Genetic Diversity in Prokaryotes

8 Key excerpts on "Genetic Diversity in Prokaryotes"

• 

  eBook - ePub

  Microbial Ecology

  • Larry L. Barton, Diana E. Northup(Authors)
  • 2011(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  Hugenholtz P. 2002. Exploring prokaryotic diversity in the genomic era. Genome Biology 3:reviews 0003.1–0003.8. Hugenholtz P, Goebel BM, Pace NR (1998), Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity, J. Bacteriol. 180:4765–4774.

  Insall R (2005), The Dictyostelium genome: The private life of a social model revealed? Genome Biol. 6:article 222.

  Kimura M, Jia Z-J, Nakayama N, Asakawa S (2008), Ecology of viruses in soils: Past, present and future, Soil Sci. Plant Nutr. 54:1–32. Kneip C, Lockhart P, Vo ß C, Maier U-G (2007), BMC Evolut. Biol. 7:55. Konhauser K (2007), Introduction to Geomicrobiology, Malden, MA: Blackwell Publishing. Kröger N, Poulsen N (2008), Diatoms—from cell wall biogenesis to nanotechnology, Annu. Rev. Genetics 42:83–107. Madigan MT, Mrtinko JM, Dunlap PV, Clark DP (2009), Brock Biology of Microorganisms, 12th ed., San Francisco: Pearson Benjamin Cummings. Margulis L, Schwartz KV (1998), Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth, 3rd ed., New York: Freeman. Martin W, Koonin EV (2006), A positive definition of prokaryotes, Nature 442:868. Mendell JE, Clements KD, Choat JH, Angert ER (2008), Extreme polyploidy in a large bacterium, Proc. Natl. Acad. Sci. (USA) 105:6730–6734. Oren A (2006), The order Halobacteriales, in Dworkin M, Falkow S, eds., The Prokaryotes: A Handbook on the Biology of Bacteria, New York: Springer, pp. 113–164. Pace NR (2006), Time for a change, Nature 441:289. Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, Patterson DJ, Katz LA (2006), Evaluating support for the current classification of eukaryotic diversity, PLoS Genetics 2:2062–2072. Rappé MS, Giovannoni SJ (2003), The uncultured microbial majority, Annu. Rev. Microbiol. 57:369–394. Robertson CE, Harris JK, Spear JR, Pace NR (2005), Phylogenetic diversity and ecology of environmental Archaea, Curr. Opin. Microbiol. 8:638–642.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  The Molecular Basis of Plant Genetic Diversity

  • Mahmut Caliskan(Author)
  • 2012(Publication Date)
  • IntechOpen

    (Publisher)

  Part 1 Genetic Diversity in Plant Populations 1 Genomics Meets Biodiversity: Advances in Molecular Marker Development and Their Applications in Plant Genetic Diversity Assessment Péter Poczai 1,2 , Ildikó Varga 2 , Neil E. Bell 1,3 and Jaakko Hyvönen 1 1 Plant Biology, University of Helsinki, Helsinki 2 Department of Plant Science and Biotechnology, Georgikon Faculty University of Pannonia, Keszthely 3 Botanical Museum, University of Helsinki, Helsinki 1,3 Finland 2 Hungary 1. Introduction Genetic diversity is the fundamental source of biodiversity – the total number of genetic characters contributing to variation within species. In other words it is the measure that quantifies the variation found within a population of a given species. Genetic diversity among individuals reflects the presence of different alleles in the gene pool, and hence different genotypes within populations. Genetic diversity should be distinguished from genetic variability, which describes the tendency of genetic traits found within populations to vary (Laikre et al., 2009). Since the beginning of the 20 th century, the study of genetic diversity has been the major focus of core evolutionary biology. The theoretical metrics developed, such as genetic variance and heritability (Fisher, 1930; Wright, 1931), provided the quantitative standards necessary for the evolutionary synthesis. Further research has focused on the origin of genetic diversity, its maintenance and its role in evolution. Simple questions such as “who breeds with whom” initiated studies on the relatedness of populations. These investigations led to the formation of metapopulation theory, where a group of spatially separated populations of the same species interact at some level and form a coherent larger group (Hanski, 1998). The discovery of spatial structure in populations was a key element in the early concepts and models of population ecology, genetics and adaptive evolution (Wright, 1931; Andrewartha & Birch, 1954).

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Textbook of Biodiversity

  • K V Krishnamurthy(Author)
  • 2003(Publication Date)
  • CRC Press

    (Publisher)

  2 GENETIC DIVERSITY Introduction In the last chapter it was recorded that Biodiversity can be studied at four levels: Gene, Species, Ecosystem and Landscape. In this chapter attention will be focused on details of genetic diversity, which is also referred to as within-species divemity, or intra-or infra-specific divemity. A number of infra-specific categories have often been recognised and most of them also enjoy taxonomic implications without necessarily being defined in genetic terms (UNEP 1995): subspecies, varieties, land races, clines, cultivars, ecotypes, chemotypes, cytotypes, hybrids, polytypes, polyploid complexes, aggregated species, etc. The recognition of these 'taxonomic' categories often poses problems in defining and conceptualizing genetic diversity. It should thus be emphasised that 'there is no single definition of genetic diversity that can be used for all purposes' (UNEP 1995, p. 213). Nature and Origin of Genetic Variations It is a well-known fact that the blueprints for all living beings are genes and that they consist of discrete segments of deoxyribonucleic acid (DNA). Meadows (1990) was correct in making the following remark: 'Nature's knowledge is contained in the DNA within living cells'. DNA is a linear molecule composed of sequences of four different nucleotide bases: adenine, guanine, thymine and cytosine. These four bases form the four base pairs: adenine-thymine, guanine-cytosine, thymine-adenine and cytosine-guanine. Genes are 'linearly arranged' along the length of the DNA molecule. All observed variations are invariably due to variations in the sequences of the four base pairs of the DNA molecule. The number of possible combinations of these base pairs exceeds the number of atoms in the universe. From this, one can imagine the magnitude of variations that can be produced. The combinations of these four base pairs in various permutations result in the Genetic code.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Biology of the Prokaryotes

  • Joseph W. Lengeler, Gerhart Drews, Hans G. Schlegel(Authors)
  • 2009(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  In this context, one of the most outstanding capacities of the prokaryotes is their extended horizontal gene transfer under natural condi- tions. A bacterium has access to any useful gene of any other strain and the sum of all the genes of all organisms of a community constitutes a large collective genome. Gene transfer, however, is optional and involves only a small percentage of the genes in a single transfer event. Of these, only the species-specific genes will recombine into the cellular chromosome of a cell. All others will be lost by curing unless under counter- selection. life in temporary ecosystems of mixed populations with complementary metabolic and mor- v vi Preface phological capacIties is the prokaryotic equivalent of multicellular life. AIry bacterium with its cellular chromosome and variable autonomous genetic ele- ments which is a member of an ecosystem thus resembles a differentiated cell in an eukaryotic multi- cellular organism. Furthermore. because no strict genetic isolation exists. speciation is not as pronounced in the prokaryotic world as in the eukaryotic world. This requires a new type of systematics. Viewed in this way. the lifestyle of the archaea (archaebacteria) resembles. despite important biochemical differences. the lifestyle ofthe bacteria (eubacteria) more than it resembles that of the eukaryotes. How Is the Book Organized? This book is based on a physiological and functional approach in which the diversity of the prokaryotic world is made visible by characteristic examples and in which up.:.and-coming developments are indicated. The book is divided into nine sections; the beginning sections provide the basic facts needed to understand the later sections. In this way, the book proceeds from the description of cellular structures through metabolic pathways and metabolic reactions to the genes and regulatory mechanisms.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Genetic Diversity in Microorganisms

  • Mahmut Caliskan(Author)
  • 2012(Publication Date)
  • IntechOpen

    (Publisher)

  Theoretical Population Biology , Vol.3, No.1, pp. 87-112 Patterns of Microbial Genetic Diversity and the Correlation Between Bacterial Demographic History and Geohistory 143 Excoffier, L., Laval, G. & Schneider, S. (2005). Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online , Vol.1, pp. 47-50 Fang, J.S., Shizuka, A., Kato, C. & Schouten, S. (2006). Microbial diversity of cold-seep sediments in Sagami Bay, Japan, as determined by 16S rRNA gene and lipid analyses. Fems Microbiology Ecology , Vol.57, No.3, pp. 429-441 Field, K.G., Gordon, D., Wright, T., Rappe, M., Urbach, E., Vergin, K. & Giovannoni, S.J. (1997). Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Applied and Environmental Microbiology , Vol.63, No.1, pp. 63-70 Flagstad, O. & Roed, K.H. (2003). Refugial origins of reindeer ( Rangifer tarandus L.) inferred from mitochondrial DNA sequences. Evolution , Vol.57, No.3, pp. 658-670 Foerstner, K.U., von Mering, C., Hooper, S.D. & Bork, P. (2005). Environments shape the nucleotide composition of genomes. Embo Reports , Vol.6, No.12, pp. 1208-1213 Franzmann, P.D. (1996). Examination of Antarctic prokaryotic diversity through molecular comparisons. Biodiversity and Conservation , Vol.5, No.11, pp. 1295-1305 Fu, Y.X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics , Vol.147, No.2, pp. 915-925 Fu, Y.X. & Li, W.H. (1999). Coalescing into the 21st century: An overview and prospects of coalescent theory. Theoretical Population Biology , Vol.56, No.1, pp. 1-10 Giovannoni, S.J. & Stingl, U. (2005). Molecular diversity and ecology of microbial plankton. Nature , Vol.437, No.7057, pp. 343-348 Gray, R.R., Tatem, A.J., Johnson, J.A., Alekseyenko, A.V., Pybus, O.G., Suchard, M.A.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Rates of Evolution

  • K.S.W Campbell, M.F. Day, K.S.W. Campbell(Authors)
  • 2019(Publication Date)
  • Routledge

    (Publisher)

  13

  The origin, nature and significance of genetic variation in prokaryotes and eukaryotes

  D. C. REANNEY

  ABSTRACT

  This chapter is based on the premise that natural selection acted to minimise the deleterious effects of (expressed) genetic errors during the early phases of evolution, when many familiar features of the genetic apparatus were ‘fixed’. According to this thesis many key features of the information- transmitting system of cells may be viewed as adaptive responses to the heavy error load placed on early genomes by their inability to correct errors made during copying or introduced from the environment. These features include;

  (1) diploidy and reciprocal recombination in eukaryotes;

  (2) genome segmentation among RNA viruses and;

  (3) the processing system which excises introns from RNA precursors.

  INTRODUCTION

  The title of this chapter is something of a misnomer. I am less concerned with the origin and nature of genetic variation than with its significance for evolution. Let me start by showing how sloppy use of language unconsciously shapes our ideas, often to the detriment of the facts. Compare the words ‘variation’ and ‘error’. In the context of genetics, both usually refer to mutations in DNA (or RNA), that is, they refer to the same thing. But the mental images they evoke are quite different: variation somehow implies ‘useful change’ it links with the notion that mutation is a ‘good’ thing because it fuels evolution. By contrast error implies ‘malfunction — it links with the idea that mutation is a ‘bad’ thing because it causes information to decay. This confusion of meanings must be avoided. The hard fact is that although mutations may cause genomes to ‘vary’ they almost always do so in a destructive

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Biodiversity In Agricultural Production Systems

  • Gero Benckiser, Sylvia Schnell, Gero Benckiser, Sylvia Schnell(Authors)
  • 2006(Publication Date)
  • CRC Press

    (Publisher)

  15 Soil prokaryotes can also be found in more highly evolved animals (e.g., nematodes, insects, or earthworms). They participate in digestion processes as gut inhabitants, but they can also occur in other regions of the body. The types of interactions between prokaroytes and eukaryotes in soil are manifold and they range from pathenogenicity to symbiosis. 5.2 THE PROBLEM OF DIVERSITY MEASUREMENTS OF SOIL PROKARYOTES The determination of “diversity” requires information on the number of different species (“rich-ness”) and the number of individuals within each species (“evenness”). For “richness,” clear, reproducible assignments of individual organisms to species are needed and for “evenness” it is important to have a reliable quantification method. 53,59 Both parameters, richness and evenness, however, cannot be unequivocally determined for prokaryotes in soil samples. 83 The species concept, which is the basis for any biodiversity assessment of eukaryotes, is not directly applicable to the prokaryotes, as prokaryotes lack the existence of groups that are repro-ductively isolated from each other. Even though there are clear definitions of what a prokaroytic species is, these definitions are for practical rather than biological reasons. 113 Type strains for most defined species are deposited in culture collections as reference organisms. Alternative approaches to define species today are debated in light of new insights gained from genome sequencing, bioinformatics, and molecular phylogeny (“phylogenomics”). 3,8,14 For ecological studies, perfect Discerning the Diversity of Soil Prokaryotes 83 species description may not be needed and, thus, the problem of species definitions for environ-mental isolates can be circumvented.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Plant Microbiology

  • Michael Gillings, Andrew Holmes(Authors)
  • 2004(Publication Date)
  • Taylor & Francis

    (Publisher)

  10

  Genetic diversity of bacterial plant pathogens

  Mark Fegan and Chris Hayward

  Plant Microbiology, Michael Gillings and Andrew Holmes© 2004 Garland Science/BIOS Scientific Publishers, Abingdon.

  10.1 Introduction

  The capacity to cause plant disease has evolved in a relatively small number of bacterial species which are phenotypically and genetically diverse. Below the level of the species the strains that make up these species also vary in genotype and phenotype. Traditionally phenotypic techniques such as substrate utilisation profiles and total fatty acid composition have been employed to characterise plant-pathogenic bacteria. Recently more reliable DNA-based methods have been applied which provide a more complete understanding of genetic and evolutionary relationships of bacteria.

  The genetic diversity of phytopathogenic prokaryotes can be assessed by employing molecular methods which differ in the taxonomic level at which they can discriminate (Figure 10.1 ). The phylogenetic diversity of plant-pathogenic bacteria, primarily assessed by phylogenetic analysis of 16S rRNA gene sequences, is of primary importance in the description of bacterial species (Stackebrandt and Goebel, 1994). Another taxonomically important technique for the assessment of genetic diversity of bacteria is the estimation of total DNA-DNA homology. If two strains share 70% DNA-DNA homology they are considered to be related at the species level (Wayne et al., 1987). However, in the absence of differential phenotypic or chemotaxonomic characteristics between strains, which exhibit less than 70% DNA-DNA homology, genomic species or genomospecies have been defined instead of a new species being described (Schloter et al., 2000).

  The basic premise for the assessment of the genetic diversity of any organism is to establish a taxonomic structure from which a nomenclature and classification system for the organism can be generated. The classification system thus generated can then be used to identify the organism and facilitate the prediction of the properties of new isolates, which will hopefully, in the case of plant pathogens, include plant pathogenicity. This improved taxonomy of plant-pathogenic bacteria aids in the development of targeted diagnostic tests, permits the definition of subspecific groups for use in the development of quarantine regulations and is useful in the study of the epidemiology and ecology of the organisms and the study of population genetics and evolution.

  Sign up to read

  Learn more about book