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Title: Evolution of genes and genomes on the Drosophila phylogenyClark AG , Eisen MB , Smith DR , Bergman CM , Oliver B , Markow TA , Kaufman TC , Kellis M , Gelbart W and MacCallum I <405 more author(s)> Clark AG , Eisen MB , Smith DR , Bergman CM , Oliver B , Markow TA , Kaufman TC , Kellis M , Gelbart W , Iyer VN , Pollard DA , Sackton TB , Larracuente AM , Singh ND , Abad JP , Abt DN , Adryan B , Aguade M , Akashi H , Anderson WW , Aquadro CF , Ardell DH , Arguello R , Artieri CG , Barbash DA , Barker D , Barsanti P , Batterham P , Batzoglou S , Begun D , Bhutkar A , Blanco E , Bosak SA , Bradley RK , Brand AD , Brent MR , Brooks AN , Brown RH , Butlin RK , Caggese C , Calvi BR , Bernardo de Carvalho A , Caspi A , Castrezana S , Celniker SE , Chang JL , Chapple C , Chatterji S , Chinwalla A , Civetta A , Clifton SW , Comeron JM , Costello JC , Coyne JA , Daub J , David RG , Delcher AL , Delehaunty K , Do CB , Ebling H , Edwards K , Eickbush T , Evans JD , Filipski A , Findeiss S , Freyhult E , Fulton L , Fulton R , Garcia AC , Gardiner A , Garfield DA , Garvin BE , Gibson G , Gilbert D , Gnerre S , Godfrey J , Good R , Gotea V , Gravely B , Greenberg AJ , Griffiths-Jones S , Gross S , Guigo R , Gustafson EA , Haerty W , Hahn MW , Halligan DL , Halpern AL , Halter GM , Han MV , Heger A , Hillier L , Hinrichs AS , Holmes I , Hoskins RA , Hubisz MJ , Hultmark D , Huntley MA , Jaffe DB , Jagadeeshan S , Jeck WR , Johnson J , Jones CD , Jordan WC , Karpen GH , Kataoka E , Keightley PD , Kheradpour P , Kirkness EF , Koerich LB , Kristiansen K , Kudrna D , Kulathinal RJ , Kumar S , Kwok R , Lander E , Langley CH , Lapoint R , Lazzaro BP , Lee SJ , Levesque L , Li R , Lin CF , Lin MF , Lindblad-Toh K , Llopart A , Long M , Low L , Lozovsky E , Lu J , Luo M , Machado CA , Makalowski W , Marzo M , Matsuda M , Matzkin L , McAllister B , McBride CS , McKernan B , McKernan K , Mendez-Lago M , Minx P , Mollenhauer MU , Montooth K , Mount SM , Mu X , Myers E , Negre B , Newfeld S , Nielsen R , Noor MA , O'Grady P , Pachter L , Papaceit M , Parisi MJ , Parisi M , Parts L , Pedersen JS , Pesole G , Phillippy AM , Ponting CP , Pop M , Porcelli D , Powell JR , Prohaska S , Pruitt K , Puig M , Quesneville H , Ram KR , Rand D , Rasmussen MD , Reed LK , Reenan R , Reily A , Remington KA , Rieger TT , Ritchie MG , Robin C , Rogers YH , Rohde C , Rozas J , Rubenfield MJ , Ruiz A , Russo S , Salzberg SL , Sanchez-Gracia A , Saranga DJ , Sato H , Schaeffer SW , Schatz MC , Schlenke T , Schwartz R , Segarra C , Singh RS , Sirot L , Sirota M , Sisneros NB , Smith CD , Smith TF , Spieth J , Stage DE , Stark A , Stephan W , Strausberg RL , Strempel S , Sturgill D , Sutton G , Sutton GG , Tao W , Teichmann S , Tobari YN , Tomimura Y , Tsolas JM , Valente VL , Venter E , Venter JC , Vicario S , Vieira FG , Vilella AJ , Villasante A , Walenz B , Wang J , Wasserman M , Watts T , Wilson D , Wilson RK , Wing RA , Wolfner MF , Wong A , Wong GK , Wu CI , Wu G , Yamamoto D , Yang HP , Yang SP , Yorke JA , Yoshida K , Zdobnov E , Zhang P , Zhang Y , Zimin AV , Baldwin J , Abdouelleil A , Abdulkadir J , Abebe A , Abera B , Abreu J , Acer SC , Aftuck L , Alexander A , An P , Anderson E , Anderson S , Arachi H , Azer M , Bachantsang P , Barry A , Bayul T , Berlin A , Bessette D , Bloom T , Blye J , Boguslavskiy L , Bonnet C , Boukhgalter B , Bourzgui I , Brown A , Cahill P , Channer S , Cheshatsang Y , Chuda L , Citroen M , Collymore A , Cooke P , Costello M , D'Aco K , Daza R , De Haan G , DeGray S , DeMaso C , Dhargay N , Dooley K , Dooley E , Doricent M , Dorje P , Dorjee K , Dupes A , Elong R , Falk J , Farina A , Faro S , Ferguson D , Fisher S , Foley CD , Franke A , Friedrich D , Gadbois L , Gearin G , Gearin CR , Giannoukos G , Goode T , Graham J , Grandbois E , Grewal S , Gyaltsen K , Hafez N , Hagos B , Hall J , Henson C , Hollinger A , Honan T , Huard MD , Hughes L , Hurhula B , Husby ME , Kamat A , Kanga B , Kashin S , Khazanovich D , Kisner P , Lance K , Lara M , Lee W , Lennon N , Letendre F , LeVine R , Lipovsky A , Liu X , Liu J , Liu S , Lokyitsang T , Lokyitsang Y , Lubonja R , Lui A , Macdonald P , Magnisalis V , Maru K , Matthews C , McCusker W , McDonough S , Mehta T , Meldrim J , Meneus L , Mihai O , Mihalev A , Mihova T , Mittelman R , Mlenga V , Montmayeur A , Mulrain L , Navidi A , Naylor J , Negash T , Nguyen T , Nguyen N , Nicol R , Norbu C , Norbu N , Novod N , O'Neill B , Osman S , Markiewicz E , Oyono OL , Patti C , Phunkhang P , Pierre F , Priest M , Raghuraman S , Rege F , Reyes R , Rise C , Rogov P , Ross K , Ryan E , Settipalli S , Shea T , Sherpa N , Shi L , Shih D , Sparrow T , Spaulding J , Stalker J , Stange-Thomann N , Stavropoulos S , Stone C , Strader C , Tesfaye S , Thomson T , Thoulutsang Y , Thoulutsang D , Topham K , Topping I , Tsamla T , Vassiliev H , Vo A , Wangchuk T , Wangdi T , Weiand M , Wilkinson J , Wilson A , Yadav S , Young G , Yu Q , Zembek L , Zhong D , Zimmer A , Zwirko Z , Alvarez P , Brockman W , Butler J , Chin C , Grabherr M , Kleber M , Mauceli E , MacCallum I (- 405) Ref: Nature, 450 :203, 2007 : PubMed Abstract ESTHER: Clark_2007_Nature_450_203 PubMedSearch: Clark 2007 Nature 450 203 PubMedID: 17994087 Gene_locus related to this paper: droan-ACHE ,
droan-b3lx10 ,
droan-b3lx75 ,
droan-b3lxv7 ,
droan-b3ly87 ,
droan-b3lyh4 ,
droan-b3lyh5 ,
droan-b3lyh7 ,
droan-b3lyh9 ,
droan-b3lyi0 ,
droan-b3lyi2 ,
droan-b3lyi3 ,
droan-b3lyi4 ,
droan-b3lyj8 ,
droan-b3lyj9 ,
droan-b3lyx4 ,
droan-b3lyx5 ,
droan-b3lyx6 ,
droan-b3lyx7 ,
droan-b3lyx9 ,
droan-b3lz72 ,
droan-b3m1x3 ,
droan-b3m2d4 ,
droan-b3m3d9 ,
droan-b3m4e3 ,
droan-b3m5w1 ,
droan-b3m6i7 ,
droan-b3m7v2 ,
droan-b3m9a5 ,
droan-b3m9f4 ,
droan-b3m9p3 ,
droan-b3m254 ,
droan-b3m259 ,
droan-b3m260 ,
droan-b3m262 ,
droan-b3m524 ,
droan-b3m635 ,
droan-b3m845 ,
droan-b3m846 ,
droan-b3md01 ,
droan-b3mdh7 ,
droan-b3mdm6 ,
droan-b3mdw8 ,
droan-b3mee1 ,
droan-b3mf47 ,
droan-b3mf48 ,
droan-b3mg94 ,
droan-b3mgk2 ,
droan-b3mgn6 ,
droan-b3mii3 ,
droan-b3mjk2 ,
droan-b3mjk3 ,
droan-b3mjk4 ,
droan-b3mjk5 ,
droan-b3mjl2 ,
droan-b3mjl4 ,
droan-b3mjl7 ,
droan-b3mjl9 ,
droan-b3mjm8 ,
droan-b3mjm9 ,
droan-b3mjs6 ,
droan-b3mkr0 ,
droan-b3ml20 ,
droan-b3mly4 ,
droan-b3mly5 ,
droan-b3mly6 ,
droan-b3mmm8 ,
droan-b3mnb5 ,
droan-b3mny9 ,
droan-b3mtj5 ,
droan-b3muw4 ,
droan-b3muw8 ,
droan-b3n0e7 ,
droan-b3n2j7 ,
droan-b3n247 ,
droan-c5idb2 ,
droer-ACHE ,
droer-b3n5c7 ,
droer-b3n5d0 ,
droer-b3n5d8 ,
droer-b3n5d9 ,
droer-b3n5t7 ,
droer-b3n5y4 ,
droer-b3n7d2 ,
droer-b3n7d3 ,
droer-b3n7d4 ,
droer-b3n7k8 ,
droer-b3n8e4 ,
droer-b3n8f7 ,
droer-b3n8f8 ,
droer-b3n9e1 ,
droer-b3n319 ,
droer-b3n547 ,
droer-b3n549 ,
droer-b3n558 ,
droer-b3n560 ,
droer-b3n577 ,
droer-b3n612 ,
droer-b3nar5 ,
droer-b3nb91 ,
droer-b3nct9 ,
droer-b3nd53 ,
droer-b3ndh9 ,
droer-b3ndq8 ,
droer-b3ne66 ,
droer-b3ne67 ,
droer-b3ne97 ,
droer-b3nfk3 ,
droer-b3nfq9 ,
droer-b3nim7 ,
droer-b3nkn2 ,
droer-b3nm11 ,
droer-b3nmh4 ,
droer-b3nmy2 ,
droer-b3npx2 ,
droer-b3npx3 ,
droer-b3nq76 ,
droer-b3nqg9 ,
droer-b3nqm8 ,
droer-b3nr28 ,
droer-b3nrd3 ,
droer-b3nst4 ,
droer-b3nwa7 ,
droer-b3nyp5.1 ,
droer-b3nyp5.2 ,
droer-b3nyp6 ,
droer-b3nyp7 ,
droer-b3nyp8 ,
droer-b3nyp9 ,
droer-b3nyq3 ,
droer-b3nz06 ,
droer-b3nz14 ,
droer-b3nzj0 ,
droer-b3p0c0 ,
droer-b3p0c1 ,
droer-b3p0c2 ,
droer-b3p2x6 ,
droer-b3p2x7 ,
droer-b3p2x9 ,
droer-b3p2y1 ,
droer-b3p2y2 ,
droer-b3p6d4 ,
droer-b3p6d5 ,
droer-b3p6w3 ,
droer-b3p7b4 ,
droer-b3p7h9 ,
droer-b3p152 ,
droer-b3p486 ,
droer-b3p487 ,
droer-b3p488 ,
droer-b3p489 ,
droer-EST6 ,
droer-q670j5 ,
drogr-ACHE ,
drogr-b4iwp3 ,
drogr-b4iww3 ,
drogr-b4iwy3 ,
drogr-b4ixf7 ,
drogr-b4ixh4 ,
drogr-b4iyz5 ,
drogr-b4j2s2 ,
drogr-b4j2u8 ,
drogr-b4j3u1 ,
drogr-b4j3v3 ,
drogr-b4j4g7 ,
drogr-b4j4x9 ,
drogr-b4j6e6 ,
drogr-b4j9c9 ,
drogr-b4j9y4 ,
drogr-b4j156 ,
drogr-b4j384 ,
drogr-b4j605 ,
drogr-b4j685 ,
drogr-b4ja76 ,
drogr-b4jay5 ,
drogr-b4jcf0 ,
drogr-b4jcf1 ,
drogr-b4jdg6 ,
drogr-b4jdg7 ,
drogr-b4jdh6 ,
drogr-b4jdz1 ,
drogr-b4jdz2 ,
drogr-b4jdz4 ,
drogr-b4je66 ,
drogr-b4je79 ,
drogr-b4je82 ,
drogr-b4je88 ,
drogr-b4je89 ,
drogr-b4je90 ,
drogr-b4je91 ,
drogr-b4jf76 ,
drogr-b4jf79 ,
drogr-b4jf80 ,
drogr-b4jf81 ,
drogr-b4jf82 ,
drogr-b4jf83 ,
drogr-b4jf84 ,
drogr-b4jf85 ,
drogr-b4jf87 ,
drogr-b4jf91 ,
drogr-b4jf92 ,
drogr-b4jg66 ,
drogr-b4jgh0 ,
drogr-b4jgh1 ,
drogr-b4jgr9 ,
drogr-b4ji67 ,
drogr-b4jls2 ,
drogr-b4jnh9 ,
drogr-b4jpc6 ,
drogr-b4jpq3 ,
drogr-b4jpx9 ,
drogr-b4jql2 ,
drogr-b4jrh5 ,
drogr-b4jsb2 ,
drogr-b4jth3 ,
drogr-b4jti1 ,
drogr-b4jul5 ,
drogr-b4jur4 ,
drogr-b4jvh3 ,
drogr-b4jz00 ,
drogr-b4jz03 ,
drogr-b4jz04 ,
drogr-b4jz05 ,
drogr-b4jzh2 ,
drogr-b4k0u2 ,
drogr-b4k2r1 ,
drogr-b4k234 ,
drogr-b4k235 ,
drome-BEM46 ,
drome-CG3734 ,
drome-CG9953 ,
drome-CG11626 ,
drome-GH02439 ,
dromo-ACHE ,
dromo-b4k6a7 ,
dromo-b4k6a8 ,
dromo-b4k6q8 ,
dromo-b4k6q9 ,
dromo-b4k6r1 ,
dromo-b4k6r3 ,
dromo-b4k6r4 ,
dromo-b4k6r5 ,
dromo-b4k6r6 ,
dromo-b4k6r7 ,
dromo-b4k6r8 ,
dromo-b4k6r9 ,
dromo-b4k6s0 ,
dromo-b4k6s1 ,
dromo-b4k6s2 ,
dromo-b4k9c7 ,
dromo-b4k9d3 ,
dromo-b4k571 ,
dromo-b4k721 ,
dromo-b4ka74 ,
dromo-b4ka89 ,
dromo-b4kaj4 ,
dromo-b4kc20 ,
dromo-b4kcl2 ,
dromo-b4kcl3 ,
dromo-b4kd55.1 ,
dromo-b4kd55.2 ,
dromo-b4kd56 ,
dromo-b4kd57 ,
dromo-b4kde1 ,
dromo-b4kdg2 ,
dromo-b4kdh4 ,
dromo-b4kdh5 ,
dromo-b4kdh6 ,
dromo-A0A0Q9XDF2 ,
dromo-b4kdh8.1 ,
dromo-b4kdh8.2 ,
dromo-b4kg04 ,
dromo-b4kg05 ,
dromo-b4kg06 ,
dromo-b4kg16 ,
dromo-b4kg44 ,
dromo-b4kg90 ,
dromo-b4kh20 ,
dromo-b4kh21 ,
dromo-b4kht7 ,
dromo-b4kid3 ,
dromo-b4kik0 ,
dromo-b4kjx0 ,
dromo-b4kki1 ,
dromo-b4kkp6 ,
dromo-b4kkp8 ,
dromo-b4kkq8 ,
dromo-b4kkr0 ,
dromo-b4kkr3 ,
dromo-b4kkr4 ,
dromo-b4kks0 ,
dromo-b4kks1 ,
dromo-b4kks2 ,
dromo-b4kla1 ,
dromo-b4klv8 ,
dromo-b4knt4 ,
dromo-b4kp08 ,
dromo-b4kp16 ,
dromo-b4kqa6 ,
dromo-b4kqa7 ,
dromo-b4kqa8 ,
dromo-b4kqh1 ,
dromo-b4kst4 ,
dromo-b4ksy6 ,
dromo-b4kt84 ,
dromo-b4ktf5 ,
dromo-b4ktf6 ,
dromo-b4kvl3 ,
dromo-b4kvw2 ,
dromo-b4kwv4 ,
dromo-b4kwv5 ,
dromo-b4kxz6 ,
dromo-b4ky12 ,
dromo-b4ky36 ,
dromo-b4ky44 ,
dromo-b4kzu7 ,
dromo-b4l0n8 ,
dromo-b4l4u5 ,
dromo-b4l6l9 ,
dromo-b4l084 ,
drope-ACHE ,
drope-b4g3s6 ,
drope-b4g4p7 ,
drope-b4g6v4 ,
drope-b4g8m0 ,
drope-b4g8n6 ,
drope-b4g8n7 ,
drope-b4g9p2 ,
drope-b4g815 ,
drope-b4g816 ,
drope-b4gat7 ,
drope-b4gav5 ,
drope-b4gb05 ,
drope-b4gc08 ,
drope-b4gcr3 ,
drope-b4gdk2 ,
drope-b4gdl9 ,
drope-b4gdv9 ,
drope-b4gei8 ,
drope-b4gei9 ,
drope-b4gej0 ,
drope-b4ghz9 ,
drope-b4gj62 ,
drope-b4gj64 ,
drope-b4gj74 ,
drope-b4gkf4 ,
drope-b4gkv2 ,
drope-b4gky9 ,
drope-b4gl76 ,
drope-b4glf3 ,
drope-b4gmt3 ,
drope-b4gmt7 ,
drope-b4gmt9 ,
drope-b4gmu2 ,
drope-b4gmu3 ,
drope-b4gmu4 ,
drope-b4gmu5 ,
drope-b4gmu6 ,
drope-b4gmu7 ,
drope-b4gmv1 ,
drope-b4gn08 ,
drope-b4gpa7 ,
drope-b4gq13 ,
drope-b4grh7 ,
drope-b4gsf9 ,
drope-b4gsw4 ,
drope-b4gsw5 ,
drope-b4gsx2 ,
drope-b4gsx7 ,
drope-b4gsy6 ,
drope-b4gsy7 ,
drope-b4guj8 ,
drope-b4gw36 ,
drope-b4gzc2 ,
drope-b4gzc6 ,
drope-b4gzc7 ,
drope-b4h4p9 ,
drope-b4h5l3 ,
drope-b4h6a0 ,
drope-b4h6a8 ,
drope-b4h6a9 ,
drope-b4h6b0 ,
drope-b4h7m7 ,
drope-b4h462 ,
drope-b4h601 ,
drope-b4h602 ,
drope-b4hay1 ,
drope-b4hb18 ,
drope-est5a ,
drope-est5b ,
drope-est5c ,
drops-ACHE ,
drops-b5dhd2 ,
drops-b5dk96 ,
drops-b5dpe3 ,
drops-b5drp9 ,
drops-b5dwa7 ,
drops-b5dwa8 ,
drops-b5dz85 ,
drops-b5dz86 ,
drops-est5a ,
drops-est5b ,
drops-q29bq2 ,
drops-q29dd7 ,
drops-q29ew0 ,
drops-q291d5 ,
drops-q291e8 ,
drops-q293n1 ,
drops-q293n4 ,
drops-q293n5 ,
drops-q293n6 ,
drops-q294n6 ,
drops-q294n7 ,
drops-q294n9 ,
drops-q294p4 ,
drose-b4he97 ,
drose-b4hfu2 ,
drose-b4hg54 ,
drose-b4hga0 ,
drose-b4hgu9 ,
drose-b4hgv0 ,
drose-b4hgv3 ,
drose-b4hgv4 ,
drose-b4hhm8 ,
drose-b4hhs6 ,
drose-b4hie4 ,
drose-b4him9 ,
drose-b4hk63 ,
drose-b4hkj5 ,
drose-b4hr07 ,
drose-b4hr81 ,
drose-b4hre7 ,
drose-b4hs13 ,
drose-b4hsj9 ,
drose-b4hsk0 ,
drose-b4hsm8 ,
drose-b4hvr5 ,
drose-b4hwr7 ,
drose-b4hwr8 ,
drose-b4hwr9 ,
drose-b4hws6 ,
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drose-b4hwt0 ,
drose-b4hwt2 ,
drose-b4hwu1 ,
drose-b4hwu2 ,
drose-b4hxs9 ,
drose-b4hxu4 ,
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drose-b4i1k8 ,
drose-b4i2f3 ,
drose-b4i2w5 ,
drose-b4i4u3 ,
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drose-b4i4w0 ,
drose-b4i7s6 ,
drose-b4i133 ,
drose-b4i857 ,
drose-b4iam7 ,
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drose-b4iaq6 ,
drose-b4icf6 ,
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drose-b4id80 ,
drose-b4ifc5 ,
drose-b4ihv9 ,
drose-b4iie9 ,
drose-b4ilj8 ,
drose-b4in13 ,
drose-b4inj9 ,
drosi-ACHE ,
drosi-aes04a ,
drosi-b4nsh8 ,
drosi-b4q3d7 ,
drosi-b4q4w5 ,
drosi-b4q4y7 ,
drosi-b4q6h6 ,
drosi-b4q7u2 ,
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drosi-b4q9c6 ,
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drosi-b4q9d3 ,
drosi-b4q9d4 ,
drosi-b4q9r0 ,
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drosi-b4q429 ,
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drosi-b4qs01 ,
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drosi-b4qs82 ,
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drosi-b4quk6 ,
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drosi-b4qzp6 ,
drosi-b4qzp7 ,
drosi-b4r1a4 ,
drosi-b4r025 ,
drosi-b4r207 ,
drosi-b4r662 ,
drosi-este6 ,
drosi-q670k8 ,
drovi-ACHE ,
drovi-b4lev2 ,
drovi-b4lf33 ,
drovi-b4lf51 ,
drovi-b4lg54 ,
drovi-b4lg72 ,
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droya-b4ppc7 ,
droya-b4ppc8 ,
droya-b4pq03 ,
droya-b4prg6B ,
droya-b4prg9 ,
droya-b4prh3 ,
droya-b4prh4 ,
droya-b4prh6 ,
droya-b4prh7 ,
droya-b4psz8 ,
droya-b4psz9 ,
droya-b4pv22 ,
droya-b4q0g5 ,
droya-b4q246 ,
droya-EST6 ,
droya-q71d76 ,
drowi-b4n7m9 ,
drope-b4gkk1 ,
droer-b3n5s3 ,
drose-b4i1w5 ,
drowi-a0a0q9x0t3 ,
drogr-b4jvm7 ,
dromo-b4ku70 ,
drovi-b4mcn9 ,
drovi-b4lty2 ,
drogr-b4jdu1 ,
drovi-a0a0q9wiq8 ,
dromo-b4kf70 ,
drosi-b2zi86 ,
droya-b4p2y4 ,
drose-b2zic5 ,
droer-b3n895 Abstract
Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
Title: The sequence of the human genomeVenter JC , Adams MD , Myers EW , Li PW , Mural RJ , Sutton GG , Smith HO , Yandell M , Evans CA and Zhu X <264 more author(s)> Venter JC , Adams MD , Myers EW , Li PW , Mural RJ , Sutton GG , Smith HO , Yandell M , Evans CA , Holt RA , Gocayne JD , Amanatides P , Ballew RM , Huson DH , Wortman JR , Zhang Q , Kodira CD , Zheng XH , Chen L , Skupski M , Subramanian G , Thomas PD , Zhang J , Gabor Miklos GL , Nelson C , Broder S , Clark AG , Nadeau J , McKusick VA , Zinder N , Levine AJ , Roberts RJ , Simon M , Slayman C , Hunkapiller M , Bolanos R , Delcher A , Dew I , Fasulo D , Flanigan M , Florea L , Halpern A , Hannenhalli S , Kravitz S , Levy S , Mobarry C , Reinert K , Remington K , Abu-Threideh J , Beasley E , Biddick K , Bonazzi V , Brandon R , Cargill M , Chandramouliswaran I , Charlab R , Chaturvedi K , Deng Z , Di Francesco V , Dunn P , Eilbeck K , Evangelista C , Gabrielian AE , Gan W , Ge W , Gong F , Gu Z , Guan P , Heiman TJ , Higgins ME , Ji RR , Ke Z , Ketchum KA , Lai Z , Lei Y , Li Z , Li J , Liang Y , Lin X , Lu F , Merkulov GV , Milshina N , Moore HM , Naik AK , Narayan VA , Neelam B , Nusskern D , Rusch DB , Salzberg S , Shao W , Shue B , Sun J , Wang Z , Wang A , Wang X , Wang J , Wei M , Wides R , Xiao C , Yan C , Yao A , Ye J , Zhan M , Zhang W , Zhang H , Zhao Q , Zheng L , Zhong F , Zhong W , Zhu S , Zhao S , Gilbert D , Baumhueter S , Spier G , Carter C , Cravchik A , Woodage T , Ali F , An H , Awe A , Baldwin D , Baden H , Barnstead M , Barrow I , Beeson K , Busam D , Carver A , Center A , Cheng ML , Curry L , Danaher S , Davenport L , Desilets R , Dietz S , Dodson K , Doup L , Ferriera S , Garg N , Gluecksmann A , Hart B , Haynes J , Haynes C , Heiner C , Hladun S , Hostin D , Houck J , Howland T , Ibegwam C , Johnson J , Kalush F , Kline L , Koduru S , Love A , Mann F , May D , McCawley S , McIntosh T , McMullen I , Moy M , Moy L , Murphy B , Nelson K , Pfannkoch C , Pratts E , Puri V , Qureshi H , Reardon M , Rodriguez R , Rogers YH , Romblad D , Ruhfel B , Scott R , Sitter C , Smallwood M , Stewart E , Strong R , Suh E , Thomas R , Tint NN , Tse S , Vech C , Wang G , Wetter J , Williams S , Williams M , Windsor S , Winn-Deen E , Wolfe K , Zaveri J , Zaveri K , Abril JF , Guigo R , Campbell MJ , Sjolander KV , Karlak B , Kejariwal A , Mi H , Lazareva B , Hatton T , Narechania A , Diemer K , Muruganujan A , Guo N , Sato S , Bafna V , Istrail S , Lippert R , Schwartz R , Walenz B , Yooseph S , Allen D , Basu A , Baxendale J , Blick L , Caminha M , Carnes-Stine J , Caulk P , Chiang YH , Coyne M , Dahlke C , Mays A , Dombroski M , Donnelly M , Ely D , Esparham S , Fosler C , Gire H , Glanowski S , Glasser K , Glodek A , Gorokhov M , Graham K , Gropman B , Harris M , Heil J , Henderson S , Hoover J , Jennings D , Jordan C , Jordan J , Kasha J , Kagan L , Kraft C , Levitsky A , Lewis M , Liu X , Lopez J , Ma D , Majoros W , McDaniel J , Murphy S , Newman M , Nguyen T , Nguyen N , Nodell M , Pan S , Peck J , Peterson M , Rowe W , Sanders R , Scott J , Simpson M , Smith T , Sprague A , Stockwell T , Turner R , Venter E , Wang M , Wen M , Wu D , Wu M , Xia A , Zandieh A , Zhu X (- 264) Ref: Science, 291 :1304, 2001 : PubMed Abstract ESTHER: Venter_2001_Science_291_1304 PubMedSearch: Venter 2001 Science 291 1304 PubMedID: 11181995 Gene_locus related to this paper: human-AADAC ,
human-ABHD1 ,
human-ABHD10 ,
human-ABHD11 ,
human-ACHE ,
human-BCHE ,
human-LDAH ,
human-ABHD18 ,
human-CMBL ,
human-ABHD17A ,
human-KANSL3 ,
human-LIPA ,
human-LYPLAL1 ,
human-NDRG2 ,
human-NLGN3 ,
human-NLGN4X ,
human-NLGN4Y ,
human-PAFAH2 ,
human-PREPL ,
human-RBBP9 ,
human-SPG21 Abstract
A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.
