Genome

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, a genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses). The genome includes both the genes, (the coding regions), the noncoding DNA[1] and the genomes of the mitochondria[2] and chloroplasts.

Origin of term

The term genome was created in 1920 by Hans Winkler,[3] professor of botany at the University of Hamburg, Germany. The Oxford Dictionary suggests the name is a blend of the words gene and chromosome.[4] However, see omics for a more thorough discussion. A few related -ome words already existed—such as biome, rhizome, forming a vocabulary into which genome fits systematically.[5]

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 the number of chromosomes of the somatic cell and the genome is a full set of chromosomes in a diploid cell. The halving of the genetic material in gametes is accomplished by the segregation of homologous chromosomes during meiosis.[6] 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.[7]

Typically, when it is said that the genome of a sexually reproducing species has been "sequenced", it refers 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. 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 is 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:

Sequencing and mapping

For more details on this topic, see Genome project.
Part of DNA sequence - prototypification of complete genome of virus

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 Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174, of 5386 base pairs.[8] The first complete genome sequences among all three 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 sequences of the 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, 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.[9] Among the thousands of completed genome sequencing projects include those for rice, a mouse, the plant Arabidopsis thaliana, the puffer fish, and the bacteria E. coli. In December 2013, scientists first sequenced 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.[10][11]

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.[12]

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.[13][14]

Reference genome sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity.[15] The decreasing cost of genomic mapping has permitted genealogical sites to offer it as a service,[16] to the extent that one may submit one's genome to crowd sourced scientific endeavours such as DNA.land at the New York Genome Center, an example both of the economies of scale and of citizen science.[17]

Genome compositions

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 there are significant differences with contents structure. 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.[18] 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. In mammals and plants, the major part of the genome is composed of repetitive DNA.[19]

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 in 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

Log-log plot of the total number of annotated proteins in genomes submitted to GenBank as a function of genome size.[20]

Genome size is the total number of DNA base pairs in one copy of a haploid genome. In humans, the nuclear genome comprises approximately 3.2 billion nucleotides of DNA, divided into 24 linear molecules, the shortest 50 000 000 nucleotides in length and the longest 260 000 000 nucleotides, each contained in a different chromosome.[21] 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.[19][22] 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.[23][24]

Here is a table of some significant or representative genomes. See #See also for lists of sequenced genomes.

Organism type Organism Genome size
(base pairs)		 Approx. no. of genes Note
Virus Porcine circovirus type 1 1,759 1.8kb Smallest viruses replicating autonomously in eukaryotic cells.[25]
Virus Bacteriophage MS2 3,569 3.5kb First sequenced RNA-genome[26]
Virus SV40 5,224 5.2kb [27]
Virus Phage Φ-X174 5,386 5.4kb First sequenced DNA-genome[28]
Virus HIV 9,749 9.7kb [29]
Virus Phage λ 48,502 48kb Often used as a vector for the cloning of recombinant DNA.

[30] [31] [32]

Virus Megavirus 1,259,197 1.3Mb Until 2013 the largest known viral genome.[33]
Virus Pandoravirus salinus 2,470,000 2.47Mb Largest known viral genome.[34]
Bacterium Nasuia deltocephalinicola (strain NAS-ALF) 112,091 112kb Smallest non-viral genome.[35]
Bacterium Carsonella ruddii 159,662 160kb
Bacterium Buchnera aphidicola 600,000 600kb [36]
Bacterium Wigglesworthia glossinidia 700,000 700Kb
Bacterium Haemophilus influenzae 1,830,000 1.8Mb First genome of a living organism sequenced, July 1995[37]
Bacterium Escherichia coli 4,600,000 4.6Mb 4288 [38]
Bacterium Solibacter usitatus (strain Ellin 6076) 9,970,000 10Mb [39]
Bacterium – cyanobacterium Prochlorococcus spp. (1.7 Mb) 1,700,000 1.7Mb 1884 Smallest known cyanobacterium genome[40][41]
Bacterium – cyanobacterium Nostoc punctiforme 9,000,000 9Mb 7432 7432 "open reading frames"[42]
Amoeboid Polychaos dubium ("Amoeba" dubia) 670,000,000,000 670Gb Largest known genome.[43] (Disputed)[44]
Plant Genlisea tuberosa 61,000,000 61Mb Smallest recorded flowering plant genome, 2014.[45]
Plant Arabidopsis thaliana 157,000,000 157Mb 25498 First plant genome sequenced, December 2000.[46]
Plant Populus trichocarpa 480,000,000 480Mb 73013 First tree genome sequenced, September 2006[47]
Plant Fritillaria assyrica 130,000,000,000 130Gb
Plant Paris japonica (Japanese-native, pale-petal) 150,000,000,000 150Gb Largest plant genome known[48]
Plant – moss Physcomitrella patens 480,000,000 480Mb First genome of a bryophyte sequenced, January 2008.[49]
Fungus – yeast Saccharomyces cerevisiae 12,100,000 12.1Mb 6294 First eukaryotic genome sequenced, 1996[50]
Fungus Aspergillus nidulans 30,000,000 30Mb 9541 [51]
Nematode Pratylenchus coffeae 20,000,000 20Mb [52] Smallest animal genome known[53]
Nematode Caenorhabditis elegans 100,300,000 100Mb 19000 First multicellular animal genome sequenced, December 1998[54]
Insect Drosophila melanogaster (fruit fly) 175,000,000 175Mb 13600 Size variation based on strain (175-180Mb; standard y w strain is 175Mb)[55]
Insect Apis mellifera (honey bee) 236,000,000 236Mb 10157 [56])
Insect Bombyx mori (silk moth) 432,000,000 432Mb 14623 14,623 predicted genes[57]
Insect Solenopsis invicta (fire ant) 480,000,000 480Mb 16569 [58]
Mammal Mus musculus 2,700,000,000 2.7Gb 20210 [59]
Mammal Homo sapiens 3,289,000,000 3.3Gb 20000 Homo sapiens estimated genome size 3.2 billion bp[60]

Initial sequencing and analysis of the human genome[61]

Mammal Bonobo 3,286,640,000 3.3Gb 20000 Pan paniscus estimated genome size 3.29 billion bp[62]
Fish Tetraodon nigroviridis (type of puffer fish) 385,000,000 390Mb Smallest vertebrate genome known estimated to be 340 Mb[63][64] – 385 Mb.[65]
Fish Protopterus aethiopicus (marbled lungfish) 130,000,000,000 130Gb Largest vertebrate genome known

Proportion of non-repetitive DNA

The proportion of non-repetitive DNA is calculated by using the length of non-repetitive DNA divided by genome size. Protein-coding genes and RNA-coding genes are generally non-repetitive DNA.[66] A bigger genome does not mean more genes, and the proportion of non-repetitive DNA decreases along with increasing genome size in higher eukaryotes.[19]

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.[19][67] Higher eukaryotes tend to have more repetitive DNA than non-repetitive ones. In some plants and amphibians, the proportion of non-repetitive DNA is no more than 20%, becoming a minority component.[19]

Proportion of repetitive DNA

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.[68]

Tandem repeats

Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion,[69] satellite DNA and microsatellites are forms of tandem repeats in the genome.[70] Although tandem repeats count for a significant proportion in genome, the largest proportion in mammalian is the other type, interspersed repeats.

Interspersed repeats

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.[18][71] It is believed that TEs are an important driving force on genome evolution of higher eukaryotes.[72] TEs can be classified into two categories, Class 1 (retrotransposons) and Class 2 (DNA transposons).[71]

Retrotransposons

Retrotransposons can be transcribed into RNA, which are then duplicated at another site into the genome.[73] Retrotransposons can be divided into Long terminal repeats (LTRs) and Non-Long Terminal Repeats (Non-LTR).[72]

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.[71] 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.[74]
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.[75]
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.[76]
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.[77] 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.[72]
DNA transposons

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.[72]

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 karyotype (chromosome number), 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 an 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

References

  1. ↑ Brosius, J (2009), "The Fragmented Gene", Annals of the New York Academy of Sciences, doi:10.1111/j.1749-6632.2009.05004.x
  2. ↑ Ridley, M. (2006), Genome: the autobiography of a species in 23 chapters (PDF), New York: Harper Perennial, ISBN 0-06-019497-9
  3. ↑ Winkler, HL (1920). Verbreitung und Ursache der Parthenogenesis im Pflanzen- und Tierreiche. Jena: Verlag Fischer.
  4. ↑ "definition of Genome in Oxford dictionary". Retrieved 25 March 2014.
  5. ↑ Lederberg, Joshua; McCray, Alexa T. (2001). "'Ome Sweet 'Omics – A Genealogical Treasury of Words" (PDF). The Scientist. 15 (7). Archived from the original (PDF) on 29 September 2006.
  6. ↑ 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.
  7. ↑ Madigan M; Martinko J, eds. (2006). Brock Biology of Microorganisms (11th ed.). Prentice Hall. ISBN 0-13-144329-1.
  8. ↑
  9. ↑ "Genome Home". 2010-12-08. Retrieved 27 January 2011.
  10. ↑ Zimmer, Carl (December 18, 2013). "Toe Fossil Provides Complete Neanderthal Genome". New York Times. Retrieved 18 December 2013.
  11. ↑ 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. 505 (7481): 43–49. Bibcode:2014Natur.505...43P. doi:10.1038/nature12886. Retrieved 18 December 2013.
  12. ↑ Wade, Nicholas (2007-05-31). "Genome of DNA Pioneer Is Deciphered". The New York Times. Retrieved 2 April 2010.
  13. ↑ "What's a Genome?". Genomenewsnetwork.org. 2003-01-15. Retrieved 27 January 2011.
  14. ↑ NCBI_user_services (29 March 2004). "Mapping Factsheet". Archived from the original on 19 July 2010. Retrieved 27 January 2011.
  15. ↑ Genome Reference Consortium. "Assembling the Genome". Retrieved 23 August 2016.
  16. ↑ Kaplan, Sarah (2016-04-17). "How do your 20,000 genes determine so many wildly different traits? They multitask.". The Washington Post. Retrieved 2016-08-27.
  17. ↑ Zimmer, Carl. "Game of Genomes, Episode 13: Answers and Questions". STAT. Retrieved 2016-08-27.
  18. 1 2 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 3273317Freely accessible. PMID 20548290.
  19. 1 2 3 4 5 Lewin, Benjamin (2004). Genes VIII (8th ed.). Upper Saddle River, NJ: Pearson/Prentice Hall. ISBN 0-13-143981-2.
  20. ↑ Koonin, Eugene V. (2011-08-31). The Logic of Chance: The Nature and Origin of Biological Evolution. FT Press. ISBN 9780132542494.
  21. ↑ "Human genome". Retrieved 19 August 2016.
  22. ↑ 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.
  23. ↑ 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. Bibcode:2006PNAS..103..425G. doi:10.1073/pnas.0510013103. PMC 1324956Freely accessible. PMID 16407165.
  24. ↑ Forster AC; Church GM (2006). "Towards synthesis of a minimal cell". Mol Syst Biol. 2 (1): 45. doi:10.1038/msb4100090. PMC 1681520Freely accessible. PMID 16924266.
  25. ↑ Mankertz P (2008). "Molecular Biology of Porcine Circoviruses". Animal Viruses: Molecular Biology. Caister Academic Press. ISBN 978-1-904455-22-6.
  26. ↑ Fiers W; 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.
  27. ↑ 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.
  28. ↑ 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.
  29. ↑ "Virology – Human Immunodeficiency Virus And Aids, Structure: The Genome And Proteins Of HIV". Pathmicro.med.sc.edu. 2010-07-01. Retrieved 27 January 2011.
  30. ↑ 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.
  31. ↑ 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 1797383Freely accessible. PMID 17085553.
  32. ↑ 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.
  33. ↑ 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 3291303Freely accessible. PMID 22482024.
  34. ↑ 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): 281–6. Bibcode:2013Sci...341..281P. doi:10.1126/science.1239181. PMID 23869018.
  35. ↑ 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. PMID 23918810.
  36. ↑ 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.
  37. ↑ Fleischmann R; Adams M; White O; Clayton R; Kirkness E; Kerlavage A; Bult C; Tomb J; Dougherty B; Merrick J; 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.
  38. ↑ 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.
  39. ↑ Challacombe, Jean F.; Eichorst, Stephanie A.; Hauser, Loren; Land, Miriam; Xie, Gary; Kuske, Cheryl R.; Steinke, Dirk (15 September 2011). Steinke, Dirk, ed. "Biological Consequences of Ancient Gene Acquisition and Duplication in the Large Genome of Candidatus Solibacter usitatus Ellin6076". PLoS ONE. 6 (9): e24882. Bibcode:2011PLoSO...624882C. doi:10.1371/journal.pone.0024882. PMC 3174227Freely accessible. PMID 21949776.
  40. ↑ Rocap, G.; Larimer, F. W.; Lamerdin, J.; Malfatti, S.; Chain, P.; Ahlgren, N. A.; Arellano, A.; Coleman, M.; Hauser, L.; Hess, W. R.; Johnson, Z. I.; Land, M.; Lindell, D.; Post, A. F.; Regala, W.; Shah, M.; Shaw, S. L.; Steglich, C.; Sullivan, M. B.; Ting, C. S.; Tolonen, A.; Webb, E. A.; Zinser, E. R.; Chisholm, S. W. (2003). "Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation". Nature. 424 (6952): 1042–7. Bibcode:2003Natur.424.1042R. doi:10.1038/nature01947. PMID 12917642.
  41. ↑ Dufresne, A.; Salanoubat, M.; Partensky, F.; Artiguenave, F.; Axmann, I. M.; Barbe, V.; Duprat, S.; Galperin, M. Y.; Koonin, E. V.; Le Gall, F.; Makarova, K. S.; Ostrowski, M.; Oztas, S.; Robert, C.; Rogozin, I. B.; Scanlan, D. J.; De Marsac, N. T.; Weissenbach, J.; Wincker, P.; Wolf, Y. I.; Hess, W. R. (2003). "Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome". Proceedings of the National Academy of Sciences. 100 (17): 10020–5. Bibcode:2003PNAS..10010020D. doi:10.1073/pnas.1733211100. PMC 187748Freely accessible. PMID 12917486.
  42. ↑ Meeks, J. C.; Elhai, J; Thiel, T; Potts, M; Larimer, F; Lamerdin, J; Predki, P; Atlas, R (2001). "An overview of the genome of Nostoc punctiforme, a multicellular, symbiotic cyanobacterium". Photosynthesis Research. 70 (1): 85–106. doi:10.1023/A:1013840025518. PMID 16228364.
  43. ↑ 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 2933061Freely accessible. PMID 18258610.
  44. ↑ 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."
  45. ↑ Fleischmann A; Michael TP; Rivadavia F; Sousa A; Wang W; Temsch EM; Greilhuber J; Müller KF & Heubl G (2014). "Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms". Annals of Botany. 114 (8): 1651–1663. doi:10.1093/aob/mcu189. PMID 25274549.
  46. ↑ Greilhuber J; Borsch T; Müller K; Worberg A; Porembski S & 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.
  47. ↑ 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.
  48. ↑ PELLICER, JAUME; FAY, MICHAEL F.; LEITCH, ILIA J. (15 September 2010). "The largest eukaryotic genome of them all?". Botanical Journal of the Linnean Society. 164 (1): 10–15. doi:10.1111/j.1095-8339.2010.01072.x.
  49. ↑ 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.
  50. ↑ "Saccharomyces Genome Database". Yeastgenome.org. Retrieved 27 January 2011.
  51. ↑ Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Baştürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D'Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Peñalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW (2005). "Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae". Nature. 438 (7071): 1105–15. Bibcode:2005Natur.438.1105G. doi:10.1038/nature04341. PMID 16372000.
  52. ↑ Leroy, S., S. Bouamer, S. Morand, and M. Fargette (2007). Genome size of plant-parasitic nematodes. Nematology 9: 449-450.
  53. ↑ Gregory TR (2005). "Animal Genome Size Database". Gregory, T.R. (2016). Animal Genome Size Database.
  54. ↑ 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.
  55. ↑ Ellis LL; Huang W; Quinn AM; et al. (2014). "Intrapopulation Genome Size Variation in "Drosophila melanogaster" Reflects Life History Variation and Plasticity". PLoS Genetics. 10 (7): e1004522. doi:10.1371/journal.pgen.1004522. Retrieved 17 March 2016.
  56. ↑ Honeybee Genome Sequencing Consortium; Weinstock; Robinson; Gibbs; Weinstock; Weinstock; Robinson; Worley; Evans; Maleszka; Robertson; Weaver; Beye; Bork; Elsik; Evans; Hartfelder; Hunt; Robertson; Robinson; Maleszka; Weinstock; Worley; Zdobnov; Hartfelder; Amdam; Bitondi; Collins; Cristino; Evans (October 2006). "Insights into social insects from the genome of the honeybee Apis mellifera". Nature. 443 (7114): 931–49. Bibcode:2006Natur.443..931T. doi:10.1038/nature05260. PMC 2048586Freely accessible. PMID 17073008.
  57. ↑ 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.
  58. ↑ Wurm Y; 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 3078418Freely accessible. PMID 21282665. Retrieved 1 February 2011.
  59. ↑ 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). Roberts, Richard J, ed. "Lineage-specific biology revealed by a finished genome assembly of the mouse". PLoS Biology. 7 (5): e1000112. doi:10.1371/journal.pbio.1000112. PMC 2680341Freely accessible. PMID 19468303.
  60. ↑ "Human Genome Project Information Site Has Been Updated". Ornl.gov. 2013-07-23. Retrieved 6 February 2014.
  61. ↑ 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.
  62. ↑ "Pan paniscus (pygmy chimpanzee)". nih.gov. Retrieved 30 June 2016.
  63. ↑ 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 310905Freely accessible. PMID 10899143.
  64. ↑ Olivier Jaillon; et al. (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.
  65. ↑ "Tetraodon Project Information". Retrieved 17 October 2012.
  66. ↑ 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.
  67. ↑ 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.
  68. ↑ Stojanovic, edited by Nikola (2007). Computational genomics : current methods. Wymondham: Horizon Bioscience. ISBN 1-904933-30-0.
  69. ↑ 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.
  70. ↑ 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.
  71. 1 2 3 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.
  72. 1 2 3 4 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.
  73. ↑ 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.
  74. ↑ 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.
  75. ↑ 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 2593564Freely accessible. PMID 19052325.
  76. ↑ 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 2884099Freely accessible. PMID 19763152.
  77. ↑ 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.

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