Genome

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For a non-technical introduction to the topic, see Introduction to genetics. For other uses, see Genome (disambiguation).
An image of the 46 chromosomes making up the diploid genome of a human male. (The mitochondrial chromosome is not shown.)

In modern molecular biology and genetics, the genome is the genetic material of an organism. It is encoded either in DNA or, for many types of viruses, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA.[1]

Origin of term[edit]

The term was created in 1920 by Hans Winkler,[2] professor of botany at the University of Hamburg, Germany. The Oxford English Dictionary suggests the name to be a blend of the words gene and chromosome.[3] A few related -ome words already existed—such as biome, rhizome and, more recently, connectome—forming a vocabulary into which genome fits systematically.[4]

Overview[edit]

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 the number of chromosomes of the somatic cell and the genome is a full set of chromosomes in a gamete. The halving of the genetic material in gametes is accomplished by the segregation of homologous chromosomes during meiosis.[5] 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 or linear chains of DNA (or RNA for some viruses), likewise constitute the genome. The term genome can be applied specifically to mean what is stored on a complete set of nuclear DNA (i.e., the "nuclear genome") but can also be applied to what is stored within organelles that contain their own DNA, as with the "mitochondrial genome" or the "chloroplast genome". Additionally, the genome can comprise non-chromosomal genetic elements such as viruses, plasmids, and transposable elements.[6]

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. Colloquially, the phrase "genetic makeup" is sometimes used to signify the genome of a particular individual or organism.[citation needed] 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 book:

  • The book (genome) would contain 23 chapters (chromosomes);
  • Each chapter contains 48 to 250 million letters (A,C,G,T) without spaces;
  • Hence, the book contains over 3.2 billion letters total;
  • The book fits into a cell nucleus the size of a pinpoint;
  • At least one copy of the book (all 23 chapters) is contained in most cells of our body. The only exception in humans is found in mature red blood cells which become enucleated during development and therefore lack a genome.

Sequencing and mapping[edit]

For more details on this topic, see Genome project.

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 next year, Phage Φ-X174, with only 5386 base pairs, became the first DNA-genome project to be completed, by Fred Sanger. The first complete genome sequences for representatives from all 3 domains of life were released within a short period during the mid-1990s. The first bacterial genome to be sequenced was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995. A few months later, the first eukaryotic genome was completed, with the 16 chromosomes of budding yeast Saccharomyces cerevisiae being released as the result of a European-led effort begun in the mid-1980s. Shortly afterward, in 1996, the first genome sequence for an archaeon, Methanococcus jannaschii, was completed, again by The Institute for Genomic Research.

The development of new technologies has made it dramatically easier and cheaper to do sequencing, and the number of complete genome sequences is growing rapidly. The US National Institutes of Health maintains one of several comprehensive databases of genomic information.[7] Among the thousands of completed genome sequencing projects include those for mouse, rice, the plant Arabidopsis thaliana, the puffer fish, and bacteria like E. coli. In December 2013, scientists reported, for the first time, the entire genome of a Neanderthal, an extinct species of humans. The genome was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave.[8][9]

New sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine. A major step toward that goal was the completion in 2007 of the full genome of James D. Watson, one of the co-discoverers of the structure of DNA.[10]

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. The Human Genome Project was organized to map and to sequence the human genome. A fundamental step in the project was the release of a detailed genomic map by Jean Weissenbach and his team at the Genoscope in Paris.[11][12]

Genome compositions[edit]

Genome composition is used to describe the make up of contents of a haploid genome, which should include genome size, proportions of non-repetitive DNA and repetitive DNA in details. By comparing the genome compositions between genomes, scientists can better understand the evolutionary history of a given genome.

When talking about genome composition, one should distinguish between prokaryotes and eukaryotes as the big differences on contents structure they have. In prokaryotes, most of the genome (85-90%) is non-repetitive DNA, which means coding DNA mainly forms it, while non-coding regions only take a small part.[13] On the contrary, eukaryotes have the feature of exon-intron organization of protein coding genes; the variation of repetitive DNA content in eukaryotes is also extremely high. When refer to mammalians and plants, the major part of genome is composed by repetitive DNA.[14]

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 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".

Genome size[edit]

Log-log plot of the total number of annotated proteins in genomes submitted to GenBank as a function of genome size.[15]

Genome size is the total number of DNA base pairs in one copy of a haploid genome. The genome size is positively correlated with the morphological complexity among prokaryotes and lower eukaryotes; however, after mollusks and all the other higher eukaryotes above, this correlation is no longer effective.[14][16] This phenomenon also indicates the mighty influence coming from repetitive DNA act on the genomes.

Since genomes 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 multi-cellular organisms (see Developmental biology). The work is both in vivo and in silico.[17][18]

Organism type Organism Genome size
(base pairs)
Note
Virus Porcine circovirus type 1 1,759 1.8kb Smallest viruses replicating autonomously in eukaryotic cells.[19]
Virus Bacteriophage MS2 3,569 3.5kb First sequenced RNA-genome[20]
Virus SV40 5,224 5.2kb [21]
Virus Phage Φ-X174 5,386 5.4kb First sequenced DNA-genome[22]
Virus HIV 9,749 9.7kb [23]
Virus Phage λ 48,502 48kb Often used as a vector for the cloning of recombinant DNA.

[24] [25] [26]

Virus Megavirus 1,259,197 1.3Mb Until 2013 the largest known viral genome.[27]
Virus Pandoravirus salinus 2,470,000 2.47Mb Largest known viral genome.[28]
Bacterium Haemophilus influenzae 1,830,000 1.8Mb First genome of a living organism sequenced, July 1995[29]
Bacterium Nasuia deltocephalinicola (strain NAS-ALF) 112,091 112kb Smallest non-viral genome.[30]
Bacterium Carsonella ruddii 159,662 160kb
Bacterium Buchnera aphidicola 600,000 600kb [31]
Bacterium Wigglesworthia glossinidia 700,000 700Kb
Bacterium Escherichia coli 4,600,000 4.6Mb [32]
Bacterium Solibacter usitatus (strain Ellin 6076) 9,970,000 10Mb [33]
Amoeboid Polychaos dubium ("Amoeba" dubia) 670,000,000,000 670Gb Largest known genome.[34] (Disputed)[35]
Plant Arabidopsis thaliana 157,000,000 157Mb First plant genome sequenced, December 2000.[36]
Plant Genlisea margaretae 63,400,000 63Mb Smallest recorded flowering plant genome, 2006.[36]
Plant Fritillaria assyrica 130,000,000,000 130Gb
Plant Populus trichocarpa 480,000,000 480Mb First tree genome sequenced, September 2006[37]
Plant Paris japonica (Japanese-native, pale-petal) 150,000,000,000 150Gb Largest plant genome known
Moss Physcomitrella patens 480,000,000 480Mb First genome of a bryophyte sequenced, January 2008.[38]
Yeast Saccharomyces cerevisiae 12,100,000 12.1Mb First eukaryotic genome sequenced, 1996[39]
Fungus Aspergillus nidulans 30,000,000 30Mb
Nematode Caenorhabditis elegans 100,300,000 100Mb First multicellular animal genome sequenced, December 1998[40]
Nematode Pratylenchus coffeae 20,000,000 20Mb Smallest animal genome known[41]
Insect Drosophila melanogaster (fruit fly) 130,000,000 130Mb [42]
Insect Bombyx mori (silk moth) 432,000,000 432Mb

14,623 predicted genes[43]

Insect Apis mellifera (honey bee) 236,000,000 236Mb
Insect Solenopsis invicta (fire ant) 480,000,000 480Mb [44]
Fish Tetraodon nigroviridis (type of puffer fish) 385,000,000 390Mb Smallest vertebrate genome known estimated to be 340 Mb[45][46] - 385 Mb.[47]
Mammal Mus musculus 2,700,000,000 2.7Gb [48]
Mammal Homo sapiens 3,200,000,000 3.2Gb Homo sapiens estimated genome size 3.2 billion bp[49]

Initial sequencing and analysis of the human genome[50]

Fish Protopterus aethiopicus (marbled lungfish) 130,000,000,000 130Gb Largest vertebrate genome known

Proportion of non-repetitive DNA[edit]

The proportion of non-repetitive DNA is calculated by using length of non-repetitive DNA divided by genome size. Protein-coding genes and RNA-coding genes are generally non-repetitive DNA.[51] Bigger genome does not mean more genes, and the proportion of non-repetitive DNA decreases along with the increase of genome size in higher eukaryotes.[14]

It had been found that the proportion of non-repetitive DNA can vary a lot between species. Some E. coli as prokaryotes only have non-repetitive DNA, lower eukaryotes such as C. elegans and fruit fly, still possess more non-repetitive DNA than repetitive DNA.[14][52] Higher eukaryotes tend to have more repetitive DNA than non-repetitive one. In some plants and amphibians, the proportion of non-repetitive DNA is no more than 20%, becoming a minority component.[14]

Proportion of repetitive DNA[edit]

The proportion of repetitive DNA is calculated by using length of repetitive DNA divide by genome size. There are two categories of repetitive DNA in genome: tandem repeats and interspersed repeats.[53]

Tandem repeats[edit]

Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion,[54] satellite DNA and microsatellites are forms of tandem repeats in the genome.[55] Although tandem repeats count for a significant proportion in genome, the largest proportion in mammalian is the other type, interspersed repeats.

Interspersed repeats[edit]

Interspersed repeats mainly come from transposable elements (TEs), but they also include some protein coding gene families and pseudogenes. Transposable elements are able to integrate into the genome at another site within the cell.[13][56] It is believed that TEs are an important driving force on genome evolution of higher eukaryotes.[57] TEs can be classified into two categories, Class 1 (retrotransposons) and Class 2 (DNA transposons).[56]

Retrotransposons[edit]

Retrotransposons can be transcribed into RNA, which are then duplicated at another site into the genome.[58] Retrotransposons can be divided into Long terminal repeats (LTRs) and Non-Long Terminal Repeats (Non-LTR).[57]

Long Terminal Repeats (LTRs) 
similar to retroviruses, which have both gag and pol genes to make cDNA from RNA and proteins to insert into genome, but LTRs can only act within the cell as they lack the env gene in retroviruses.[56] It has been reported that LTRs consist of the largest fraction in most plant genome and might account for the huge variation in genome size.[59]
Non-Long Terminal Repeats (Non-LTRs) 
can be divided into long interspersed elements (LINEs), short interspersed elements (SINEs) and Penelope-like elements. In Dictyostelium discoideum, there is another DIRS-like elements belong to Non-LTRs. Non-LTRs are widely spread in eukaryotic genomes.[60]
Long interspersed elements (LINEs) 
are able to encode two Open Reading Frames (ORFs) to generate transcriptase and endonuclease, which are essential in retrotransposition. The human genome has around 500,000 LINEs, taking around 17% of the genome.[61]
Short interspersed elements (SINEs) 
are usually less than 500 base pairs and need to co-opt with the LINEs machinery to function as nonautonomous retrotransposons.[62] The Alu element is the most common SINEs found in primates, it has a length of about 350 base pairs and takes about 11% of the human genome with around 1,500,000 copies.[57]
DNA transposons[edit]

DNA transposons generally move by "cut and paste" in the genome, but duplication has also been observed. Class 2 TEs do not use RNA as intermediate and are popular in bacteria, in metazoan it has also been found.[57]

Genome evolution[edit]

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. Duplication may range from extension of short tandem repeats, to duplication of a cluster of genes, and all the way to duplication 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.

See also[edit]

References[edit]

  1. ^ Ridley, M. (2006). Genome. New York, NY: Harper Perennial. ISBN 0-06-019497-9
  2. ^ Winkler, HL (1920). Verbreitung und Ursache der Parthenogenesis im Pflanzen- und Tierreiche. Jena: Verlag Fischer. 
  3. ^ "definition of Genome in Oxford dictionary". Retrieved 25 March 2014. 
  4. ^ Lederberg, Joshua; McCray, Alexa T. (2001). "'Ome Sweet 'Omics -- A Genealogical Treasury of Words" (PDF). The Scientist 15 (7). 
  5. ^ Griffiths JF, Gelbart WM, Lewontin RC, Wessler SR, Suzuki DT, Miller JH (2005). Introduction to Genetic Analysis. New York: W.H. Freeman and Co. pp. 34–40, 473–476, 626–629. ISBN 0-7167-4939-4. 
  6. ^ Madigan M, Martinko J (editors) (2006). Brock Biology of Microorganisms (11th ed.). Prentice Hall. ISBN 0-13-144329-1. 
  7. ^ "Genome Home". 2010-12-08. Retrieved 27 January 2011. 
  8. ^ Zimmer, Carl (December 18, 2013). "Toe Fossil Provides Complete Neanderthal Genome". New York Times. Retrieved 18 December 2013. 
  9. ^ Prüfer, Kay; Racimo, Fernando; Patterson, Nick; Jay, Flora; Sankararaman, Sriram; Sawyer, Susanna; Heinze, Anja; Renaud, Gabriel; Sudmant, Peter H.; De Filippo, Cesare; Li, Heng; Mallick, Swapan; Dannemann, Michael; Fu, Qiaomei; Kircher, Martin; Kuhlwilm, Martin; Lachmann, Michael; Meyer, Matthias; Ongyerth, Matthias; Siebauer, Michael; Theunert, Christoph; Tandon, Arti; Moorjani, Priya; Pickrell, Joseph; Mullikin, James C.; Vohr, Samuel H.; Green, Richard E.; Hellmann, Ines; Johnson, Philip L. F. et al. (December 18, 2013). "The complete genome sequence of a Neanderthal from the Altai Mountains". Nature (journal) 505 (7481): 43. doi:10.1038/nature12886. Retrieved 18 December 2013. 
  10. ^ Wade, Nicholas (2007-05-31). "Genome of DNA Pioneer Is Deciphered". The New York Times. Retrieved 2 April 2010. 
  11. ^ "What's a Genome?". Genomenewsnetwork.org. 2003-01-15. Retrieved 27 January 2011. 
  12. ^ NCBI_user_services (2004-03-29). "Mapping Factsheet". Retrieved 27 January 2011. 
  13. ^ a b Koonin, Eugene V.; Wolf, Yuri I. (2010). "Constraints and plasticity in genome and molecular-phenome evolution". Nature Reviews Genetics 11 (7): 487–498. doi:10.1038/nrg2810. PMC 3273317. PMID 20548290. 
  14. ^ a b c d e Lewin, Benjamin (2004). Genes VIII (8th ed.). Upper Saddle River, NJ: Pearson/Prentice Hall. ISBN 0-13-143981-2. 
  15. ^ Koonin, Eugene V. (2011-08-31). The Logic of Chance: The Nature and Origin of Biological Evolution. FT Press. ISBN 9780132542494. 
  16. ^ Gregory TR, Nicol JA, Tamm H, Kullman B, Kullman K, Leitch IJ, Murray BG, Kapraun DF, Greilhuber J, Bennett MD (3 January 2007). "Eukaryotic genome size databases". Nucleic Acids Research 35 (Database): D332–D338. doi:10.1093/nar/gkl828. 
  17. ^ Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison CA 3rd, Smith HO, Venter JC; Assad-Garcia; Alperovich; Yooseph; Lewis; Maruf; Hutchison; Smith; Venter (2006). "Essential genes of a minimal bacterium". Proc Natl Acad Sci USA 103 (2): 425–30. Bibcode:2006PNAS..103..425G. doi:10.1073/pnas.0510013103. PMC 1324956. PMID 16407165. 
  18. ^ Forster AC, Church GM (2006). "Towards synthesis of a minimal cell". Mol Syst Biol. 2 (1): 45. doi:10.1038/msb4100090. PMC 1681520. PMID 16924266. 
  19. ^ Mankertz P (2008). "Molecular Biology of Porcine Circoviruses". Animal Viruses: Molecular Biology. Caister Academic Press. ISBN 978-1-904455-22-6. 
  20. ^ Fiers W, et al.; Contreras, R.; Duerinck, F.; Haegeman, G.; Iserentant, D.; Merregaert, J.; Min Jou, W.; Molemans, F.; Raeymaekers, A.; Van Den Berghe, A.; Volckaert, G.; Ysebaert, M. (1976). "Complete nucleotide-sequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene". Nature 260 (5551): 500–507. Bibcode:1976Natur.260..500F. doi:10.1038/260500a0. PMID 1264203. 
  21. ^ Fiers, W.; Contreras, R.; Haegeman, 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. Bibcode:1978Natur.273..113F. doi:10.1038/273113a0. PMID 205802. 
  22. ^ Sanger, F.; Air, G.M.; Barrell, B.G.; Brown, N.L.; Coulson, A.R.; Fiddes, J.C.; Hutchison, C.A.; Slocombe, P. M.; Smith, M. (1977). "Nucleotide sequence of bacteriophage phi X174 DNA". Nature 265 (5596): 687–695. Bibcode:1977Natur.265..687S. doi:10.1038/265687a0. PMID 870828. 
  23. ^ "Virology - Human Immunodeficiency Virus And Aids, Structure: The Genome And Proteins Of HIV". Pathmicro.med.sc.edu. 2010-07-01. Retrieved 27 January 2011. 
  24. ^ Thomason, Lynn; Court, Donald L.; Bubunenko, Mikail; Costantino, Nina; Wilson, Helen; Datta, Simanti; Oppenheim, Amos (2007). "Recombineering: genetic engineering in bacteria using homologous recombination". Current Protocols in Molecular Biology. Chapter 1: Unit 1.16. doi:10.1002/0471142727.mb0116s78. ISBN 0471142727. PMID 18265390. 
  25. ^ Court, D. L.; Oppenheim, A. B.; Adhya, S. L. (2007). "A new look at bacteriophage lambda genetic networks". Journal of Bacteriology 189 (2): 298–304. doi:10.1128/JB.01215-06. PMC 1797383. PMID 17085553. 
  26. ^ Sanger, F.; Coulson, A.R.; Hong, G.F.; Hill, D.F.; Petersen, G.B. (1982). "Nucleotide sequence of bacteriophage lambda DNA". Journal of Molecular Biology 162 (4): 729–73. doi:10.1016/0022-2836(82)90546-0. PMID 6221115. 
  27. ^ Legendre, M; Arslan, D; Abergel, C; Claverie, JM (2012). "Genomics of Megavirus and the elusive fourth domain of life| journal". Communicative & Integrative Biology 5 (1): 102–106. doi:10.4161/cib.18624. PMC 3291303. 
  28. ^ Philippe, N.; Legendre, M.; Doutre, G.; Coute, Y.; Poirot, O.; Lescot, M.; Arslan, D.; Seltzer, V.; Bertaux, L.; Bruley, C.; Garin, J.; Claverie, J.-M.; Abergel, C. (2013). "Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes". Science 341 (6143): 281. doi:10.1126/science.1239181. PMID 23869018. 
  29. ^ Fleischmann R, Adams M, White O, Clayton R, Kirkness E, Kerlavage A, Bult C, Tomb J, Dougherty B, Merrick J; Adams; White; Clayton; Kirkness; Kerlavage; Bult; Tomb; Dougherty; Merrick; McKenney; Sutton; Fitzhugh; Fields; Gocyne; Scott; Shirley; Liu; Glodek; Kelley; Weidman; Phillips; Spriggs; Hedblom; Cotton; Utterback; Hanna; Nguyen; Saudek et al. (1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd". Science 269 (5223): 496–512. Bibcode:1995Sci...269..496F. doi:10.1126/science.7542800. PMID 7542800. 
  30. ^ Bennett, G. M.; Moran, N. A. (5 August 2013). "Small, Smaller, Smallest: The Origins and Evolution of Ancient Dual Symbioses in a Phloem-Feeding Insect". Genome Biology and Evolution 5 (9): 1675–1688. doi:10.1093/gbe/evt118. 
  31. ^ Shigenobu, S; Watanabe, H; Hattori, M; Sakaki, Y; Ishikawa, H (Sep 7, 2000). "Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS". Nature 407 (6800): 81–6. doi:10.1038/35024074. PMID 10993077. 
  32. ^ 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. 
  33. ^ Challacombe, Jean F.; Eichorst, Stephanie A.; Hauser, Loren; Land, Miriam; Xie, Gary; Kuske, Cheryl R.; Steinke, Dirk (15 September 2011). "Biological Consequences of Ancient Gene Acquisition and Duplication in the Large Genome of Candidatus Solibacter usitatus Ellin6076". In Steinke, Dirk. PLoS ONE 6 (9): e24882. Bibcode:2011PLoSO...624882C. doi:10.1371/journal.pone.0024882. PMC 3174227. PMID 21949776. 
  34. ^ Parfrey LW, Lahr DJG, Katz LA (2008). "The Dynamic Nature of Eukaryotic Genomes". Molecular Biology and Evolution 25 (4): 787–94. doi:10.1093/molbev/msn032. PMC 2933061. PMID 18258610. 
  35. ^ ScienceShot: Biggest Genome Ever, comments: "The measurement for Amoeba dubia and other protozoa which have been reported to have very large genomes were made in the 1960s using a rough biochemical approach which is now considered to be an unreliable method for accurate genome size determinations."
  36. ^ 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. 
  37. ^ Tuskan, GA; Difazio, S; Jansson, S; Bohlmann, J; Grigoriev, I; Hellsten, U; Putnam, N; Ralph, S; Rombauts, S; Salamov, A; Schein, J; Sterck, L; Aerts, A; Bhalerao, RR; Bhalerao, RP; Blaudez, D; Boerjan, W; Brun, A; Brunner, A; Busov, V; Campbell, M; Carlson, J; Chalot, M; Chapman, J; Chen, GL; Cooper, D; Coutinho, PM; Couturier, J; Covert, S; Cronk, Q; Cunningham, R; Davis, J; Degroeve, S; Déjardin, A; Depamphilis, C; Detter, J; Dirks, B; Dubchak, I; Duplessis, S; Ehlting, J; Ellis, B; Gendler, K; Goodstein, D; Gribskov, M; Grimwood, J; Groover, A; Gunter, L; Hamberger, B; Heinze, B; Helariutta, Y; Henrissat, B; Holligan, D; Holt, R; Huang, W; Islam-Faridi, N; Jones, S; Jones-Rhoades, M; Jorgensen, R; Joshi, C; Kangasjärvi, J; Karlsson, J; Kelleher, C; Kirkpatrick, R; Kirst, M; Kohler, A; Kalluri, U; Larimer, F; Leebens-Mack, J; Leplé, JC; Locascio, P; Lou, Y; Lucas, S; Martin, F; Montanini, B; Napoli, C; Nelson, DR; Nelson, C; Nieminen, K; Nilsson, O; Pereda, V; Peter, G; Philippe, R; Pilate, G; Poliakov, A; Razumovskaya, J; Richardson, P; Rinaldi, C; Ritland, K; Rouzé, P; Ryaboy, D; Schmutz, J; Schrader, J; Segerman, B; Shin, H; Siddiqui, A; Sterky, F; Terry, A; Tsai, CJ; Uberbacher, E; Unneberg, P; Vahala, J; Wall, K; Wessler, S; Yang, G; Yin, T; Douglas, C; Marra, M; Sandberg, G; Van de Peer, Y; Rokhsar, D (Sep 15, 2006). "The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)". Science 313 (5793): 1596–604. Bibcode:2006Sci...313.1596T. doi:10.1126/science.1128691. PMID 16973872. 
  38. ^ Lang D, Zimmer AD, Rensing SA, Reski R (October 2008). "Exploring plant biodiversity: the Physcomitrella genome and beyond". Trends Plant Sci 13 (10): 542–549. doi:10.1016/j.tplants.2008.07.002. PMID 18762443. 
  39. ^ "Saccharomyces Genome Database". Yeastgenome.org. Retrieved 27 January 2011. 
  40. ^ 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. 
  41. ^ Gregory TR (2005). "Animal Genome Size Database". http://www.genomesize.com. 
  42. ^ Adams MD, Celniker SE, Holt RA, et al. (2000). "The genome sequence of Drosophila melanogaster". Science 287 (5461): 2185–95. Bibcode:2000Sci...287.2185.. doi:10.1126/science.287.5461.2185. PMID 10731132. Retrieved 25 May 2007. 
  43. ^ The International Silkworm Genome (2008). "The genome of a lepidopteran model insect, the silkworm Bombyx mori". Insect Biochemistry and Molecular Biology 38 (12): 1036–1045. doi:10.1016/j.ibmb.2008.11.004. PMID 19121390.  edit
  44. ^ Wurm Y et al.; Wang, J.; Riba-Grognuz, O.; Corona, M.; Nygaard, S.; Hunt, B. G.; Ingram, K. K.; Falquet, L.; Nipitwattanaphon, M.; Gotzek, D.; Dijkstra, M. B.; Oettler, J.; Comtesse, F.; Shih, C.-J.; Wu, W.-J.; Yang, C.-C.; Thomas, J.; Beaudoing, E.; Pradervand, S.; Flegel, V.; Cook, E. D.; Fabbretti, R.; Stockinger, H.; Long, L.; Farmerie, W. G.; Oakey, J.; Boomsma, J. J.; Pamilo, P.; Yi, S. V. et al. (2011). "The genome of the fire ant Solenopsis invicta". PNAS 108 (14): 5679–5684. Bibcode:2011PNAS..108.5679W. doi:10.1073/pnas.1009690108. PMC 3078418. PMID 21282665. Retrieved 1 February 2011. 
  45. ^ Crollius, HR; Jaillon, O; Dasilva, C; Ozouf-Costaz, C; Fizames, C; Fischer, C; Bouneau, L; Billault, A; Quetier, F; Saurin, W; Bernot, A; Weissenbach, J (2000). "Characterization and Repeat Analysis of the Compact Genome of the Freshwater Pufferfish Tetraodon nigroviridis". Genome Research 10 (7): 939–949. doi:10.1101/gr.10.7.939. PMC 310905. PMID 10899143. 
  46. ^ Jaillon, Olivier; Aury, Jean-Marc; Brunet, Frédéric; Petit, Jean-Louis; Stange-Thomann, Nicole; Mauceli, Evan; Bouneau, Laurence; Fischer, Cécile; Ozouf-Costaz, Catherine; Bernot, Alain; Nicaud, Sophie; Jaffe, David; Fisher, Sheila; Lutfalla, Georges; Dossat, Carole; Segurens, Béatrice; Dasilva, Corinne; Salanoubat, Marcel; Levy, Michael; Boudet, Nathalie; Castellano, Sergi; Anthouard, Véronique; Jubin, Claire; Castelli, Vanina; Katinka, Michael; Vacherie, Benoît; Biémont, Christian; Skalli, Zineb; Cattolico, Laurence; Poulain, Julie; de Berardinis, Véronique; Cruaud, Corinne; Duprat, Simone; Brottier, Philippe; Coutanceau, Jean-Pierre; Gouzy, Jérôme; Parra, Genis; Lardier, Guillaume; Chapple, Charles; McKernan, Kevin J.; McEwan, Paul; Bosak, Stephanie; Kellis, Manolis; Volff, Jean-Nicolas; Guigó, Roderic; Zody, Michael C.; Mesirov, Jill; Lindblad-Toh, Kerstin; Birren, Bruce; Nusbaum, Chad; Kahn, Daniel; Robinson-Rechavi, Marc; Laudet, Vincent; Schachter, Vincent; Quétier, Francis; Saurin, William; Scarpelli, Claude; Wincker, Patrick; Lander, Eric S.; Weissenbach, Jean; Roest Crollius, Hugues (21 October 2004). "Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype". Nature 431 (7011): 946–957. Bibcode:2004Natur.431..946J. doi:10.1038/nature03025. PMID 15496914. 
  47. ^ "Tetraodon Project Information". Retrieved 17 October 2012. 
  48. ^ Church, DM; Goodstadt, L; Hillier, LW; Zody, MC; Goldstein, S; She, X; Bult, CJ; Agarwala, R; Cherry, JL; DiCuccio, M; Hlavina, W; Kapustin, Y; Meric, P; Maglott, D; Birtle, Z; Marques, AC; Graves, T; Zhou, S; Teague, B; Potamousis, K; Churas, C; Place, M; Herschleb, J; Runnheim, R; Forrest, D; Amos-Landgraf, J; Schwartz, DC; Cheng, Z; Lindblad-Toh, K; Eichler, EE; Ponting, CP; Mouse Genome Sequencing, Consortium (May 5, 2009). "Lineage-specific biology revealed by a finished genome assembly of the mouse". In Roberts, Richard J. PLoS Biology 7 (5): e1000112. doi:10.1371/journal.pbio.1000112. PMC 2680341. PMID 19468303. 
  49. ^ "Human Genome Project Information Site Has Been Updated". Ornl.gov. 2013-07-23. Retrieved 6 February 2014. 
  50. ^ Venter, J. C.; Adams, M.; Myers, E.; Li, P.; Mural, R.; Sutton, G.; Smith, H.; Yandell, M.; Evans, C.; Holt, R. A.; Gocayne, J. D.; Amanatides, P.; Ballew, R. M.; Huson, D. H.; Wortman, J. R.; Zhang, Q.; Kodira, C. D.; Zheng, X. H.; Chen, L.; Skupski, M.; Subramanian, G.; Thomas, P. D.; Zhang, J.; Gabor Miklos, G. L.; Nelson, C.; Broder, S.; Clark, A. G.; Nadeau, J.; McKusick, V. A.; Zinder, N. (2001). "The Sequence of the Human Genome". Science 291 (5507): 1304–1351. Bibcode:2001Sci...291.1304V. doi:10.1126/science.1058040. PMID 11181995.  edit
  51. ^ Britten, RJ; Davidson, EH (June 1971). "Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty". The Quarterly review of biology 46 (2): 111–38. doi:10.1086/406830. PMID 5160087. 
  52. ^ Naclerio, G; Cangiano, G, Coulson, A, Levitt, A, Ruvolo, V, La Volpe, A (1992-07-05). "Molecular and genomic organization of clusters of repetitive DNA sequences in Caenorhabditis elegans". Journal of Molecular Biology 226 (1): 159–68. doi:10.1016/0022-2836(92)90131-3. PMID 1619649. 
  53. ^ Stojanovic, edited by Nikola (2007). Computational genomics : current methods. Wymondham: Horizon Bioscience. ISBN 1-904933-30-0. 
  54. ^ Li, YC; Korol, AB, Fahima, T, Beiles, A, Nevo, E (December 2002). "Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review". Molecular ecology 11 (12): 2453–65. doi:10.1046/j.1365-294X.2002.01643.x. PMID 12453231. 
  55. ^ Schlötterer, C (December 2000). "Microsatellite analysis indicates genetic differentiation of the neo-sex chromosomes in Drosophila americana americana". Heredity 85 (Pt 6): 610–6. doi:10.1046/j.1365-2540.2000.00797.x. PMID 11240628. 
  56. ^ a b c Wessler, S. R. (13 November 2006). "Eukaryotic Transposable Elements and Genome Evolution Special Feature: Transposable elements and the evolution of eukaryotic genomes". Proceedings of the National Academy of Sciences 103 (47): 17600–17601. Bibcode:2006PNAS..10317600W. doi:10.1073/pnas.0607612103. 
  57. ^ a b c d Kazazian, H. H. (12 March 2004). "Mobile Elements: Drivers of Genome Evolution". Science 303 (5664): 1626–1632. Bibcode:2004Sci...303.1626K. doi:10.1126/science.1089670. PMID 15016989. 
  58. ^ Deininger PL, Moran JV, Batzer MA, Kazazian, HH Jr (December 2003). "Mobile elements and mammalian genome evolution". Current opinion in genetics & development 13 (6): 651–8. doi:10.1016/j.gde.2003.10.013. PMID 14638329. 
  59. ^ Kidwell MG, Lisch DR (March 2000). "Transposable elements and host genome evolution". Trends in ecology & evolution 15 (3): 95–99. doi:10.1016/S0169-5347(99)01817-0. PMID 10675923. 
  60. ^ Richard G.-F., Kerrest A, Dujon B (3 December 2008). "Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes". Microbiology and Molecular Biology Reviews 72 (4): 686–727. doi:10.1128/MMBR.00011-08. PMC 2593564. PMID 19052325. 
  61. ^ Cordaux R, Batzer MA (1 October 2009). "The impact of retrotransposons on human genome evolution". Nature Reviews Genetics 10 (10): 691–703. doi:10.1038/nrg2640. PMC 2884099. PMID 19763152. 
  62. ^ Han, Jeffrey S.; Boeke, Jef D. (1 August 2005). "LINE-1 retrotransposons: Modulators of quantity and quality of mammalian gene expression?". BioEssays 27 (8): 775–784. doi:10.1002/bies.20257. PMID 16015595. 

Further reading[edit]

  • Benfey, P.; Protopapas, A.D. (2004). Essentials of Genomics. Prentice Hall. 
  • Brown, Terence A. (2002). Genomes 2. Oxford: Bios Scientific Publishers. ISBN 978-1-85996-029-5. 
  • 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[edit]