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Structural Biochemistry/Genome Analysis/Sequenced Genomes

< Structural Biochemistry | Genome Analysis

Due to modern techniques of DNA analysis, many genomes have been sequenced and analyzed. A famous example is the human genome through the Human Genome Project.

Human Genome Project

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The human genome project was an international scientific research effort to fully map out the human genome. This project was started by James D. Watson at the US Institute of Health, but research centers worked on the project all over the world; such as France, Germany, Japan, China, the United Kingdom, and India. So far about 92.3% of the genome has been sequenced, but its difficult to determine due to non-coding sequences of DNA or "junk" DNA.

The genome project uncovered some key findings such as the genome of the human race is 99.9% alike.

Homology

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Sequencing genomes allow scientists to identify homologous proteins and establish evolutionary relationships. Furthermore if a newly discovered protein is homologous to a known protein, through homology scientists can make an educated guess on how the new protein functions.

The Impact of Sequencing on Medicine

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The ability to quickly sequence the human genome in the future may have significant impacts on medicine. Knowledge about genes and an individual's DNA have already given scientists a way to predict the likelihood of certain diseases among individuals. This also allows one to analyze the chromosomal structure, the effects of evolution upon the genome, and protein structures and functions. In the future, gene therapy, genomic medicine, and preventative treatments may reduce the likelihood of disease and allow manufacturers to tailor drugs to specific individuals.

Sequenced Eukaryotic Genomes

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Eukaryotes are organisms containing cells that enclose complex organelles within a well-defined cell membrane. The defining characteristic that sets Eukaryotes and Prokaryotes apart is Eukaryotes' nucleus, or nuclear envelope, in which an organism's genetic information is contained.

The first eukaryotic genome to be sequenced is that of Saccharomyces cerevisiae (S. cerevisiae) in 1996, and it is commonly known as brewer's yeast. S. cerevisiae is the most useful type of yeast due to its utility in baking and brewing, so it is the most studied eukaryotic model organisms in molecular and cell biology, similar to E. coli's role in the study of prokayortic organisms. Many proteins that are important to humans are studied by examining their homologs in yeasts. For example, signaling proteins and protein-processing enzymes are all discovered through the help of yeast genome.

Other fully sequenced organisms include: roundworm, fruitfly, pufferfish (first vertebrate to be sequenced after humans), and Arabidopsis thaliana.

The tables from below are taken from Wikipedia's list of sequenced eukaryotic genomes.

Protists

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Chromista

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The Chromista are a group of protists that contains the algal phyla Heterokontophyta, Haptophyta and Cryptophyta. Members of this group are mostly studied for evolutionary interest.

Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Guillardia theta Cryptomonad Model organism 0.551 Mb
(nucleomorph genome only) 		464[1] Canadian Institute of Advanced Research, Philipps-University Marburg and the University of British Columbia 2001[1]
Thalassiosira pseudonana
Strain:CCMP 1335 		Diatom 2.5 Mb 11,242[2] Joint Genome Institute and the University of Washington 2004[2]
Phaeodactylum tricornutum
Strain: CCAP1055/1 		Diatom 27.4 Mb 10,402 Joint Genome Institute 2008 [3]

Alveolata

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Alveolata are a group of protists which includes the Ciliophora, Apicomplexa and Dinoflagellata. Members of this group are of particular interest to science as the cause of serious human and livestock diseases.

Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Babesia bovis Parasitic protozoan Cattle pathogen 8.2 Mb 3,671 2007[4]
Cryptosporidium hominis
Strain:TU502 		Parasitic protozoan Human pathogen 10.4 Mb 3,994[5] Virginia Commonwealth University 2004[5]
Cryptosporidium parvum
C- or genotype 2 isolate 		Parasitic protozoan Human pathogen 16.5 Mb 3,807[6] UCSF and University of Minnesota 2004[6]
Paramecium tetraurelia Ciliate Model organism 72 Mb 39,642[7] Genoscope 2006[7]
Plasmodium falciparum
Clone:3D7 		Parasitic protozoan Human pathogen (malaria) 22.9 Mb 5,268[8] Malaria Genome Project Consortium 2002[8]
Plasmodium knowlesi Parasitic protozoan Primate pathogen (malaria) 23.5 Mb 5,188[9] 2008[9]
Plasmodium vivax Parasitic protozoan Human pathogen (malaria) 26.8 Mb 5,433[10] 2008[10]
Plasmodium yoelii yoelii
Strain:17XNL 		Parasitic protozoan Rodent pathogen (malaria) 23.1 Mb 5,878[11] TIGR and NMRC 2002[11]
Tetrahymena thermophila Ciliate Model organism 104 Mb 27,000[12] 2006[12]
Theileria parva
Strain:Muguga 		Parasitic protozoan Cattle pathogen (African east coast fever) 8.3 Mb 4,035[13] TIGR and the International Livestock Research Institute 2005[13]
Theileria annulata
Ankara clone C9 		Parasitic protozoan Cattle pathogen 8.3 Mb 3,792 Sanger 2005[14]

Excavata

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Excavata is a group of related free living and symbiotic protists; it includes the Metamonada, Loukozoa, Euglenozoa and Percolozoa. They are researched for their role in human disease.

Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Leishmania major
Strain:Friedlin 		Parasitic protozoan Human pathogen 32.8 Mb 8,272[15] Sanger Institute 2005[15]
Giardia lamblia Parasitic protozoan Human pathogen 11.7 Mb 6,470[16] 2007[16]
Trichomonas vaginalis Parasitic protozoan Human pathogen (Trichomoniasis) 160 Mb 59,681[17] TIGR 2007[17]
Trypanosoma brucei
Strain:TREU927/4 GUTat10.1 		Parasitic protozoan Human pathogen (Sleeping sickness) 26 Mb 9,068 [18] Sanger Institute and TIGR 2005[18]
Trypanosoma cruzi
Strain:CL Brener TC3 		Parasitic protozoan Human pathogen (Chagas disease) 34 Mb 22,570[19] TIGR, Seattle Biomedical Research Institute and Uppsala University 2005[19]

Amoebozoa

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Amoebozoa are a group of motile amoeboid protists, members of this group move or feed by means of temporary projections, called pseudopods. The best known member of this group is the slime mold which has been studied for centuries; other members include the Archamoebae, Tubulinea and Flabellinea. Some Amoeboza cause disease.

Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Dictyostelium discoideum
Strain:AX4 		Slime mold Model organism 34 Mb 12,500[20] Consortium from University of Cologne, Baylor College of Medicine and the Sanger Centre 2005[20]
Entamoeba histolytica
HM1:IMSS 		Parasitic protozoan Human pathogen (amoebic dysentery) 23.8 Mb 9,938[21] TIGR, Sanger Institute and the London School of Hygiene and Tropical Medicine 2005[21]

Plants

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Higher plants

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Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Arabidopsis thaliana
Ecotype:Columbia 		Wild mustard Model plant 120 Mb 25,498[22] Arabidopsis Genome Initiative[23] 2000[22]
Brassica napus Rapeseed Oil plant 1,100 Mb Bayer CropScience 2009[24]
Oryza sativa
ssp indica 		Rice Crop and model organism 420 Mb 32-50,000[25] Beijing Genomics Institute, Zhejiang University and the Chinese Academy of Sciences 2002[25]
Oryza sativa
ssp japonica 		Rice Crop and model organism 466 Mb 46,022-55,615[26] Syngenta and Myriad Genetics 2002[26]
Ostreococcus tauri Green alga Simple eukaryote 12.6 Mb Laboratoire Arago 2006[27]
Physcomitrella patens Bryophyte Model organism

early diverging land plant

500 Mb 39,458[28] US Department of Energy Office of Science Joint Genome Institute 2008[28]
Populus trichocarpa Balsam poplar or Black Cottonwood Carbon sequestration, model tree, commercial use (timber), and comparison to A. thaliana 550 Mb 45,555[29] The International Poplar Genome Consortium 2006[29]
Vitis vinifera Grapevine PN40024 Fruit crop 490 Mb[30] 30,434[30] The French-Italian Public Consortium for Grapevine Genome Characterization 2007[30]
Zea mays
ssp mays 		Corn (maize) Fruit crop 2,800 Mb 50,000-60,000 NSF 2008[31]

Algae

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Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Cyanidioschyzon merolae
Strain:10D 		Red alga Simple eukaryote 16.5 Mb 5,331[32] University of Tokyo, Rikkyo University, Saitama University and Kumamoto University 2004[32]
Thalassiosira pseudonoana[33] Heterokont
Chlamydomonas reinhardtii[34] Model organism 2007[34]
Ostreococcus tauri[33] Chlorophyte

Fungi

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Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Ashbya gossypii
Strain:ATCC 10895 		Fungus Plant pathogen 9.2 Mb 4,718[35] SyngentaAG and University of Basel 2004[35]
Aspergillus fumigatus
Strain:Af293 		Fungus Human pathogen 29.4 Mb 9,926[36] Sanger Institute, University of Manchester, TIGR, Institut Pasteur, Nagasaki University, University of Salamanca and OpGen 2005[36]
Aspergillus nidulans
Strain:FGSC A4 		Fungus Model organism 30 Mb 9,500[37] 2005[37]
Aspergillus niger
Strain:CBS 513.88 		Fungus Biotechnology - fermentation 33.9 Mb 14,165[38] 2007[38]
Aspergillus oryzae
Strain:RIB40 		Fungus Used to ferment soy 37 Mb 12,074[39] National Institute of Technology and Evaluation 2005[39]
Candida glabrata
Strain:CBS138 		Fungus Human pathogen 12.3 Mb 5,283[40] Génolevures Consortium [41] 2004[40]
Cryptococcus (Filobasidiella) neoformans
JEC21 		Fungus Human pathogen 20 Mb 6,500[42] TIGR and Stanford University 2005[42]
Debaryomyces hansenii
Strain:CBS767 		Yeast Cheese ripening 12.2 Mb 6,906[40] Génolevures Consortium 2004[40]
Encephalitozoon cuniculi Microsporidium Human pathogen 2.9 Mb 1,997[43] Genoscope and Université Blaise Pascal 2001[43]
Kluyveromyces lactis
Strain:CLIB210 		Yeast 10-12 Mb 5,329[40] Génolevures Consortium 2004[40]
Magnaporthe grisea Fungus Plant pathogen 37.8 Mb 11,109[44] 2005[44]
Neurospora crassa Fungus Model eukaryote 40 Mb 10,082[37] Broad Institute, Oregon Health and Science University, University of Kentucky, and the University of Kansas 2003[37]
Saccharomyces cerevisiae
Strain:S288C 		Baker's yeast Model eukaryote 12.1 Mb 6,294[45] International Collaboration for the Yeast Genome Sequencing[46] 1996[45]
Schizosaccharomyces pombe
Strain:972h 		Yeast Model eukaryote 14 Mb 4,824[47] Sanger Institute and Cold Spring Harbor Laboratory 2002[47]
Yarrowia lipolytica
Strain:CLIB99 		Yeast Industrial uses 20 Mb 6,703[40] Génolevures Consortium 2004[40]

Animals

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Mammals

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Organism Type Shotgun Coverage Genome size Number of genes predicted Organization Year of completion
Bos taurus Cow 6* 3.0 Gb[48][49] 22000[50] Cattle Genome Sequencing International Consortium 2009
Canis lupus familiaris Dog 7.6* 2.4 Gb[51] 19,300[51] Broad Institute and Agencourt Bioscience 2005[51]
Cavia porcellus Guinea Pig 2* 3.4 Gb The Genome Sequencing Platform, The Genome Assembly Team[49]
Dasypus novemcinctus Nine-banded Armadillo 2* [52] 3.0 Gb Broad Institute[49]
Echinops telfairi Hedgehog-Tenrec 2* [52] Broad Institute
Equus caballus Horse 6.8* 2.1 Gb [49] Broad Institute et al.[49] 2007 [53]
Erinaceus europaeus Western European Hedgehog 2* [52] Broad Institute
Felis catus Cat 2* 3 Gb 20,285 The Genome Sequencing Platform, The Genome Assembly Team[49] 2007[54]
Homo sapiens Human 3.2 Gb [55] 25,000[55] Human Genome Project Consortium and Celera Genomics Draft 2001[56][57]
Complete 2006[58]
Loxodonta africana African Elephant 2* [52] 3 Gb Broad Institute
Macaca mulatta Rhesus Macaque 6* Macaque Genome Sequencing Consortium[49]
Microcebus murinus Gray Mouse Lemur 2* [52] The Genome Sequencing Platform, The Genome Assembly Team[49]
Monodelphis domestica Gray Short-tailed Opossum 3.5 Gb 18 - 20,000 Broad Institute et al. 2007[49][59]
Mus musculus
Strain: C57BL/6J 		Mouse 2.5 Gb 24,174[60] International Collaboration for the Mouse Genome Sequencing[61] 2002[60]
Myotis lucifugus Little Brown Bat 2* [49] Broad Institute
Ochotona princeps American Pika 2* [52] Broad Institute
Ornithorhynchus anatinus [62] Platypus 6* [49] Washington University
Oryctolagus cuniculus Rabbit 2* [52] 2.5 Gb Broad Institute et al. [49]
Otolemur garnettii Small-eared Galago, or Bushbaby 2* [52] Broad Institute
Pan troglodytes Chimpanzee 6* [49] 3.1 Gb Chimpanzee Sequencing and Analysis Consortium 2005[63]
Pongo pygmaeus Orangutan 3.0 Gb Institute for Molecular Biotechnology [49]
Rattus norvegicus Rat 1.8* or better 2.8 Gb [49] 21,166[64] Rat Genome Sequencing Project Consortium 2004[64]
Sorex araneus European Shrew 2* [52] 3.0 Gb [49] The Genome Sequencing Platform, The Genome Assembly Team[49]
Spermophilus tridecemlineatus Thirteen-lined Ground Squirrel 2* The Genome Sequencing Platform, The Genome Assembly Team[49]
Tupaia belangeri Northern Tree Shrew 2* Broad Institute[49]

Insects

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Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Anopheles gambiae
Strain: PEST 		Mosquito Vector of malaria 278 Mb 13,683[65] Celera Genomics and Genoscope 2002[65]
Apis mellifera Honey bee Model for eusocial behavior 1800 Mb 10,157[66] The Honeybee Genome Sequencing Consortium 2006[66]
Bombyx mori
Strain:p50T 		Moth (domestic silk worm) Silk production 530 Mb University of Tokyo and National Institute of Agrobiological Sciences 2004[67]
Drosophila melanogaster Fruit fly Model animal 165 Mb 13,600[68] Celera, UC Berkeley, Baylor College of Medicine, European DGP 2000[68]

Nematodes

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Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Caenorhabditis briggsae Nematode worm For comparison with C. elegans 104 Mb 19,500[69] Washington University, Sanger Institute and Cold Spring Harbor Laboratory 2003[69]
Caenorhabditis elegans
Strain:Bristol N2 		Nematode worm Model animal 100 Mb 19,000[70] Washington University and the Sanger Institute 1998[70]
Meloidogyne hapla Northern root-knot nematode Vegetable pathogen 54 Mb 14,420[71] 2008[71]
Meloidogyne incognita Southern root-knot nematode Plant pathogen 86 Mb 19,212[72] INRA, Genoscope and International M.incognita Genome Consortium[73] 2008[72]
Pristionchus pacificus Nematode worm Model invertebrate 169 Mb 23,500[74] Max-Planck Institute for Developmental Biology &

Genome Sequencing Center, Washington University School of Medicine

2008[74]

Other animals

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Organism Type Relevance Genome size Number of genes predicted Organization Year of completion
Ciona intestinalis Tunicate Simple chordate 116.7 Mb 16,000[75] Joint Genome Institute 2003[75]
Ciona savignyi Tunicate 174 Mb Broad Institute 2007[76]
Gallus gallus Chicken 1000 Mb 20-23,000[77] International Chicken Genome Sequencing Consortium 2004[77]
Strongylocentrotus purpuratus Sea urchin Model eukaryote 814 Mb 23,300[78] Sea Urchin Genome Sequencing Consortium 2006[78]
Takifugu rubripes Puffer fish Vertebrate with small genome 390 Mb 22-29,000[79] International Fugu Genome Consortium[80] 2002[81]
Tetraodon nigroviridis Puffer fish Vertebrate with compact genome 340 Mb[82] 22,400[82] Genoscope and the Broad Institute 2004[82]

Sequenced Bacterial Genomes

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There are some techniques which are improving to be fast and high volume DNA sequencing like fluorescent dideoxynucleotide chain terminators, "shot gun" method etc. The bacterial genome of Haemophilus influenza wa determined in 1995 with a "short gun" method. The genomic DNA is cut randomly into fragments and then the computer programs brings out the whole sequence by matching the overlapping regions between these fragments. The H. influenzae genome consists of 1,830,137 base pairs and encodes approximately 1740 proteins. With these similar approaches, more than 100 bacterial and archaeal species including key model of organisms such as E.coli, Salmonella typhimurium, and Archaeoglobus fulgidus, as well as pathogenic organisms such as Yersina pestis (causing bubonic plague) and Bacillus anthracis (anthrax).1

References

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1. Berg, Jeremy M. 2007. Biochemistry. Sixth Ed. New York: W.H. Freeman. 68-69, 78. 2. Voet, Voet, Pratt (2004). - Fundamentals of Biochemistry

  1. ↑ a b Douglas S, Zauner S, Fraunholz M; et al. (2001). "The highly reduced genome of an enslaved algal nucleus". Nature. 410 (6832): 1091–6. doi:10.1038/35074092. PMID 11323671. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ↑ a b Armbrust EV, Berges JA, Bowler C; et al. (2004). "The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism". Science (journal). 306 (5693): 79–86. doi:10.1126/science.1101156. PMID 15459382. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  3. ↑ Bowler C, Allen AE, Badger JH; et al. (2008). "The Phaeodactylum genome reveals the evolutionary history of diatom genomes". Nature. 456: 239–244. doi:10.1038/nature07410. PMID 18923393. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  4. ↑ Brayton KA, Lau AOT, Herndon DR; et al. (2007). "Genome Sequence of Babesia bovis and Comparative Analysis of Apicomplexan Hemoprotozoa". PLoS Pathogens. 3 (10): e148. doi:10.1371/journal.ppat.0030148. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
  5. ↑ a b Xu P, Widmer G, Wang Y; et al. (2004). "The genome of Cryptosporidium hominis". Nature. 431 (7012): 1107–12. doi:10.1038/nature02977. PMID 15510150. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  6. ↑ a b Abrahamsen MS, Templeton TJ, Enomoto S; et al. (2004). "Complete genome sequence of the apicomplexan, Cryptosporidium parvum". Science (journal). 304 (5669): 441–5. doi:10.1126/science.1094786. PMID 15044751. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  7. ↑ a b Aury JM, Jaillon O, Duret L; et al. (2006). "Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia". Nature. 444 (7116): 171–8. doi:10.1038/nature05230. PMID 17086204. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  8. ↑ a b Gardner MJ, Hall N, Fung E; et al. (2002). "Genome sequence of the human malaria parasite Plasmodium falciparum". Nature. 419 (6906): 498–511. doi:10.1038/nature01097. PMID 12368864. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  9. ↑ a b A. Pain, U. Böhme, A. E. Berry, K. Mungall, R. D. Finn, A. P. Jackson, T. Mourier, J. Mistry, E. M. Pasini, M. A. Aslet, S. Balasubrammaniam, K. Borgwardt, K. Brooks, C. Carret, T. J. Carver, I. Cherevach, T. Chillingworth, T. G. Clark, M. R. Galinski, N. Hall, D. Harper, D. Harris, H. Hauser, A. Ivens, C. S. Janssen, T. Keane, N. Larke, S. Lapp, M. Marti, S. Moule, I. M. Meyer, D. Ormond, N. Peters, M. Sanders, S. Sanders, T. J. Sargeant, M. Simmonds, F. Smith, R. Squares, S. Thurston, A. R. Tivey, D. Walker, B. White, E. Zuiderwijk, C. Churcher, M. A. Quail, A. F. Cowman, C. M. R. Turner, M. A. Rajandream, C. H. M. Kocken, A. W. Thomas, C. I. Newbold, B. G. Barrell & M. Berriman (9 October 2008). "The genome of the simian and human malaria parasite Plasmodium knowlesi". Nature. 455: 799–803. doi:10.1038/nature07306.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  10. ↑ a b JM Carlton, JH Adams, JC Silva; et al. (9 October 2008). "Comparative genomics of the neglected human malaria parasite Plasmodium vivax". Nature. 455: 757–763. doi:10.1038/nature07327. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
  11. ↑ a b Carlton JM, Angiuoli SV, Suh BB; et al. (2002). "Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii". Nature. 419 (6906): 512–9. doi:10.1038/nature01099. PMID 12368865. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  12. ↑ a b Eisen JA, Coyne RS, Wu M; et al. (2006). "Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote". PLoS Biol. 4 (9): e286. doi:10.1371/journal.pbio.0040286. PMC 1557398. PMID 16933976. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  13. ↑ a b Gardner MJ, Bishop R, Shah T; et al. (2005). "Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes". Science (journal). 309 (5731): 134–7. doi:10.1126/science.1110439. PMID 15994558. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  14. ↑ Pain A, Renauld H, Berriman M; et al. (2005). "Genome of the host-cell transforming parasite Theileria annulata compared with T. parva". Science (journal). 309 (5731): 131–3. doi:10.1126/science.1110418. PMID 15994557. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  15. ↑ a b Ivens AC, Peacock CS, Worthey EA; et al. (2005). "The genome of the kinetoplastid parasite, Leishmania major". Science (journal). 309 (5733): 436–42. doi:10.1126/science.1112680. PMC 1470643. PMID 16020728. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  16. ↑ a b HG Morrison, AG McArthur, FD Gillin; et al. (2007). "Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia". Science (journal). 317 (5846): 1921–26. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  17. ↑ a b Carlton JM, Hirt RP, Silva JC; et al. (2007). "Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis". Science (journal). 315 (5809): 207–12. doi:10.1126/science.1132894. PMC 2080659. PMID 17218520. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  18. ↑ a b Berriman M, Ghedin E, Hertz-Fowler C; et al. (2005). "The genome of the African trypanosome Trypanosoma brucei". Science (journal). 309 (5733): 416–22. doi:10.1126/science.1112642. PMID 16020726. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  19. ↑ a b El-Sayed NM, Myler PJ, Bartholomeu DC; et al. (2005). "The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease". Science (journal). 309 (5733): 409–15. doi:10.1126/science.1112631. PMID 16020725. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  20. ↑ a b Eichinger L, Pachebat JA, Glöckner G; et al. (2005). "The genome of the social amoeba Dictyostelium discoideum". Nature. 435 (7038): 43–57. doi:10.1038/nature03481. PMC 1352341. PMID 15875012. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  21. ↑ a b Loftus B, Anderson I, Davies R; et al. (2005). "The genome of the protist parasite Entamoeba histolytica". Nature. 433 (7028): 865–8. doi:10.1038/nature03291. PMID 15729342. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  22. ↑ a b The Arabidopsis Genome Initiative, (2000). "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana". Nature. 408 (6814): 796–815. doi:10.1038/35048692. PMID 11130711. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: extra punctuation (link)
  23. ↑ Arabidopsis Genome Initiative
  24. ↑ http://www.research-in-germany.de/coremedia/generator/dachportal/en/07__News_20and_20Events/VDITZ_20-_20News_26Events/Archiv/2009-10-25_2C_20Full_20oilseed_20rape_20genome_20deciphered,sourcePageId=34814.html
  25. ↑ a b Goff SA, Ricke D, Lan TH; et al. (2002). "A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)". Science (journal). 296 (5565): 92–100. doi:10.1126/science.1068275. PMID 11935018. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  26. ↑ a b Yu J, Hu S, Wang J; et al. (2002). "A draft sequence of the rice genome (Oryza sativa L. ssp. indica)". Science (journal). 296 (5565): 79–92. doi:10.1126/science.1068037. PMID 11935017. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  27. ↑ Derelle E, Ferraz C, Rombauts S; et al. (2006). "Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features". Proc. Natl. Acad. Sci. U.S.A. 103 (31): 11647–52. doi:10.1073/pnas.0604795103. PMC 1544224. PMID 16868079. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  28. ↑ a b Rensing SA, Lang D, Zimmer AD; et al. (2008). "The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants". Science (journal). 319 (5859): 64–9. doi:10.1126/science.1150646. PMID 18079367. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  29. ↑ a b Tuskan GA, Difazio S, Jansson S; et al. (2006). "The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)". Science (journal). 313 (5793): 1596–604. doi:10.1126/science.1128691. PMID 16973872. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  30. ↑ a b c Jaillon O, Aury JM, Noel B; et al. (2007). "The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla". Nature. 449 (7161): 463–7. doi:10.1038/nature06148. PMID 17721507. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  31. ↑ First Draft Of Corn Genome Completed
  32. ↑ a b Matsuzaki M, Misumi O, Shin-I T; et al. (2004). "Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D". Nature. 428 (6983): 653–7. doi:10.1038/nature02398. PMID 15071595. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  33. ↑ a b Walker, Tara (16 Nov 2005). "ALGAL TRANSGENICS IN THE GENOMIC ERA". Journal of Phycology. 41 (6): 1077–1093. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  34. ↑ a b Merchant; et al. (2007). "The Chlamydomonas genome reveals the evolution of key animal and plant functions". Science. 318: 245–250. doi:10.1126/science.1143609. PMID 17932292. {{cite journal}}: Explicit use of et al. in: |author= (help)
  35. ↑ a b Dietrich FS, Voegeli S, Brachat S; et al. (2004). "The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome". Science (journal). 304 (5668): 304–7. doi:10.1126/science.1095781. PMID 15001715. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  36. ↑ a b Nierman WC, Pain A, Anderson MJ; et al. (2005). "Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus". Nature. 438 (7071): 1151–6. doi:10.1038/nature04332. PMID 16372009. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  37. ↑ a b c d Galagan JE, Calvo SE, Cuomo C; et al. (2005). "Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae". Nature. 438 (7071): 1105–15. doi:10.1038/nature04341. PMID 16372000. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) Invalid <ref> tag; name "Galagan" defined multiple times with different content
  38. ↑ a b Pel HJ, de Winde JH, Archer DB; et al. (2007). "Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88". Nat. Biotechnol. 25 (2): 221–31. doi:10.1038/nbt1282. PMID 17259976. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  39. ↑ a b Machida M, Asai K, Sano M; et al. (2005). "Genome sequencing and analysis of Aspergillus oryzae". Nature. 438 (7071): 1157–61. doi:10.1038/nature04300. PMID 16372010. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  40. ↑ a b c d e f g h Dujon B, Sherman D, Fischer G; et al. (2004). "Genome evolution in yeasts". Nature. 430 (6995): 35–44. doi:10.1038/nature02579. PMID 15229592. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  41. ↑ About Génolevures
  42. ↑ a b Loftus BJ, Fung E, Roncaglia P; et al. (2005). "The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans". Science (journal). 307 (5713): 1321–4. doi:10.1126/science.1103773. PMID 15653466. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  43. ↑ a b Katinka MD, Duprat S, Cornillot E; et al. (2001). "Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi". Nature. 414 (6862): 450–3. doi:10.1038/35106579. PMID 11719806. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  44. ↑ a b Dean RA, Talbot NJ, Ebbole DJ; et al. (2005). "The genome sequence of the rice blast fungus Magnaporthe grisea". Nature. 434 (7036): 980–6. doi:10.1038/nature03449. PMID 15846337. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  45. ↑ a b Goffeau A, Barrell BG, Bussey H; et al. (1996). "Life with 6000 genes". Science (journal). 274 (5287): 546, 563–7. PMID 8849441. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  46. ↑ International Collaboration for the Yeast Genome Sequencing
  47. ↑ a b Wood V, Gwilliam R, Rajandream MA; et al. (2002). "The genome sequence of Schizosaccharomyces pombe". Nature. 415 (6874): 871–80. doi:10.1038/nature724. PMID 11859360. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  48. ↑ The Bovine Genome Sequencing and Analysis Consortium (2009-04-24). "The genome sequence of taurine cattle: a window to ruminant biology and evolution". Science. 324 (5926): 522–528. doi:10.1126/science.1169588. Retrieved 2009-04-24.
  49. ↑ a b c d e f g h i j k l m n o p q r s PubMed Home
  50. ↑ http://news.bbc.co.uk/1/hi/sci/tech/8014598.stm Cow genome 'to transform farming'
  51. ↑ a b c Lindblad-Toh K, Wade CM, Mikkelsen TS; et al. (2005). "Genome sequence, comparative analysis and haplotype structure of the domestic dog". Nature. 438 (7069): 803–19. doi:10.1038/nature04338. PMID 16341006. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  52. ↑ a b c d e f g h i Mammalian Genome Project - Broad
  53. ↑ Horse Genome Assembled, February 7, 2007 News Release - National Institutes of Health (NIH)
  54. ↑ Pontius JU, Mullikin JC, Smith DR; et al. (2007). "Initial sequence and comparative analysis of the cat genome". Genome Res. 17 (11): 1675–89. doi:10.1101/gr.6380007. PMC 2045150. PMID 17975172. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  55. ↑ a b Human Genome Sequencing Consortium, International (2004). "Finishing the euchromatic sequence of the human genome". Nature. 431 (7011): 931–45. doi:10.1038/nature03001. PMID 15496913. {{cite journal}}: Unknown parameter |month= ignored (help)
  56. ↑ McPherson JD, Marra M, Hillier L; et al. (2001). "A physical map of the human genome". Nature. 409 (6822): 934–41. doi:10.1038/35057157. PMID 11237014. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  57. ↑ Venter JC, Adams MD, Myers EW; et al. (2001). "The sequence of the human genome". Science (journal). 291 (5507): 1304–51. doi:10.1126/science.1058040. PMID 11181995. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  58. ↑ Gregory SG, Barlow KF, McLay KE; et al. (2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315–21. doi:10.1038/nature04727. PMID 16710414. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  59. ↑ Mikkelsen TS, Wakefield MJ, Aken B; et al. (2007). "Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences". Nature. 447 (7141): 167–77. doi:10.1038/nature05805. PMID 17495919. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  60. ↑ a b Waterston RH, Lindblad-Toh K, Birney E; et al. (2002). "Initial sequencing and comparative analysis of the mouse genome". Nature. 420 (6915): 520–62. doi:10.1038/nature01262. PMID 12466850. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  61. ↑ International Collaboration for the Mouse Genome Sequencing
  62. ↑ Whole Genome Shotgun sequencing project list
  63. ↑ Chimpanzee Sequencing and Analysis Consortium. (2005). "Initial sequence of the chimpanzee genome and comparison with the human genome". Nature. 437 (7055): 69–87. doi:10.1038/nature04072. PMID 16136131. {{cite journal}}: Unknown parameter |month= ignored (help)
  64. ↑ a b Gibbs RA, Weinstock GM, Metzker ML; et al. (2004). "Genome sequence of the Brown Norway rat yields insights into mammalian evolution". Nature. 428 (6982): 493–521. doi:10.1038/nature02426. PMID 15057822. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  65. ↑ a b Holt RA, Subramanian GM, Halpern A; et al. (2002). "The genome sequence of the malaria mosquito Anopheles gambiae". Science (journal). 298 (5591): 129–49. doi:10.1126/science.1076181. PMID 12364791. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)H
  66. ↑ a b Honeybee Genome Sequencing Consortium. (2006). "Insights into social insects from the genome of the honeybee Apis mellifera". Nature. 443 (7114): 931–49. doi:10.1038/nature05260. PMC 2048586. PMID 17073008. {{cite journal}}: Unknown parameter |month= ignored (help)
  67. ↑ Mita K, Kasahara M, Sasaki S; et al. (2004). "The genome sequence of silkworm, Bombyx mori". DNA Res. 11 (1): 27–35. doi:10.1093/dnares/11.1.27. PMID 15141943. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  68. ↑ a b Adams MD, Celniker SE, Holt RA; et al. (2000). "The genome sequence of Drosophila melanogaster". Science (journal). 287 (5461): 2185–95. PMID 10731132. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  69. ↑ a b Stein LD, Bao Z, Blasiar D; et al. (2003). "The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics". PLoS Biol. 1 (2): E45. doi:10.1371/journal.pbio.0000045. PMC 261899. PMID 14624247. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  70. ↑ a b C. elegans Sequencing Consortium. (1998). "Genome sequence of the nematode C. elegans: a platform for investigating biology". Science (journal). 282 (5396): 2012–8. PMID 9851916. {{cite journal}}: Unknown parameter |month= ignored (help)
  71. ↑ a b Charles Opperman, David McK. Bird, Mark Burke, Jonathan Cohn, John Cromer, Steve Diener, Jim Gajan, Steve Graham, T. D. Houfek, Jennifer Schaff, Reenah Schaffer, Elizabeth Scholl, Eric Windham, Bryon R. Sosinski, Valerie M. Williamson, Qingli Liu, Varghese P. Thomas, Dan S. Rokhsar, Therese Mitros (2008). "Sequence and Genetic Map of Meloidogyne hapla: A Compact Nematode Genome for Plant Parasitism". Proceedings of the National Academy of Sciences. 105: 14802. doi:10.1073/pnas.0805946105. PMID 18809916.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  72. ↑ a b Pierre Abad, Jerome Gouzy, Jean-Marc Aury, Philippe Castagnone-Sereno, Etienne G.J. Danchin, Emeline Deleury, Laetitia Perfus-Barbeoch et al. vol. 26, pp. 909-915. (2008). "Genome sequence of the metazoan plant-parasitic nematode : Meloidogyne incognita". Nature Biotechnology. 26: 909–915. doi:10.1038/nbt.1482. PMID 18660804. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  73. ↑ International M.incognita Genome Consortium
  74. ↑ a b Christoph Dieterich, Sandra W Clifton, Lisa N Schuster, Asif Chinwalla, Kimberly Delehaunty, Iris Dinkelacker, Lucinda Fulton, Robert Fulton, Jennifer Godfrey, Pat Minx, Makedonka Mitreva, Waltraud Roeseler, Huiyu Tian, Hanh Witte, Shiaw-Pyng Yang, Richard K Wilson & Ralf J Sommer (2008). "The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism". Nature Genetics. 40: 1193. doi:10.1038/ng.227. PMID 17095691. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  75. ↑ a b Dehal P, Satou Y, Campbell RK; et al. (2002). "The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins". Science (journal). 298 (5601): 2157–67. doi:10.1126/science.1080049. PMID 12481130. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  76. ↑ Small KS, Brudno M, Hill MM, Sidow A (2007). "A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome". Genome Biol. 8 (3): R41. doi:10.1186/gb-2007-8-3-r41. PMC 1868934. PMID 17374142.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  77. ↑ a b International Chicken Genome Sequencing Consortium. (2004). "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution". Nature. 432 (7018): 695–716. doi:10.1038/nature03154. PMID 15592404. {{cite journal}}: Unknown parameter |month= ignored (help)
  78. ↑ a b Sodergren E, Weinstock GM, Davidson EH; et al. (2006). "The genome of the sea urchin Strongylocentrotus purpuratus". Science (journal). 314 (5801): 941–52. doi:10.1126/science.1133609. PMID 17095691. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  79. ↑ International Fugu Genome Consortium. Forth Genome Assembly
  80. ↑ International Fugu Genome Consortium
  81. ↑ Aparicio S, Chapman J, Stupka E; et al. (2002). "Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes". Science (journal). 297 (5585): 1301–10. doi:10.1126/science.1072104. PMID 12142439. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  82. ↑ a b c Jaillon O, Aury JM, Brunet F; et al. (2004). "Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype". Nature. 431 (7011): 946–57. doi:10.1038/nature03025. PMID 15496914. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
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