Genome

DNA
RNA

Codon

PCR

 

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 and rhizome, 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

For more details on this topic, see Genome project.

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]

Comparison of different genome sizes

Main article: Genome size

 

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 Times. http://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:10.1038/260500a0. PMID 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:10.1038/273113a0. PMID 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:10.1038/265687a0. PMID 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.7542800. PMID 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.1134196. PMID 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.277.5331.1453. PMID 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/msn032. PMID 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-2006-924101. PMID 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.282.5396.2012. PMID 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 of Drosophila melanogaster". Science 287 (5461): 2185–95. doi:10.1126/science.287.5461.2185. PMID 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.0510013103. PMID 16407165. 
23. ^ Forster AC, Church GM (2006). "Towards synthesis of a minimal cell". Mol Syst Biol. 2:45: 45. doi:10.1038/msb4100090. PMID 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)02918-0. PMID 14678738. 

External links

• Genomics.org
• Omics.org
• Build a DNA Molecule
• Some comparative genome sizes
• DNA Interactive: The History of DNA Science
• DNA From The Beginning
• All About The Human Genome Project from Genome.gov
• Animal genome size database
• Plant genome size database
• GOLD:Genomes OnLine Database
• The Genome News Network
• NCBI Entrez Genome Project database
• NCBI Genome Primer
• BBC News - Final genome 'chapter' published
• The Plant Genome
• IMG The Integrated Microbial Genomes system, for genome analysis by the DOE-JGI.
• CAMERA Cyberinfrastructure for Metagenomics, data repository and bioinformatics tools for metagenomic research
• GeneCards an integrated database of human genes.
• Genome@IGIB Resources and News on the Zebrafish Genome Project @ IGIB.
• GeKnome Technologies Next-Gen Sequencing Data Analysis Next-Gen Sequencing Data Analysis for Illumina and 454 Service from GeKnome Technologies.
• What Genomes Can Tell Us About the Past - lecture by Sydney Brenner
• Genome metaphor, reflecting from formal-net hierarchies, and software binaries.