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Author Report for: Langley CH

Title: The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols
Martinez-Garcia PJ, Crepeau MW, Puiu D, Gonzalez-Ibeas D, Whalen J, Stevens KA, Paul R, Butterfield TS, Britton MT and Neale DB <14 more author(s)> Martinez-Garcia PJ, Crepeau MW, Puiu D, Gonzalez-Ibeas D, Whalen J, Stevens KA, Paul R, Butterfield TS, Britton MT, Reagan RL, Chakraborty S, Walawage SL, Vasquez-Gross HA, Cardeno C, Famula RA, Pratt K, Kuruganti S, Aradhya MK, Leslie CA, Dandekar AM, Salzberg SL, Wegrzyn JL, Langley CH, Neale DB (- 14)
Ref: Plant J, 87:507, 2016 : PubMed
Abstract


ESTHER: Martinez-Garcia_2016_Plant.J_87_507
PubMedSearch: Martinez-Garcia 2016 Plant.J 87 507
PubMedID: 27145194
Gene_locus related to this paper: jugre-a0a2i4fez2, jugre-a0a2i4h0n2, jugre-a0a2i4gzr6, jugre-a0a2i4hni2, jugre-a0a2i4gla1, jugre-a0a2i4e0e6, jugre-a0a2i4es54, jugre-a0a2i4e9m5, jugre-a0a2i4hql8, jugre-a0a2i4gf09, jugre-a0a2i4fj48, jugre-a0a2i4flz2

Abstract

The Persian walnut (Juglans regia L.), a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich array of polyphenolic compounds, whose complete biosynthetic pathways are still unknown. A J. regia genome sequence was obtained from the cultivar 'Chandler' to discover target genes and additional unknown genes. The 667-Mbp genome was assembled using two different methods (SOAPdenovo2 and MaSuRCA), with an N50 scaffold size of 464 955 bp (based on a genome size of 606 Mbp), 221 640 contigs and a GC content of 37%. Annotation with MAKER-P and other genomic resources yielded 32 498 gene models. Previous studies in walnut relying on tissue-specific methods have only identified a single polyphenol oxidase (PPO) gene (JrPPO1). Enabled by the J. regia genome sequence, a second homolog of PPO (JrPPO2) was discovered. In addition, about 130 genes in the large gallate 1-beta-glucosyltransferase (GGT) superfamily were detected. Specifically, two genes, JrGGT1 and JrGGT2, were significantly homologous to the GGT from Quercus robur (QrGGT), which is involved in the synthesis of 1-O-galloyl-beta-d-glucose, a precursor for the synthesis of hydrolysable tannins. The reference genome for J. regia provides meaningful insight into the complex pathways required for the synthesis of polyphenols. The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits.



        

Title: First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Ne (Fagaceae)
Sork VL, Fitz-Gibbon ST, Puiu D, Crepeau M, Gugger PF, Sherman R, Stevens K, Langley CH, Pellegrini M, Salzberg SL
Ref: G3 (Bethesda), 6:3485, 2016 : PubMed
Abstract


ESTHER: Sork_2016_G3.(Bethesda)_6_3485
PubMedSearch: Sork 2016 G3.(Bethesda) 6 3485
PubMedID: 27621377
Gene_locus related to this paper: quelo-a0a7n2rbl4, quelo-a0a7n2mne3, quelo-a0a7n2mpu3

Abstract

Oak represents a valuable natural resource across Northern Hemisphere ecosystems, attracting a large research community studying its genetics, ecology, conservation, and management. Here we introduce a draft genome assembly of valley oak (Quercus lobata) using Illumina sequencing of adult leaf tissue of a tree found in an accessible, well-studied, natural southern California population. Our assembly includes a nuclear genome and a complete chloroplast genome, along with annotation of encoded genes. The assembly contains 94,394 scaffolds, totaling 1.17 Gb with 18,512 scaffolds of length 2 kb or longer, with a total length of 1.15 Gb, and a N50 scaffold size of 278,077 kb. The k-mer histograms indicate an diploid genome size of -720-730 Mb, which is smaller than the total length due to high heterozygosity, estimated at 1.25%. A comparison with a recently published European oak (Q. robur) nuclear sequence indicates 93% similarity. The Q. lobata chloroplast genome has 99% identity with another North American oak, Q. rubra Preliminary annotation yielded an estimate of 61,773 predicted protein-coding genes, of which 71% had similarity to known protein domains. We searched 956 Benchmarking Universal Single-Copy Orthologs, and found 863 complete orthologs, of which 450 were present in > 1 copy. We also examined an earlier version (v0.5) where duplicate haplotypes were removed to discover variants. These additional sources indicate that the predicted gene count in Version 1.0 is overestimated by 37-52%. Nonetheless, this first draft valley oak genome assembly represents a high-quality, well-annotated genome that provides a tool for forest restoration and management practices.



        

Title: Evolution of genes and genomes on the Drosophila phylogeny
Clark 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, drose-b4hws7, drose-b4hwt0, drose-b4hwt2, drose-b4hwu1, drose-b4hwu2, drose-b4hxs9, drose-b4hxu4, drose-b4hxz1, drose-b4hyp8, drose-b4hyp9, drose-b4hyq0, drose-b4hyz4, drose-b4hyz5, drose-b4i1k8, drose-b4i2f3, drose-b4i2w5, drose-b4i4u3, drose-b4i4u7, drose-b4i4u9, drose-b4i4v0, drose-b4i4v1, drose-b4i4v4, drose-b4i4v5, drose-b4i4v6, drose-b4i4v7, drose-b4i4v8, drose-b4i4w0, drose-b4i7s6, drose-b4i133, drose-b4i857, drose-b4iam7, drose-b4iam9, drose-b4iaq6, drose-b4icf6, drose-b4icf7, 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, drosi-b4q7u3, drosi-b4q9c6, drosi-b4q9c7, drosi-b4q9d3, drosi-b4q9d4, drosi-b4q9r0, drosi-b4q9r1, drosi-b4q9r3, drosi-b4q9s2, drosi-b4q9s3, drosi-b4q429, drosi-b4q530, drosi-b4q734, drosi-b4q782, drosi-b4q783, drosi-b4q942, drosi-b4qet1, drosi-b4qfv6, drosi-b4qge5, drosi-b4qgh5, drosi-b4qgs5, drosi-b4qhf3, drosi-b4qhf4, drosi-b4qhi5, drosi-b4qjr2, drosi-b4qjr3, drosi-b4qjv6, drosi-b4qk23, drosi-b4qk51, drosi-b4qlt1, drosi-b4qlz9, drosi-b4qmn9, drosi-b4qrq7, drosi-b4qs01, drosi-b4qs57, drosi-b4qs82, drosi-b4qs83, drosi-b4qs84, drosi-b4qs85, drosi-b4qs86, drosi-b4qsq1, drosi-b4quk6, drosi-b4qvg5, drosi-b4qvg6, drosi-b4qzn2, drosi-b4qzn3, drosi-b4qzn5, drosi-b4qzn7, drosi-b4qzn8, drosi-b4qzp2, drosi-b4qzp3, drosi-b4qzp4, drosi-b4qzp5, 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, drovi-b4lgc6, drovi-b4lgd5, drovi-b4lgg0, drovi-b4lgk5, drovi-b4lgn2, drovi-b4lh17, drovi-b4lh18, drovi-b4lk43, drovi-b4ll59, drovi-b4ll60, drovi-b4llm5, drovi-b4lln3, drovi-b4lmk4, drovi-b4lmp0, drovi-b4lnr4, drovi-b4lp47, drovi-b4lpd0, drovi-b4lps0, drovi-b4lqc6, drovi-b4lr00, drovi-b4lrp6, drovi-b4lrw2, drovi-b4lse7, drovi-b4lse9, drovi-b4lsf0, drovi-b4lsn0, drovi-b4lsq5, drovi-b4lt32, drovi-b4ltr1, drovi-b4lui7, drovi-b4lui9, drovi-b4luj8, drovi-b4luk0, drovi-b4luk3, drovi-b4luk8, drovi-b4luk9, drovi-b4lul0, drovi-b4lve2, drovi-b4lxi9, drovi-b4lxj8, drovi-b4lyf3, drovi-b4lyq2, drovi-b4lyq3, drovi-b4lz07, drovi-b4lz13, drovi-b4lz14, drovi-b4lz15, drovi-b4m0j7, drovi-b4m0s0, drovi-b4m2b6, drovi-b4m4h7, drovi-b4m4h8, drovi-b4m4i0, drovi-b4m4i2, drovi-b4m4i3.A, drovi-b4m4i3.B, drovi-b4m4i4, drovi-b4m4i5, drovi-b4m4i6, drovi-b4m4i7, drovi-b4m4i8, drovi-b4m4i9, drovi-b4m4j2, drovi-b4m5a0, drovi-b4m5a1, drovi-b4m5a2, drovi-b4m6b9, drovi-b4m7k9, drovi-b4m9g9, drovi-b4m9h0, drovi-b4m564, drovi-b4m599, drovi-b4m918, drovi-b4mb87, drovi-b4mc71, drovi-b4mfa4, drowi-ACHE, drowi-b4mjb9, drowi-b4mkt7, drowi-b4mlc1, drowi-b4mp68, drowi-b4mqe9, drowi-b4mqf0.2, drowi-b4mqf1, drowi-b4mqf3, drowi-b4mqf4, drowi-b4mqf5, drowi-b4mqq6, drowi-b4mrd1, drowi-b4mrk3, drowi-b4mtl5, drowi-b4mug2, drowi-b4muj8, drowi-b4mv18, drowi-b4mw32, drowi-b4mw85, drowi-b4mwp2, drowi-b4mwp6, drowi-b4mwq5, drowi-b4mwr0, drowi-b4mwr8, drowi-b4mwr9, drowi-b4mwt1, drowi-b4mwz7, drowi-b4mxn5, drowi-b4my54, drowi-b4myg1, drowi-b4myh5, drowi-b4n0d4, drowi-b4n1a7, drowi-b4n1c8, drowi-b4n3s9, drowi-b4n3x7, drowi-b4n4x9, drowi-b4n4y0, drowi-b4n6m1, drowi-b4n6n0, drowi-b4n6n7, drowi-b4n6u6, drowi-b4n7s6, drowi-b4n7s7, drowi-b4n7s8, drowi-b4n899.1, drowi-b4n8a1, drowi-b4n8a2, drowi-b4n8a3, drowi-b4n8a4, drowi-b4n8a9, drowi-b4n023, drowi-b4n075, drowi-b4n543, drowi-b4n888, drowi-b4n889, drowi-b4n891, drowi-b4n893, drowi-b4n895, drowi-b4n897, drowi-b4n898, drowi-b4n899.2, drowi-b4nae3, drowi-b4ner8, drowi-b4ng76, drowi-b4nga7, drowi-b4ngb5, drowi-b4nhz9, drowi-b4nj18, drowi-b4nj19, drowi-b4nja7, drowi-b4nja8, drowi-b4nja9, drowi-b4njk8, drowi-b4nkc8, drowi-b4nky0, drowi-b4nl36, drowi-b4nm27, drowi-b4nn59, drowi-b4nnc1, drowi-b4nng1, drowi-b4nng2, droya-ACHE, droya-aes04, droya-b4itg2, droya-b4itg6, droya-b4itu9, droya-b4iuv4, droya-b4iuv5, droya-b4nxe6, droya-b4nxg5, droya-b4nxg6, droya-b4nxg8, droya-b4nxw4, droya-b4ny57, droya-b4ny58, droya-b4ny86, droya-b4nzz8, droya-b4p0b5, droya-b4p0q9, droya-b4p0r0, droya-b4p0r7, droya-b4p0r8, droya-b4p0r9, droya-b4p0s0, droya-b4p0s2, droya-b4p0t0, droya-b4p0t1, droya-b4p3h4, droya-b4p3x8, droya-b4p5g8, droya-b4p6c9, droya-b4p6l9, droya-b4p6r1, droya-b4p6r2, droya-b4p7u4, droya-b4p8w7, droya-b4p023, droya-b4p241, droya-b4p774, droya-b4pat9, droya-b4pbl1, droya-b4pd22, droya-b4pd70, droya-b4pdm8, droya-b4pet9, droya-b4pff9, droya-b4pga7, droya-b4pgu0, droya-b4pig3, droya-b4pjt8, droya-b4pka2, droya-b4plh2, droya-b4pma3, droya-b4pmv3, droya-b4pmv4, droya-b4pmv5, droya-b4pn92, droya-b4pp65, droya-b4ppc5, droya-b4ppc6, 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.