Structural Biochemistry/Genome Analysis/Sequenced Genomes

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 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 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 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 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 Chromista 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 thetaCryptomonadModel organism0.551 Mb(nucleomorph genome only)464Douglas S, Zauner S, Fraunholz M, et al. The highly reduced genome of an enslaved algal nucleus Nature 410 6832 1091–6 2001 April 11323671 10.1038/35074092 Canadian Institute of Advanced Research, Philipps-University Marburg and the University of British Columbia2001Thalassiosira pseudonanaStrain:CCMP 1335Diatom2.5 Mb11,242Armbrust EV, Berges JA, Bowler C, et al. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism Science (journal) 306 5693 79–86 2004 October 15459382 10.1126/science.1101156 Joint Genome Institute and the University of Washington2004 Phaeodactylum tricornutumStrain: CCAP1055/1 Diatom27.4 Mb10,402 Joint Genome Institute 2008 Bowler C, Allen AE, Badger JH, et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes Nature 456 239–244 2008 November 18923393 10.1038/nature07410 http://www.nature.com/nature/journal/v456/n7219/abs/nature07410.html Alveolata 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 bovisParasitic protozoanCattle pathogen8.2 Mb3,6712007Brayton KA, Lau AOT, Herndon DR, et al. Genome Sequence of Babesia bovis and Comparative Analysis of Apicomplexan Hemoprotozoa. PLoS Pathogens 3 10 e148 2007 10.1371/journal.ppat.0030148 Cryptosporidium hominisStrain:TU502Parasitic protozoanHuman pathogen10.4 Mb3,994Xu P, Widmer G, Wang Y, et al. The genome of Cryptosporidium hominis Nature 431 7012 1107–12 2004 October 15510150 10.1038/nature02977 Virginia Commonwealth University2004Cryptosporidium parvumC- or genotype 2 isolateParasitic protozoanHuman pathogen16.5 Mb3,807Abrahamsen MS, Templeton TJ, Enomoto S, et al. Complete genome sequence of the apicomplexan, Cryptosporidium parvum Science (journal) 304 5669 441–5 2004 April 15044751 10.1126/science.1094786 UCSF and University of Minnesota2004Paramecium tetraureliaCiliateModel organism72 Mb39,642Aury JM, Jaillon O, Duret L, et al. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia Nature 444 7116 171–8 2006 November 17086204 10.1038/nature05230 Genoscope2006Plasmodium falciparumClone:3D7Parasitic protozoanHuman pathogen (malaria)22.9 Mb5,268Gardner MJ, Hall N, Fung E, et al. Genome sequence of the human malaria parasite Plasmodium falciparum Nature 419 6906 498–511 2002 October 12368864 10.1038/nature01097 Malaria Genome Project Consortium2002Plasmodium knowlesiParasitic protozoanPrimate pathogen (malaria)23.5 Mb5,188A. 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 The genome of the simian and human malaria parasite Plasmodium knowlesi Nature 455 799–803 9 October 2008 10.1038/nature07306 2008Plasmodium vivaxParasitic protozoanHuman pathogen (malaria)26.8 Mb5,433JM Carlton, JH Adams, JC Silva, et al. Comparative genomics of the neglected human malaria parasite Plasmodium vivax Nature 455 757–763 9 October 2008 10.1038/nature07327 2008Plasmodium yoelii yoeliiStrain:17XNLParasitic protozoanRodent pathogen (malaria)23.1 Mb5,878Carlton JM, Angiuoli SV, Suh BB, et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii Nature 419 6906 512–9 2002 October 12368865 10.1038/nature01099 TIGR and NMRC2002Tetrahymena thermophilaCiliateModel organism104 Mb27,000Eisen JA, Coyne RS, Wu M, et al. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote PLoS Biol. 4 9 e286 2006 September 16933976 1557398 10.1371/journal.pbio.0040286 2006Theileria parvaStrain:MugugaParasitic protozoanCattle pathogen (African east coast fever)8.3 Mb4,035Gardner MJ, Bishop R, Shah T, et al. Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes Science (journal) 309 5731 134–7 2005 July 15994558 10.1126/science.1110439 TIGR and the International Livestock Research Institute2005Theileria annulataAnkara clone C9Parasitic protozoanCattle pathogen8.3 Mb3,792Sanger2005Pain A, Renauld H, Berriman M, et al. Genome of the host-cell transforming parasite Theileria annulata compared with T. parva Science (journal) 309 5731 131–3 2005 July 15994557 10.1126/science.1110418 Excavata 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 majorStrain:FriedlinParasitic protozoanHuman pathogen32.8 Mb8,272Ivens AC, Peacock CS, Worthey EA, et al. The genome of the kinetoplastid parasite, Leishmania major Science (journal) 309 5733 436–42 2005 July 16020728 1470643 10.1126/science.1112680 Sanger Institute2005Giardia lambliaParasitic protozoanHuman pathogen11.7 Mb6,470HG Morrison, AG McArthur, FD Gillin, et al. Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia Science (journal) 317 5846 1921–26 2007 September 2007Trichomonas vaginalisParasitic protozoanHuman pathogen (Trichomoniasis)160 Mb59,681Carlton JM, Hirt RP, Silva JC, et al. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis Science (journal) 315 5809 207–12 2007 January 17218520 2080659 10.1126/science.1132894 TIGR2007Trypanosoma bruceiStrain:TREU927/4 GUTat10.1Parasitic protozoanHuman pathogen (Sleeping sickness)26 Mb9,068 Berriman M, Ghedin E, Hertz-Fowler C, et al. The genome of the African trypanosome Trypanosoma brucei Science (journal) 309 5733 416–22 2005 July 16020726 10.1126/science.1112642 Sanger Institute and TIGR2005Trypanosoma cruziStrain:CL Brener TC3Parasitic protozoanHuman pathogen (Chagas disease)34 Mb22,570El-Sayed NM, Myler PJ, Bartholomeu DC, et al. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease Science (journal) 309 5733 409–15 2005 July 16020725 10.1126/science.1112631 TIGR, Seattle Biomedical Research Institute and Uppsala University2005 Amoebozoa 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 discoideumStrain:AX4Slime moldModel organism34 Mb12,500Eichinger L, Pachebat JA, Glöckner G, et al. The genome of the social amoeba Dictyostelium discoideum Nature 435 7038 43–57 2005 May 15875012 1352341 10.1038/nature03481 Consortium from University of Cologne, Baylor College of Medicine and the Sanger Centre2005 Entamoeba histolyticaHM1:IMSSParasitic protozoanHuman pathogen (amoebic dysentery)23.8 Mb9,938Loftus B, Anderson I, Davies R, et al. The genome of the protist parasite Entamoeba histolytica Nature 433 7028 865–8 2005 February 15729342 10.1038/nature03291 TIGR, Sanger Institute and the London School of Hygiene and Tropical Medicine2005 Plants Higher plants Organism Type Relevance Genome size Number of genes predicted Organization Year of completion Arabidopsis thalianaEcotype:ColumbiaWild mustardModel plant120 Mb25,498 The Arabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 6814 796–815 2000 December 11130711 10.1038/35048692 Arabidopsis Genome InitiativeArabidopsis Genome Initiative2000Brassica napusRapeseedOil plant1,100 MbBayer CropScience2009http://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.htmlOryza sativassp indicaRiceCrop and model organism420 Mb32-50,000Goff SA, Ricke D, Lan TH, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica) Science (journal) 296 5565 92–100 2002 April 11935018 10.1126/science.1068275 Beijing Genomics Institute, Zhejiang University and the Chinese Academy of Sciences2002Oryza sativassp japonicaRiceCrop and model organism466 Mb46,022-55,615Yu J, Hu S, Wang J, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica) Science (journal) 296 5565 79–92 2002 April 11935017 10.1126/science.1068037 Syngenta and Myriad Genetics2002Ostreococcus tauriGreen algaSimple eukaryote12.6 MbLaboratoire Arago2006Derelle E, Ferraz C, Rombauts S, et al. 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 2006 August 16868079 1544224 10.1073/pnas.0604795103 Physcomitrella patensBryophyteModel organism early diverging land plant500 Mb39,458Rensing SA, Lang D, Zimmer AD, et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants Science (journal) 319 5859 64–9 2008 January 18079367 10.1126/science.1150646 US Department of Energy Office of Science Joint Genome Institute2008Populus trichocarpaBalsam poplar or Black CottonwoodCarbon sequestration, model tree, commercial use (timber), and comparison to A. thaliana550 Mb45,555Tuskan GA, Difazio S, Jansson S, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) Science (journal) 313 5793 1596–604 2006 September 16973872 10.1126/science.1128691 The International Poplar Genome Consortium2006Vitis viniferaGrapevine PN40024Fruit crop490 MbJaillon O, Aury JM, Noel B, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature 449 7161 463–7 2007 September 17721507 10.1038/nature06148 30,434The French-Italian Public Consortium for Grapevine Genome Characterization2007Zea mays ssp maysCorn (maize)Fruit crop2,800 Mb50,000-60,000NSF2008First Draft Of Corn Genome Completed Algae Organism Type Relevance Genome size Number of genes predicted Organization Year of completion Cyanidioschyzon merolaeStrain:10DRed algaSimple eukaryote16.5 Mb5,331Matsuzaki M, Misumi O, Shin-I T, et al. Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D Nature 428 6983 653–7 2004 April 15071595 10.1038/nature02398 University of Tokyo, Rikkyo University, Saitama University and Kumamoto University2004Thalassiosira pseudonoanaWalker Tara Chris Collet and Saul Purton 16 Nov 2005 ALGAL TRANSGENICS IN THE GENOMIC ERA Journal of Phycology 41 6 1077 - 1093HeterokontChlamydomonas reinhardtii Merchant et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions Science 2007 318 245–250 17932292 10.1126/science.1143609Model organism2007Ostreococcus tauriChlorophyte Fungi Organism Type Relevance Genome size Number of genes predicted Organization Year of completion Ashbya gossypiiStrain:ATCC 10895 FungusPlant pathogen9.2 Mb4,718Dietrich FS, Voegeli S, Brachat S, et al. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome Science (journal) 304 5668 304–7 2004 April 15001715 10.1126/science.1095781 SyngentaAG and University of Basel2004Aspergillus fumigatusStrain:Af293FungusHuman pathogen29.4 Mb9,926Nierman WC, Pain A, Anderson MJ, et al. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus Nature 438 7071 1151–6 2005 December 16372009 10.1038/nature04332 Sanger Institute, University of Manchester, TIGR, Institut Pasteur, Nagasaki University, University of Salamanca and OpGen2005Aspergillus nidulansStrain:FGSC A4FungusModel organism30 Mb9,500Galagan JE, Calvo SE, Cuomo C, et al. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae Nature 438 7071 1105–15 2005 December 16372000 10.1038/nature04341 2005Aspergillus nigerStrain:CBS 513.88FungusBiotechnology - fermentation33.9 Mb14,165Pel HJ, de Winde JH, Archer DB, et al. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88 Nat. Biotechnol. 25 2 221–31 2007 February 17259976 10.1038/nbt1282 2007Aspergillus oryzaeStrain:RIB40FungusUsed to ferment soy 37 Mb12,074Machida M, Asai K, Sano M, et al. Genome sequencing and analysis of Aspergillus oryzae Nature 438 7071 1157–61 2005 December 16372010 10.1038/nature04300 National Institute of Technology and Evaluation2005Candida glabrataStrain:CBS138FungusHuman pathogen12.3 Mb5,283Dujon B, Sherman D, Fischer G, et al. Genome evolution in yeasts Nature 430 6995 35–44 2004 July 15229592 10.1038/nature02579 Génolevures Consortium About Génolevures2004Cryptococcus (Filobasidiella) neoformansJEC21FungusHuman pathogen20 Mb6,500Loftus BJ, Fung E, Roncaglia P, et al. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans Science (journal) 307 5713 1321–4 2005 February 15653466 10.1126/science.1103773 TIGR and Stanford University2005Debaryomyces hanseniiStrain:CBS767YeastCheese ripening12.2 Mb6,906Génolevures Consortium2004Encephalitozoon cuniculiMicrosporidiumHuman pathogen2.9 Mb1,997Katinka MD, Duprat S, Cornillot E, et al. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi Nature 414 6862 450–3 2001 November 11719806 10.1038/35106579 Genoscope and Université Blaise Pascal2001Kluyveromyces lactisStrain:CLIB210Yeast10-12 Mb5,329Génolevures Consortium2004Magnaporthe griseaFungusPlant pathogen37.8 Mb11,109Dean RA, Talbot NJ, Ebbole DJ, et al. The genome sequence of the rice blast fungus Magnaporthe grisea Nature 434 7036 980–6 2005 April 15846337 10.1038/nature03449 2005Neurospora crassaFungusModel eukaryote40 Mb10,082Galagan JE, Calvo SE, Borkovich KA, et al. The genome sequence of the filamentous fungus Neurospora crassa Nature 422 6934 859–68 2003 April 12712197 10.1038/nature01554 Broad Institute, Oregon Health and Science University, University of Kentucky, and the University of Kansas2003Saccharomyces cerevisiaeStrain:S288CBaker's yeastModel eukaryote12.1 Mb6,294Goffeau A, Barrell BG, Bussey H, et al. Life with 6000 genes Science (journal) 274 5287 546, 563–7 1996 October 8849441 http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=8849441International Collaboration for the Yeast Genome SequencingInternational Collaboration for the Yeast Genome Sequencing1996Schizosaccharomyces pombeStrain:972hYeastModel eukaryote14 Mb4,824Wood V, Gwilliam R, Rajandream MA, et al. The genome sequence of Schizosaccharomyces pombe Nature 415 6874 871–80 2002 February 11859360 10.1038/nature724 Sanger Institute and Cold Spring Harbor Laboratory2002Yarrowia lipolyticaStrain:CLIB99YeastIndustrial uses20 Mb6,703Génolevures Consortium2004 Animals Mammals Organism Type Shotgun Coverage Genome size Number of genes predicted Organization Year of completion Bos taurus Cow 6* 3.0 Gb 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 10.1126/science.1169588 http://www.sciencemag.org/cgi/content/abstract/324/5926/522 2009-04-24PubMed Home 22000http://news.bbc.co.uk/1/hi/sci/tech/8014598.stm Cow genome 'to transform farming' Cattle Genome Sequencing International Consortium 2009Canis lupus familiaris Dog 7.6* 2.4 GbLindblad-Toh K, Wade CM, Mikkelsen TS, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog Nature 438 7069 803–19 2005 December 16341006 10.1038/nature04338 19,300Broad Institute and Agencourt Bioscience2005Cavia porcellus Guinea Pig 2* 3.4 Gb The Genome Sequencing Platform, The Genome Assembly TeamDasypus novemcinctus Nine-banded Armadillo 2* Mammalian Genome Project - Broad 3.0 Gb Broad Institute Echinops telfairi Hedgehog-Tenrec 2* Broad InstituteEquus caballus Horse 6.8* 2.1 Gb Broad Institute et al.2007 Horse Genome Assembled, February 7, 2007 News Release - National Institutes of Health (NIH)Erinaceus europaeus Western European Hedgehog 2* Broad InstituteFelis catus Cat 2* 3 Gb 20,285 The Genome Sequencing Platform, The Genome Assembly Team 2007Pontius JU, Mullikin JC, Smith DR, et al. Initial sequence and comparative analysis of the cat genome Genome Res. 17 11 1675–89 2007 November 17975172 2045150 10.1101/gr.6380007 Homo sapiens Human 3.2 Gb Human Genome Sequencing Consortium, International Finishing the euchromatic sequence of the human genome Nature 431 7011 931–45 2004 October 15496913 10.1038/nature03001 25,000Human Genome Project Consortium and Celera GenomicsDraft 2001McPherson JD, Marra M, Hillier L, et al. A physical map of the human genome Nature 409 6822 934–41 2001 February 11237014 10.1038/35057157 Venter JC, Adams MD, Myers EW, et al. The sequence of the human genome Science (journal) 291 5507 1304–51 2001 February 11181995 10.1126/science.1058040 Complete 2006Gregory SG, Barlow KF, McLay KE, et al. The DNA sequence and biological annotation of human chromosome 1 Nature 441 7091 315–21 2006 May 16710414 10.1038/nature04727 Loxodonta africana African Elephant 2* 3 Gb Broad InstituteMacaca mulatta Rhesus Macaque 6* Macaque Genome Sequencing ConsortiumMicrocebus murinus Gray Mouse Lemur 2* The Genome Sequencing Platform, The Genome Assembly TeamMonodelphis domestica Gray Short-tailed Opossum 3.5 Gb 18 - 20,000 Broad Institute et al.2007Mikkelsen TS, Wakefield MJ, Aken B, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences Nature 447 7141 167–77 2007 May 17495919 10.1038/nature05805 http://www.nature.com/nature/journal/v447/n7141/full/nature05805.htmlMus musculusStrain: C57BL/6J Mouse 2.5 Gb 24,174Waterston RH, Lindblad-Toh K, Birney E, et al. Initial sequencing and comparative analysis of the mouse genome Nature 420 6915 520–62 2002 December 12466850 10.1038/nature01262 International Collaboration for the Mouse Genome SequencingInternational Collaboration for the Mouse Genome Sequencing2002Myotis lucifugus Little Brown Bat 2* Broad InstituteOchotona princeps American Pika 2* Broad InstituteOrnithorhynchus anatinus Whole Genome Shotgun sequencing project list Platypus 6* Washington UniversityOryctolagus cuniculus Rabbit 2* 2.5 Gb Broad Institute et al. Otolemur garnettii Small-eared Galago, or Bushbaby 2* Broad InstitutePan troglodytes Chimpanzee 6* 3.1 Gb Chimpanzee Sequencing and Analysis Consortium2005Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome Nature 437 7055 69–87 2005 September 16136131 10.1038/nature04072 Pongo pygmaeus Orangutan 3.0 Gb Institute for Molecular Biotechnology Rattus norvegicus Rat 1.8* or better 2.8 Gb 21,166Gibbs RA, Weinstock GM, Metzker ML, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution Nature 428 6982 493–521 2004 April 15057822 10.1038/nature02426 Rat Genome Sequencing Project Consortium2004Sorex araneus European Shrew 2* 3.0 Gb The Genome Sequencing Platform, The Genome Assembly TeamSpermophilus tridecemlineatus Thirteen-lined Ground Squirrel 2* The Genome Sequencing Platform, The Genome Assembly TeamTupaia belangeri Northern Tree Shrew 2* Broad Institute Insects Organism Type Relevance Genome size Number of genes predicted Organization Year of completion Anopheles gambiaeStrain: PESTMosquitoVector of malaria 278 Mb13,683Holt RA, Subramanian GM, Halpern A, et al. The genome sequence of the malaria mosquito Anopheles gambiae Science (journal) 298 5591 129–49 2002 October 12364791 10.1126/science.1076181 HCelera Genomics and Genoscope2002Apis melliferaHoney beeModel for eusocial behavior1800 Mb10,157Honeybee Genome Sequencing Consortium. Insights into social insects from the genome of the honeybee Apis mellifera Nature 443 7114 931–49 2006 October 17073008 2048586 10.1038/nature05260The Honeybee Genome Sequencing Consortium2006Bombyx moriStrain:p50TMoth (domestic silk worm)Silk production530 MbUniversity of Tokyo and National Institute of Agrobiological Sciences 2004Mita K, Kasahara M, Sasaki S, et al. The genome sequence of silkworm, Bombyx mori DNA Res. 11 1 27–35 2004 February 15141943 10.1093/dnares/11.1.27 http://dnaresearch.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=15141943Drosophila melanogasterFruit flyModel animal165 Mb13,600Adams MD, Celniker SE, Holt RA, et al. The genome sequence of Drosophila melanogaster Science (journal) 287 5461 2185–95 2000 March 10731132 http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=10731132 Celera, UC Berkeley, Baylor College of Medicine, European DGP2000 Nematodes Organism Type Relevance Genome size Number of genes predicted Organization Year of completion Caenorhabditis briggsaeNematode wormFor comparison with C. elegans104 Mb19,500Stein LD, Bao Z, Blasiar D, et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics PLoS Biol. 1 2 E45 2003 November 14624247 261899 10.1371/journal.pbio.0000045 http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0000045Washington University, Sanger Institute and Cold Spring Harbor Laboratory2003Caenorhabditis elegansStrain:Bristol N2Nematode wormModel animal100 Mb19,000C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology Science (journal) 282 5396 2012–8 1998 December 9851916 http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=9851916Washington University and the Sanger Institute1998Meloidogyne haplaNorthern root-knot nematodeVegetable pathogen54 Mb14,420Charles 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 Sequence and Genetic Map of Meloidogyne hapla: A Compact Nematode Genome for Plant Parasitism Proceedings of the National Academy of Sciences 2008 10.1073/pnas.0805946105 18809916 105 148022008Meloidogyne incognitaSouthern root-knot nematodePlant pathogen86 Mb19,212Pierre 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. Genome sequence of the metazoan plant-parasitic nematode : Meloidogyne incognita Nature Biotechnology 26 909–915 2008 August 10.1038/nbt.1482 18660804INRA, Genoscope and International M.incognita Genome ConsortiumInternational M.incognita Genome Consortium2008Pristionchus pacificusNematode wormModel invertebrate169 Mb23,500Christoph 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 The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism Nature Genetics 40 1193 2008 September 17095691 10.1038/ng.227Max-Planck Institute for Developmental Biology & Genome Sequencing Center, Washington University School of Medicine2008 Other animals Organism Type Relevance Genome size Number of genes predicted Organization Year of completion Ciona intestinalisTunicateSimple chordate116.7 Mb16,000Dehal P, Satou Y, Campbell RK, et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins Science (journal) 298 5601 2157–67 2002 December 12481130 10.1126/science.1080049 http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=12481130Joint Genome Institute2003Ciona savignyiTunicate 174 MbBroad Institute2007Small KS, Brudno M, Hill MM, Sidow A A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome Genome Biol. 8 3 R41 2007 17374142 1868934 10.1186/gb-2007-8-3-r41 http://genomebiology.com/1465-6906/8/R41Gallus gallusChicken1000 Mb20-23,000International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution Nature 432 7018 695–716 2004 December 15592404 10.1038/nature03154International Chicken Genome Sequencing Consortium2004Strongylocentrotus purpuratusSea urchinModel eukaryote814 Mb23,300Sodergren E, Weinstock GM, Davidson EH, et al. The genome of the sea urchin Strongylocentrotus purpuratus Science (journal) 314 5801 941–52 2006 November 17095691 10.1126/science.1133609 http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=17095691Sea Urchin Genome Sequencing Consortium2006Takifugu rubripesPuffer fishVertebrate with small genome390 Mb22-29,000International Fugu Genome Consortium. Forth Genome AssemblyInternational Fugu Genome ConsortiumInternational Fugu Genome Consortium2002Aparicio S, Chapman J, Stupka E, et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes Science (journal) 297 5585 1301–10 2002 August 12142439 10.1126/science.1072104 http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=12142439Tetraodon nigroviridisPuffer fishVertebrate with compact genome340 MbJaillon O, Aury JM, Brunet F, et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype Nature 431 7011 946–57 2004 October 15496914 10.1038/nature0302522,400Genoscope and the Broad Institute2004 Sequenced Bacterial Genomes 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 1. Berg, Jeremy M. 2007. Biochemistry. Sixth Ed. New York: W.H. Freeman. 68-69, 78. 2. Voet, Voet, Pratt (2004). - Fundamentals of Biochemistry