Author Report for: Gardiner A No contact information in database for Gardiner A
Title: Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thalianaKemen E , Gardiner A , Schultz-Larsen T , Kemen AC , Balmuth AL , Robert-Seilaniantz A , Bailey K , Holub E , Studholme DJ and Jones JD <1 more author(s)> Kemen E , Gardiner A , Schultz-Larsen T , Kemen AC , Balmuth AL , Robert-Seilaniantz A , Bailey K , Holub E , Studholme DJ , Maclean D , Jones JD (- 1) Ref: PLoS Biol, 9 :e1001094, 2011 : PubMed Abstract ESTHER: Kemen_2011_PLoS.Biol_9_e1001094 PubMedSearch: Kemen 2011 PLoS.Biol 9 e1001094 PubMedID: 21750662 Gene_locus related to this paper: 9stra-f0vzr0 ,
9stra-f0w3s0 ,
9stra-f0whp7 ,
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9stra-f0we19 ,
9stra-f0wqy5 ,
9stra-f0w333 Abstract
Biotrophic eukaryotic plant pathogens require a living host for their growth and form an intimate haustorial interface with parasitized cells. Evolution to biotrophy occurred independently in fungal rusts and powdery mildews, and in oomycete white rusts and downy mildews. Biotroph evolution and molecular mechanisms of biotrophy are poorly understood. It has been proposed, but not shown, that obligate biotrophy results from (i) reduced selection for maintenance of biosynthetic pathways and (ii) gain of mechanisms to evade host recognition or suppress host defence. Here we use Illumina sequencing to define the genome, transcriptome, and gene models for the obligate biotroph oomycete and Arabidopsis parasite, Albugo laibachii. A. laibachii is a member of the Chromalveolata, which incorporates Heterokonts (containing the oomycetes), Apicomplexa (which includes human parasites like Plasmodium falciparum and Toxoplasma gondii), and four other taxa. From comparisons with other oomycete plant pathogens and other chromalveolates, we reveal independent loss of molybdenum-cofactor-requiring enzymes in downy mildews, white rusts, and the malaria parasite P. falciparum. Biotrophy also requires "effectors" to suppress host defence; we reveal RXLR and Crinkler effectors shared with other oomycetes, and also discover and verify a novel class of effectors, the "CHXCs", by showing effector delivery and effector functionality. Our findings suggest that evolution to progressively more intimate association between host and parasite results in reduced selection for retention of certain biosynthetic pathways, and particularly reduced selection for retention of molybdopterin-requiring biosynthetic pathways. These mechanisms are not only relevant to plant pathogenic oomycetes but also to human pathogens within the Chromalveolata.
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 ,
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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.
