion . Retrotransposon Recruitment by Host Genome . Retrotransposon-mediated Gene Duplication Richard Cordaux, University of Poitiers, Poitiers, France . Conclusion Mark A Batzer, Department of Biological Sciences, Louisiana State University, Baton Rouge, doi: 10.1002/9780470015902.a0020783 Louisiana, USA Variation in the number of genes among species indicates that new genes are continuously generated over evolutionary times. Evidence is accumulating that transposable elements, including retrotransposons (which account for about 90% of all transposable elements inserted in primate genomes), are potent mediators of new gene origination. Retrotransposons have fostered genetic innovation during human and primate evolution through: (i) alteration of structure and/or expression of pre-existing genes following their insertion, (ii) recruitment (or domestication) of their coding sequence by the host genome and (iii) their ability to mediate gene duplication via ectopic recombination, sequence transduction and gene retrotransposition. Introduction genes, respectively, and de novo origination from previ- ously noncoding genomic sequence. Genome sequencing Variation in the number of genes among species indicates projects have also highlighted that new gene structures can that new genes are continuously generated over evolution- arise as a result of the activity of transposable elements ary times. Although the emergence of new genes and (TEs), which are mobile genetic units or ‘jumping genes’ functions is of central importance to the evolution of that have been bombarding the genomes of most species species, studies on the formation of genetic innovations during evolution. For example, there are over three million have only recently become possible.
    [Show full text]
  • Genome Organization/ Human
    Genome Organization/ Secondary article Human Article Contents . Introduction David H Kass, Eastern Michigan University, Ypsilanti, Michigan, USA . Sequence Complexity Mark A Batzer, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA . Single-copy Sequences . Repetitive Sequences . The human nuclear genome is a highly complex arrangement of two sets of 23 Macrosatellites, Minisatellites and Microsatellites . chromosomes, or DNA molecules. There are various types of DNA sequences and Gene Families . chromosomal arrangements, including single-copy protein-encoding genes, repetitive Gene Superfamilies . sequences and spacer DNA. Transposable Elements . Pseudogenes . Mitochondrial Genome Introduction . Genome Evolution . Acknowledgements The human nuclear genome contains 3000 million base pairs (bp) of DNA, of which only an estimated 3% possess protein-encoding sequences. As shown in Figure 1, the DNA sequences of the eukaryotic genome can be classified sequences such as the ribosomal RNA genes. Repetitive into several types, including single-copy protein-encoding sequences with no known function include the various genes, DNA that is present in more than one copy highly repeated satellite families, and the dispersed, (repetitive sequences) and intergenic (spacer) DNA. The moderately repeated transposable element families. The most complex of these are the repetitive sequences, some of remainder of the genome consists of spacer DNA, which is which are functional and some of which are without simply a broad category of undefined DNA sequences. function. Functional repetitive sequences are classified into The human nuclear genome consists of 23 pairs of dispersed and/or tandemly repeated gene families that chromosomes, or 46 DNA molecules, of differing sizes either encode proteins (and may include noncoding (Table 1).
    [Show full text]
  • Estimation of Duplication History Under a Stochastic Model for Tandem Repeats Farzad Farnoud1* , Moshe Schwartz2 and Jehoshua Bruck3
    Farnoud et al. BMC Bioinformatics (2019) 20:64 https://doi.org/10.1186/s12859-019-2603-1 RESEARCH ARTICLE Open Access Estimation of duplication history under a stochastic model for tandem repeats Farzad Farnoud1* , Moshe Schwartz2 and Jehoshua Bruck3 Abstract Background: Tandem repeat sequences are common in the genomes of many organisms and are known to cause important phenomena such as gene silencing and rapid morphological changes. Due to the presence of multiple copies of the same pattern in tandem repeats and their high variability, they contain a wealth of information about the mutations that have led to their formation. The ability to extract this information can enhance our understanding of evolutionary mechanisms. Results: We present a stochastic model for the formation of tandem repeats via tandem duplication and substitution mutations. Based on the analysis of this model, we develop a method for estimating the relative mutation rates of duplications and substitutions, as well as the total number of mutations, in the history of a tandem repeat sequence. We validate our estimation method via Monte Carlo simulation and show that it outperforms the state-of-the-art algorithm for discovering the duplication history. We also apply our method to tandem repeat sequences in the human genome, where it demonstrates the different behaviors of micro- and mini-satellites and can be used to compare mutation rates across chromosomes. It is observed that chromosomes that exhibit the highest mutation activity in tandem repeat regions are the same as those thought to have the highest overall mutation rates. However, unlike previous works that rely on comparing human and chimpanzee genomes to measure mutation rates, the proposed method allows us to find chromosomes with the highest mutation activity based on a single genome, in essence by comparing (approximate) copies of the pattern in tandem repeats.
    [Show full text]
  • Genomic Comparison of Closely Related Giant Viruses Supports an Accordion-Like Model of Evolution
    ORIGINAL RESEARCH published: 16 June 2015 doi: 10.3389/fmicb.2015.00593 Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution Jonathan Filée * Laboratoire Evolution, Génome, Comportement, Ecologie, Centre National de la Recherche Scientifique UMR 9191, IRD UMR 247, Université Paris-Saclay, Gif-sur-Yvette, France Genome gigantism occurs so far in Phycodnaviridae and Mimiviridae (order Megavirales). Origin and evolution of these Giant Viruses (GVs) remain open questions. Interestingly, availability of a collection of closely related GV genomes enabling genomic comparisons offer the opportunity to better understand the different evolutionary forces acting on these genomes. Whole genome alignment for five groups of viruses belonging to the Mimiviridae and Phycodnaviridae families show that there is no trend of genome expansion or general tendency of genome contraction. Instead, GV genomes accumulated genomic mutations over the time with gene gains compensating the Edited by: different losses. In addition, each lineage displays specific patterns of genome evolution. Bernard La Scola, Mimiviridae (megaviruses and mimiviruses) and Chlorella Phycodnaviruses evolved Aix Marseille Université, France mainly by duplications and losses of genes belonging to large paralogous families Reviewed by: (including movements of diverse mobiles genetic elements), whereas Micromonas and Dahlene N. Fusco, Massachusetts General Hospital, USA Ostreococcus Phycodnaviruses derive most of their genetic novelties thought lateral Philippe Colson, gene transfers. Taken together, these data support an accordion-like model of evolution Aix-Marseille Université, France in which GV genomes have undergone successive steps of gene gain and gene loss, *Correspondence: Jonathan Filée, accrediting the hypothesis that genome gigantism appears early, before the diversification Laboratoire Evolution, Génome, of the different GV lineages.
    [Show full text]
  • Extrachromosomal Element Capture and the Evolution of Multiple Replication Origins in Archaeal Chromosomes
    Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes Nicholas P. Robinson† and Stephen D. Bell† Medical Research Council Cancer Cell Unit, Hutchison Medical Research Council Research Center, Hills Road, Cambridge CB2 0XZ, United Kingdom Edited by Carl R. Woese, University of Illinois at Urbana–Champaign, Urbana, IL, and approved February 15, 2007 (received for review January 9, 2007) In all three domains of life, DNA replication begins at specialized Orc2–6 act to recruit MCM to origins of replication in a reaction loci termed replication origins. In bacteria, replication initiates from that absolutely requires an additional factor, Cdt1 (6). Although a single, clearly defined site. In contrast, eukaryotic organisms archaea possess orthologs of Orc1, Cdc6, and MCM, no archaeal exploit a multitude of replication origins, dividing their genomes homolog of Cdt1 has yet been identified. into an array of short contiguous units. Recently, the multiple In the current work, we reveal that Aeropyrum pernix has at replication origin paradigm has also been demonstrated within the least two replication origins, indicating that the multiple repli- archaeal domain of life, with the discovery that the hyperthermo- cation origin paradigm is not restricted to the Sulfolobus genus. philic archaeon Sulfolobus has three replication origins. However, Comparison of the A. pernix and Sulfolobus origins reveals a clear the evolutionary mechanism driving the progression from single to relationship between these loci. Further, analyses of the gene multiple origin usage remains unclear. Here, we demonstrate that order and identity in the environment of the origins provides Aeropyrum pernix, a distant relative of Sulfolobus, has two origins.
    [Show full text]
  • Mitochondrial DNA Duplication, Recombination, and Introgression During Interspecific Hybridization
    www.nature.com/scientificreports OPEN Mitochondrial DNA duplication, recombination, and introgression during interspecifc hybridization Silvia Bágeľová Poláková1,5, Žaneta Lichtner1, Tomáš Szemes2,3,4, Martina Smolejová1 & Pavol Sulo1* mtDNA recombination events in yeasts are known, but altered mitochondrial genomes were not completed. Therefore, we analyzed recombined mtDNAs in six Saccharomyces cerevisiae × Saccharomyces paradoxus hybrids in detail. Assembled molecules contain mostly segments with variable length introgressed to other mtDNA. All recombination sites are in the vicinity of the mobile elements, introns in cox1, cob genes and free standing ORF1, ORF4. The transplaced regions involve co-converted proximal exon regions. Thus, these selfsh elements are benefcial to the host if the mother molecule is challenged with another molecule for transmission to the progeny. They trigger mtDNA recombination ensuring the transfer of adjacent regions, into the progeny of recombinant molecules. The recombination of the large segments may result in mitotically stable duplication of several genes. Hybrids between Saccharomyces species occur frequently in nature as a number of hybrids have been reported among wine and beer strains1–6. Most lager beer strains are hybrids between S. cerevisiae and S. eubayanus, combining the ability to produce ethanol with cryotolerance 6–8. Some S. cerevisiae × S. kudriavzevii strains are associated with beer, but most of them are associated with wine, where they provide unique favor8,9. S. eubayanus and S. uvarum hybrids have been associated with sparkling wine, cider fermentation, and, in some cases, with the production of of-favors in breweries 8,10,11. Interspecifc hybrids among Saccharomyces species can also be readily obtained in the laboratory 9,12–14.
    [Show full text]
  • CAGGG Repeats and the Pericentromeric Duplication of the Hominoid Genome
    Downloaded from genome.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Research CAGGG Repeats and the Pericentromeric Duplication of the Hominoid Genome Evan E. Eichler,1,3 Nicoletta Archidiacono,2 and Mariano Rocchi2 1Department of Genetics and Center for Human Genetics, Case Western Reserve School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106 USA; 2Instituto di Genetica, Via Amendola 165/A, 70126 Bari, Italy Gene duplication is one of the primary forces of evolutionary change. We present data from three different pericentromeric regions of human chromosomes, which indicate that such regions of the genome have been sites of recent genomic duplication. This form of duplication has involved the evolutionary movement of segments of genomic material, including both intronic and exonic sequence, from diverse regions of the genome toward the pericentromeric regions. Sequence analyses of the target sites of duplication have identified a novel class of interspersed GC-rich repeats located precisely at the boundaries of duplication. Estimates of the evolutionary age of these duplications indicate that they have occurred between 10 and 25 mya. In contrast, comparative analyses confirm that the GC-rich pericentromeric repeats have existed within the pericentromeric regions of primate chromosomes before the divergence of the cercopithecoid and hominoid lineages (∼30 mya). These data provide molecular evidence for considerable interchromosomal duplication of genic segments during the evolution of the hominoid genome and strongly implicate GC-rich repeat elements as playing a direct role in the pericentromeric localization of these events Genome evolution is dependent on the processes of eral independent reports indicate that genic segments, single-base-pair mutation and gene duplication.
    [Show full text]
  • Rider Transposon Insertion and Phenotypic Change in Tomato
    Chapter 15 Rider Transposon Insertion and Phenotypic Change in Tomato Ning Jiang, Sofia Visa, Shan Wu, and Esther van der Knaap Abstract The Rider retrotransposon is ubiquitous in the tomato genome and is likely an autonomous element that still transposes to date. The majority of approxi- mately 2,000 copies of Rider are located near genes. Phenotypes associated with Rider insertion are diverse and often the result of knock out of the underlying genes. One unusual Rider-mediated phenotype resulted from a gene duplication event. By means of read-through transcription, Rider copied part of the surrounding sequence to another location in the genome, leading to high expression of one of the transposed genes, SUN, resulting in an elongated fruit shape. Transcription studies demonstrated that Rider is expressed to levels comparable to the expression of other tomato genes and that control of transposition may be regulated by antisense transcription. Taken together, Rider is a unique retrotransposon that may have played important roles in the evolution of tomato and its closest relatives. Keywords LTR Copia • Phenotype • Rider • Tomato • Transcription Abbreviations ATP Adenosine triphosphate bHLH Basic helix–loop–helix BL Blind C Cut leaf or potato leaf mutation N. Jiang Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA S. Visa Department of Mathematics and Computer Science, College of Wooster, Wooster, OH 44691, USA S. Wu • E. van der Knaap (*) Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH 44691, USA e-mail: [email protected] M.-A. Grandbastien and J.M. Casacuberta (eds.), Plant Transposable Elements, 297 Topics in Current Genetics 24, DOI 10.1007/978-3-642-31842-9_15, # Springer-Verlag Berlin Heidelberg 2012 298 N.
    [Show full text]
  • Multiple Large-Scale Gene and Genome Duplications During the Evolution of Hexapods
    Multiple large-scale gene and genome duplications during the evolution of hexapods Zheng Lia,1, George P. Tileyb,c,1, Sally R. Galuskaa, Chris R. Reardona, Thomas I. Kiddera, Rebecca J. Rundella,d, and Michael S. Barkera,2 aDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721; bDepartment of Biology, University of Florida, Gainesville, FL 32611; cDepartment of Biology, Duke University, Durham, NC 27708; and dDepartment of Environmental and Forest Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210 Edited by Michael Freeling, University of California, Berkeley, CA, and approved March 12, 2018 (received for review June 14, 2017) Polyploidy or whole genome duplication (WGD) is a major contrib- than 800,000 described hexapod species (25) are known polyploids utor to genome evolution and diversity. Although polyploidy is (17, 20). However, until recently there were limited data available recognized as an important component of plant evolution, it is to search for evidence of paleopolyploidy among the hexapods generally considered to play a relatively minor role in animal and other animal clades. Thus, the contributions of polyploidy to evolution. Ancient polyploidy is found in the ancestry of some animal evolution and the differences with plant evolution have animals, especially fishes, but there is little evidence for ancient remained unclear. WGDs in other metazoan lineages. Here we use recently published To search for evidence of WGDs among the hexapods, we transcriptomes and genomes from more than 150 species across the leveraged recently released genomic data for the insects (26). insect phylogeny to investigate whether ancient WGDs occurred Combined with additional datasets from public databases, we assembled 128 transcriptomes and 27 genomes with at least one during the evolution of Hexapoda, the most diverse clade of animals.
    [Show full text]
  • Chapter 10 Toward a Theory of Multilevel Evolution: Long-Term Information Integration Shapes the Mutational Landscape and Enhances Evolvability
    1 Chapter 10 Toward a Theory of Multilevel Evolution: Long-Term Information Integration Shapes the Mutational Landscape and Enhances Evolvability Paulien Hogeweg Abstract Most of evolutionary theory has abstracted away from how information is coded in the genome and how this information is transformed into traits on which selection takes place. While in the earliest stages of biological evolution, in the RNA world, the mapping from the genotype into function was largely predefined by the physical–chemical properties of the evolving entities (RNA replicators, e.g. from sequence to folded structure and catalytic sites), in present-day organisms, the mapping itself is the result of evolution. I will review results of several in silico evolutionary studies which examine the consequences of evolving the genetic coding, and the ways this information is transformed, while adapting to prevailing environments. Such multilevel evolution leads to long-term information integration. Through genome, network, and dynamical structuring, the occurrence and/or effect of random mutations becomes nonrandom, and facilitates rapid adaptation. This is what does happen in the in silico experiments. Is it also what did happen in biological evolution? I will discuss some data that suggest that it did. In any case, these results provide us with novel search images to tackle the wealth of biological data. 1 Introduction Much of current research in biology is on the physical and biochemical basis of information processing in cells. This information processing leads to the transfor- mation of the inherited genotypic information to a living organism enough adapted to its environment to survive. P. Hogeweg () Theoretical Biology and Bioinformatics Group, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands e-mail: [email protected] O.S.
    [Show full text]
  • Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution
    cells Review Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution Syed Farhan Ahmad 1,2,3,4, Worapong Singchat 1,3,4, Thitipong Panthum 1,3,4 and Kornsorn Srikulnath 1,2,3,4,5,* 1 Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; [email protected] (S.F.A.); [email protected] (W.S.); [email protected] (T.P.) 2 The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand 3 Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand 4 Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand 5 Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan * Correspondence: [email protected] Abstract: The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is inter- linked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite re- peats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex Citation: Ahmad, S.F.; Singchat, W.; and microchromosome evolution.
    [Show full text]
  • An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice
    G C A T T A C G G C A T genes Review An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice 1, 1, 1 2 Tanguy Lallemand y , Martin Leduc y, Claudine Landès , Carène Rizzon and Emmanuelle Lerat 3,* 1 IRHS, Agrocampus-Ouest, INRAE, Université d’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France; [email protected] (T.L.); [email protected] (M.L.); [email protected] (C.L.) 2 Laboratoire de Mathématiques et Modélisation d’Evry (LaMME), Université d’Evry Val d’Essonne, Université Paris-Saclay, UMR CNRS 8071, ENSIIE, USC INRAE, 23 bvd de France, CEDEX, 91037 Evry Paris, France; [email protected] 3 Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France * Correspondence: [email protected]; Tel.: +3342432918 These authors contributed equally to this work. y Received: 30 July 2020; Accepted: 2 September 2020; Published: 4 September 2020 Abstract: Gene duplication is an important evolutionary mechanism allowing to provide new genetic material and thus opportunities to acquire new gene functions for an organism, with major implications such as speciation events. Various processes are known to allow a gene to be duplicated and different models explain how duplicated genes can be maintained in genomes. Due to their particular importance, the identification of duplicated genes is essential when studying genome evolution but it can still be a challenge due to the various fates duplicated genes can encounter. In this review, we first describe the evolutionary processes allowing the formation of duplicated genes but also describe the various bioinformatic approaches that can be used to identify them in genome sequences.
    [Show full text]