Genome

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The genome is the entire set of sequences in an organism that encodes information for survival and the continuation of the species it belongs to.

 

Main function of genomes

The main function of genome is information storaging and processing to form an entity that utilizes energy to keep processing signals to interact with other genomes in the whole eco-system.

The genome is universal in the universe and aliens living on other planets also have genomes. The chemical construction may be slightly different but the information deposition and processing function is the same.

The information is usually stored in DNA or RNA in the organisms found on Earth.

The genome is often classified into the protein coding genes and the non-coding sequences of the DNA historically.[1]

 

The essence of genome

The essence of genomes is that it is the foundation of spontaneous information processing network that can utilizes energy in time axis. The genome is a kind of linearly expressed language system.

 

Origin of Term

The term was adapted in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg, Germany. In Greek, the word genome (γίνομαι) means I become, I am born, to come into being.

The Oxford English Dictionary suggests the name to be a blend of the words gene and chromosome. A few related -ome words already existed, such as biome andrhizome, forming a vocabulary into which genome fits systematically.[2]

Overview

Some organisms have multiple copies of chromosomes, diploid, triploid, tetraploid and so on. In classical genetics, in a sexually reproducing organism (typically eukarya) the gamete has half of the number of chromosome of the somatic cell and the genome is a full set of chromosomes in a gamete. In haploid organisms, including cells of bacteria, archaea, and in organelles including mitochondria and chloroplasts, or viruses, that similarly contain genes, the single or set of circular and/or linear chains of DNA (or RNA for some viruses), likewise constitute the genome. The term genome can be applied specifically to mean that stored on a complete set of nuclear DNA (i.e., the "nuclear genome") but can also be applied to that stored within organelles that contain their own DNA, as with the "mitochondrial genome" or the "chloroplast genome". Additionally, the genome can comprise nonchromosomal genetic elements such as viruses, plasmids, and transposable elements[3]. When people say that the genome of a sexually reproducing species has been "sequenced", typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as "a genome sequence" may be a composite read from the chromosomes of various individuals. In general use, the phrase "genetic makeup" is sometimes used conversationally to mean the genome of a particular individual or organism. The study of the global properties of genomes of related organisms is usually referred to as genomics, which distinguishes it from genetics which generally studies the properties of single genes or groups of genes.

Both the number of base pairs and the number of genes vary widely from one species to another, and there is only a rough correlation between the two (an observation known as the C-value paradox). At present, the highest known number of genes is around 60,000, for the protozoan causing trichomoniasis (see List of sequenced eukaryotic genomes), almost three times as many as in the human genome.

An analogy to the human genome stored on DNA is that of instructions stored in a library:

  • The library would contain 46 books (chromosomes)
  • The books range in size from 400 to 3340 pages (genes)
  • which is 48 to 250 million letters (A,C,G,T) per book.
  • Hence the library contains over six billion letters total;
  • The library fits into a cell nucleus the size of a pinpoint;
  • A copy of the library (all 46 books) is contained in almost every cell of our body.

Types

Most biological entities that are more complex than a virus sometimes or always carry additional genetic material besides that which resides in their chromosomes. In some contexts, such as sequencing the genome of a pathogenic microbe, "genome" is meant to include information stored on this auxiliary material, which is carried in plasmids. In such circumstances then, "genome" describes all of the genes and information on non-coding DNA that have the potential to be present.

In eukaryotes such as plants, protozoa and animals, however, "genome" carries the typical connotation of only information on chromosomal DNA. So although these organisms contain chloroplasts and/or mitochondria that have their own DNA, the genetic information contained by DNA within these organelles is not considered part of the genome. In fact, mitochondria are sometimes said to have their own genome often referred to as the "mitochondrial genome". The DNA found within the chloroplast may be referred to as the "plastome".

Genomes and genetic variation

Note that a genome does not capture the genetic diversity or the genetic polymorphism of a species. For example, the human genome sequence in principle could be determined from just half the information on the DNA of one cell from one individual. To learn what variations in genetic information underlie particular traits or diseases requires comparisons across individuals. This point explains the common usage of "genome" (which parallels a common usage of "gene") to refer not to the information in any particular DNA sequence, but to a whole family of sequences that share a biological context.

Although this concept may seem counter intuitive, it is the same concept that says there is no particular shape that is the shape of a cheetah. Cheetahs vary, and so do the sequences of their genomes. Yet both the individual animals and their sequences share commonalities, so one can learn something about cheetahs and "cheetah-ness" from a single example of either.

 

Sequencing and mapping

The Human Genome Project was organized to map and to sequence the human genome. Other genome projects include mouse, rice, the plant Arabidopsis thaliana, the puffer fish, bacteria like E. coli, etc. In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome (bacteriophage MS2). The first DNA-genome project to be completed was the Phage Φ-X174, with only 5386 base pairs, which was sequenced by Fred Sanger in 1977 . The first bacterial genome to be completed was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995.

The development of new technologies has dramatically decreased the difficulty and cost of sequencing, and the number of complete genome sequences is rising rapidly. Among many genome database sites, the one maintained by the US National Institutes of Health is inclusive.[4]

These new technologies open up the prospect of personal genome sequencing as an important diagnostic tool. A major step toward that goal was the May 2007 New York Times announcement that the full genome of DNA pioneer James D. Watson was deciphered.[5]

Whereas a genome sequence lists the order of every DNA base in a genome, a genome map identifies the landmarks. A genome map is less detailed than a genome sequence and aids in navigating around the genome.[6][7]

Contents

Comparison of different genome sizes

Organism type↓ Organism↓ Genome size (base pairs)↓ mass - in pg↓ Note↓
Virus Bacteriophage MS2 3,569 0.000002 First sequenced RNA-genome[8]
Virus SV40 5,224   [9]
Virus Phage Φ-X174 5,386   First sequenced DNA-genome[10]
Virus HIV 9749[11]    
Virus Phage λ 48,502  
Virus Mimivirus 1,181,404   Largest known viral genome
Bacterium Haemophilus influenzae 1,830,000   First genome of living organism, July 1995[12]
Bacterium Carsonella ruddii 159,662   Smallest non-viral genome.[13]
Bacterium Buchnera aphidicola 600,000  
Bacterium Wigglesworthia glossinidia 700,000  
Bacterium Escherichia coli 4,600,000   [14]
Bacterium Solibacter usitatus (strain Ellin 6076) 9,970,000   Largest known Bacterial genome
Amoeboid Polychaos dubium ("Amoeba" dubia) 670,000,000,000 737 Largest known genome.[15]
Plant Arabidopsis thaliana 157,000,000   First plant genome sequenced, December 2000.[16]
Plant Genlisea margaretae 63,400,000   Smallest recorded flowering plant genome, 2006.[16]
Plant Fritillaria assyrica 130,000,000,000  
Plant Populus trichocarpa 480,000,000   First tree genome, September 2006
Moss Physcomitrella patens 480,000,000   First genome of a bryophyte, January 2008 [17]
Yeast Saccharomyces cerevisiae 12,100,000   [18]
Fungus Aspergillus nidulans 30,000,000  
Nematode Caenorhabditis elegans 100,300,000   First multicellular animal genome, December 1998[19]
Nematode Pratylenchus coffeae 20,000,000   Smallest animal genome known[20]
Insect Drosophila melanogaster (fruit fly) 130,000,000   [21]
Insect Bombyx mori (silk moth) 530,000,000  
Insect Apis mellifera (honey bee) 236,000,000  
Fish Tetraodon nigroviridis (type of puffer fish) 385,000,000   Smallest vertebrate genome known
Mammal Homo sapiens 3,200,000,000 3  
Fish Protopterus aethiopicus (marbled lungfish) 130,000,000,000 143 Largest vertebrate genome known

Note: The DNA from a single (diploid) human cell if the 46 chromosomes were connected end-to-end and straightened, would have a length of ~2 m and a width of ~2.4 nanometers.

Since genomes and their organisms are very complex, one research strategy is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive. There is experimental work being done on minimal genomes for single cell organisms as well as minimal genomes for multicellular organisms (see Developmental biology). The work is both in vivo and in silico.[22][23]

Genome evolution

Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to the details of any particular genes and their products. Researchers compare traits such as chromosome number (karyotype), genome size, gene order, codon usage bias, and GC-content to determine what mechanisms could have produced the great variety of genomes that exist today (for recent overviews, see Brown 2002; Saccone and Pesole 2003; Benfey and Protopapas 2004; Gibson and Muse 2004; Reese 2004; Gregory 2005).

Duplications play a major role in shaping the genome. Duplications may range from extension of short tandem repeats, to duplication of a cluster of genes, and all the way to duplications of entire chromosomes or even entire genomes. Such duplications are probably fundamental to the creation of genetic novelty.

Horizontal gene transfer is invoked to explain how there is often extreme similarity between small portions of the genomes of two organisms that are otherwise very distantly related. Horizontal gene transfer seems to be common among many microbes. Also, eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial genomes to their nuclear chromosomes.

References

  1. ^ Ridley, M. (2006). Genome. New York, NY: Harper Perennial. ISBN 0-06-019497-9
  2. ^ Joshua Lederberg and Alexa T. McCray (2001). "'Ome Sweet 'Omics -- A Genealogical Treasury of Words"The Scientist 15 (7).http://lhncbc.nlm.nih.gov/lhc/docs/published/2001/pub2001047.pdf.
  3. ^ Madigan M, Martinko J (editors) (2006). Brock Biology of Microorganisms (11th ed.). Prentice Hall. ISBN 0-13-144329-1.
  4. ^ http://www.ncbi.nlm.nih.gov/sites/entrez?db=Genome&itool=toolbar
  5. ^ Wade, Nicholas (2007-05-31). "Genome of DNA Pioneer Is Deciphered"The New York Timeshttp://www.nytimes.com/2007/05/31/science/31cnd-gene.html?em&ex=1180843200&en=19e1d55639350b73&ei=5087%0A. Retrieved 2010-04-02.
  6. ^ http://www.genomenewsnetwork.org/resources/whats_a_genome/Chp3_1.shtml
  7. ^ http://www.ncbi.nlm.nih.gov/About/primer/mapping.html
  8. ^ Fiers W, et al. (1976). "Complete nucleotide-sequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene"Nature 260 (5551): 500–507. doi:10.1038/260500a0PMID 1264203.http://www.nature.com/nature/journal/v260/n5551/abs/260500a0.html.
  9. ^ Fiers W, Contreras R, Haegemann G, Rogiers R, Van de Voorde A, Van Heuverswyn H, Van Herreweghe J, Volckaert G, Ysebaert M (1978). "Complete nucleotide sequence of SV40 DNA"Nature 273 (5658): 113–120.doi:10.1038/273113a0PMID 205802.http://www.nature.com/nature/journal/v273/n5658/abs/273113a0.html.
  10. ^ Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M (1977). "Nucleotide sequence of bacteriophage phi X174 DNA"Nature 265 (5596): 687–695. doi:10.1038/265687a0PMID 870828.http://www.nature.com/nature/journal/v265/n5596/abs/265687a0.html.
  11. ^ VIROLOGY - HUMAN IMMUNODEFICIENCY VIRUS AND AIDS, STRUCTURE: The Genome AND PROTEINS of HIV
  12. ^ Fleischmann R, Adams M, White O, Clayton R, Kirkness E, Kerlavage A, Bult C, Tomb J, Dougherty B, Merrick J (1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd"Science 269 (5223): 496–512.doi:10.1126/science.7542800PMID 7542800.http://www.sciencemag.org/cgi/content/abstract/269/5223/496.
  13. ^ Nakabachi A, Yamashita A, Toh H, et al. (October 2006). "The 160-kilobase genome of the bacterial endosymbiont Carsonella". Science (journal) 314 (5797): 267. doi:10.1126/science.1134196PMID 17038615.
  14. ^ Frederick R. Blattner, Guy Plunkett III, et al. (1997). "The Complete Genome Sequence of Escherichia coli K-12"Science 277 (5331): 1453–1462.doi:10.1126/science.277.5331.1453PMID 9278503.http://www.sciencemag.org/cgi/content/abstract/277/5331/1453.
  15. ^ Parfrey, L.W.; Lahr, D.J.G.; Katz, L.A. (2008). "The Dynamic Nature of Eukaryotic Genomes". Molecular Biology and Evolution 25 (4): 787.doi:10.1093/molbev/msn032PMID 18258610.
  16. a b Greilhuber, J., Borsch, T., Müller, K., Worberg, A., Porembski, S., and Barthlott, W. (2006). "Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size". Plant Biology 8 (6): 770–777. doi:10.1055/s-2006-924101PMID 17203433.
  17. ^ Daniel Lang, Andreas D. Zimmer, Stefan A. Rensing, Ralf Reski(2008): Exploring plant biodiversity: the Physcomitrella genome and beyond. Trends in Plant Science 13, 542-549. [1]
  18. ^ http://www.yeastgenome.org/
  19. ^ The C. elegans Sequencing Consortium (1998). "Genome sequence of the nematode C. elegans: a platform for investigating biology"Science 282 (5396): 2012–2018. doi:10.1126/science.282.5396.2012PMID 9851916.http://www.sciencemag.org/cgi/content/abstract/282/5396/2012.
  20. ^ "Gregory, T.R. (2005). Animal Genome Size Database. http://www.genomesize.com."http://www.genomesize.com/statistics.php?stats=entire#stats_top.
  21. ^ Adams MD, Celniker SE, Holt RA, et al. (2000). "The genome sequence ofDrosophila melanogaster"Science 287 (5461): 2185–95.doi:10.1126/science.287.5461.2185PMID 10731132.http://www.sciencemag.org/cgi/content/abstract/287/5461/2185. Retrieved 2007-05-25.
  22. ^ Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison CA 3rd, Smith HO, Venter JC (2006). "Essential genes of a minimal bacterium."Proc Natl Acad Sci USA 103 (2): 425–30.doi:10.1073/pnas.0510013103PMID 16407165.
  23. ^ Forster AC, Church GM (2006). "Towards synthesis of a minimal cell"Mol Syst Biol. 2:45: 45. doi:10.1038/msb4100090PMID 16924266.

Further reading

  • Benfey, P.; Protopapas, A.D. (2004). Essentials of Genomics. Prentice Hall.
  • Brown, Terence A. (2002). Genomes 2. Oxford: Bios Scientific Publishers. ISBN 978-1859960295.
  • Gibson, Greg; Muse, Spencer V. (2004). A Primer of Genome Science (Second ed.). Sunderland, Mass: Sinauer Assoc. ISBN 0-87893-234-8.
  • Gregory, T. Ryan (ed) (2005). The Evolution of the Genome. Elsevier. ISBN 0-12-301463-8.
  • Reece, Richard J. (2004). Analysis of Genes and Genomes. Chichester: John Wiley & Sons. ISBN 0-470-84379-9.
  • Saccone, Cecilia; Pesole, Graziano (2003). Handbook of Comparative Genomics. Chichester: John Wiley & Sons. ISBN 0-471-39128-X.
  • Werner, E. (2003). "In silico multicellular systems biology and minimal genomes". Drug Discov Today 8 (24): 1121–1127. doi:10.1016/S1359-6446(03)02918-0PMID 14678738.

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