Stanke M

References (9)

Title : Finding the missing honey bee genes: lessons learned from a genome upgrade - Elsik_2014_BMC.Genomics_15_86
Author(s) : Elsik CG , Worley KC , Bennett AK , Beye M , Camara F , Childers CP , de Graaf DC , Debyser G , Deng J , Devreese B , Elhaik E , Evans JD , Foster LJ , Graur D , Guigo R , Hoff KJ , Holder ME , Hudson ME , Hunt GJ , Jiang H , Joshi V , Khetani RS , Kosarev P , Kovar CL , Ma J , Maleszka R , Moritz RF , Munoz-Torres MC , Murphy TD , Muzny DM , Newsham IF , Reese JT , Robertson HM , Robinson GE , Rueppell O , Solovyev V , Stanke M , Stolle E , Tsuruda JM , Vaerenbergh MV , Waterhouse RM , Weaver DB , Whitfield CW , Wu Y , Zdobnov EM , Zhang L , Zhu D , Gibbs RA
Ref : BMC Genomics , 15 :86 , 2014
Abstract : BACKGROUND: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes.
RESULTS: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data.
CONCLUSIONS: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.
ESTHER : Elsik_2014_BMC.Genomics_15_86
PubMedSearch : Elsik_2014_BMC.Genomics_15_86
PubMedID: 24479613

Title : Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote - Schonknecht_2013_Science_339_1207
Author(s) : Schonknecht G , Chen WH , Ternes CM , Barbier GG , Shrestha RP , Stanke M , Brautigam A , Baker BJ , Banfield JF , Garavito RM , Carr K , Wilkerson C , Rensing SA , Gagneul D , Dickenson NE , Oesterhelt C , Lercher MJ , Weber AP
Ref : Science , 339 :1207 , 2013
Abstract : Some microbial eukaryotes, such as the extremophilic red alga Galdieria sulphuraria, live in hot, toxic metal-rich, acidic environments. To elucidate the underlying molecular mechanisms of adaptation, we sequenced the 13.7-megabase genome of G. sulphuraria. This alga shows an enormous metabolic flexibility, growing either photoautotrophically or heterotrophically on more than 50 carbon sources. Environmental adaptation seems to have been facilitated by horizontal gene transfer from various bacteria and archaea, often followed by gene family expansion. At least 5% of protein-coding genes of G. sulphuraria were probably acquired horizontally. These proteins are involved in ecologically important processes ranging from heavy-metal detoxification to glycerol uptake and metabolism. Thus, our findings show that a pan-domain gene pool has facilitated environmental adaptation in this unicellular eukaryote.
ESTHER : Schonknecht_2013_Science_339_1207
PubMedSearch : Schonknecht_2013_Science_339_1207
PubMedID: 23471408
Gene_locus related to this paper: galsu-m2y8v3 , galsu-m2xs14 , galsu-m2w341

Title : Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus) - Stajich_2010_Proc.Natl.Acad.Sci.U.S.A_107_11889
Author(s) : Stajich JE , Wilke SK , Ahren D , Au CH , Birren BW , Borodovsky M , Burns C , Canback B , Casselton LA , Cheng CK , Deng J , Dietrich FS , Fargo DC , Farman ML , Gathman AC , Goldberg J , Guigo R , Hoegger PJ , Hooker JB , Huggins A , James TY , Kamada T , Kilaru S , Kodira C , Kues U , Kupfer D , Kwan HS , Lomsadze A , Li W , Lilly WW , Ma LJ , Mackey AJ , Manning G , Martin F , Muraguchi H , Natvig DO , Palmerini H , Ramesh MA , Rehmeyer CJ , Roe BA , Shenoy N , Stanke M , Ter-Hovhannisyan V , Tunlid A , Velagapudi R , Vision TJ , Zeng Q , Zolan ME , Pukkila PJ
Ref : Proc Natl Acad Sci U S A , 107 :11889 , 2010
Abstract : The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi.
ESTHER : Stajich_2010_Proc.Natl.Acad.Sci.U.S.A_107_11889
PubMedSearch : Stajich_2010_Proc.Natl.Acad.Sci.U.S.A_107_11889
PubMedID: 20547848
Gene_locus related to this paper: copc7-a8n2b8 , copc7-a8n3e0 , copc7-a8n3e1 , copc7-a8n6a5 , copc7-a8n8h4 , copc7-a8n702 , copc7-a8n941 , copc7-a8nkc7 , copc7-a8nll5 , copc7-a8nll6 , copc7-a8nqf4 , copc7-a8nqg3 , copc7-a8nqv8 , copc7-a8nvb5 , copc7-a8nwm2 , copc7-a8nz18 , copc7-a8p0p4 , copc7-d6rlx1 , copc7-d6rnh7 , copc7-kex1 , copci-b9u444 , copc7-a8nb05 , copc7-a8nha0 , copci-b9u443 , copc7-a8nq30 , copc7-a8nh79 , copc7-d6rm78 , copc7-a8nzs7 , copc7-axe1

Title : Functional and evolutionary insights from the genomes of three parasitoid Nasonia species - Werren_2010_Science_327_343
Author(s) : Werren JH , Richards S , Desjardins CA , Niehuis O , Gadau J , Colbourne JK , Beukeboom LW , Desplan C , Elsik CG , Grimmelikhuijzen CJ , Kitts P , Lynch JA , Murphy T , Oliveira DC , Smith CD , van de Zande L , Worley KC , Zdobnov EM , Aerts M , Albert S , Anaya VH , Anzola JM , Barchuk AR , Behura SK , Bera AN , Berenbaum MR , Bertossa RC , Bitondi MM , Bordenstein SR , Bork P , Bornberg-Bauer E , Brunain M , Cazzamali G , Chaboub L , Chacko J , Chavez D , Childers CP , Choi JH , Clark ME , Claudianos C , Clinton RA , Cree AG , Cristino AS , Dang PM , Darby AC , de Graaf DC , Devreese B , Dinh HH , Edwards R , Elango N , Elhaik E , Ermolaeva O , Evans JD , Foret S , Fowler GR , Gerlach D , Gibson JD , Gilbert DG , Graur D , Grunder S , Hagen DE , Han Y , Hauser F , Hultmark D , Hunter HCt , Hurst GD , Jhangian SN , Jiang H , Johnson RM , Jones AK , Junier T , Kadowaki T , Kamping A , Kapustin Y , Kechavarzi B , Kim J , Kiryutin B , Koevoets T , Kovar CL , Kriventseva EV , Kucharski R , Lee H , Lee SL , Lees K , Lewis LR , Loehlin DW , Logsdon JM, Jr. , Lopez JA , Lozado RJ , Maglott D , Maleszka R , Mayampurath A , Mazur DJ , McClure MA , Moore AD , Morgan MB , Muller J , Munoz-Torres MC , Muzny DM , Nazareth LV , Neupert S , Nguyen NB , Nunes FM , Oakeshott JG , Okwuonu GO , Pannebakker BA , Pejaver VR , Peng Z , Pratt SC , Predel R , Pu LL , Ranson H , Raychoudhury R , Rechtsteiner A , Reese JT , Reid JG , Riddle M , Robertson HM , Romero-Severson J , Rosenberg M , Sackton TB , Sattelle DB , Schluns H , Schmitt T , Schneider M , Schuler A , Schurko AM , Shuker DM , Simoes ZL , Sinha S , Smith Z , Solovyev V , Souvorov A , Springauf A , Stafflinger E , Stage DE , Stanke M , Tanaka Y , Telschow A , Trent C , Vattathil S , Verhulst EC , Viljakainen L , Wanner KW , Waterhouse RM , Whitfield JB , Wilkes TE , Williamson MS , Willis JH , Wolschin F , Wyder S , Yamada T , Yi SV , Zecher CN , Zhang L , Gibbs RA , Williamson M
Ref : Science , 327 :343 , 2010
Abstract : We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.
ESTHER : Werren_2010_Science_327_343
PubMedSearch : Werren_2010_Science_327_343
PubMedID: 20075255
Gene_locus related to this paper: nasvi-ACHE1 , nasvi-ACHE2 , nasvi-k7in31 , nasvi-k7iwl9 , nasvi-k7iyk8 , nasvi-k7jlv1 , nasvi-k7in32 , nasvi-k7ind2 , nasvi-k7inh0 , nasvi-k7inh1 , nasvi-k7inh2 , nasvi-k7inp9 , nasvi-k7iun7 , nasvi-k7iv21 , nasvi-k7ivn5 , nasvi-k7ivn6 , nasvi-k7iw29 , nasvi-k7iwk5 , nasvi-k7iwl8 , nasvi-k7iz24 , nasvi-k7izb4 , nasvi-k7j5u6 , nasvi-k7j6y1 , nasvi-k7j6y2 , nasvi-k7j6y4 , nasvi-k7j718 , nasvi-k7j755 , nasvi-k7j756 , nasvi-k7j757 , nasvi-k7j7k5 , nasvi-k7j7n7 , nasvi-k7j7r8 , nasvi-k7j7s8 , nasvi-k7j7s9 , nasvi-k7j811 , nasvi-k7iny8 , nasvi-k7izf2 , nasvi-k7iwe2 , nasvi-k7j6w4 , nasvi-k7izl9 , nasvi-k7jf39 , nasvi-k7izl8 , nasvi-k7irf1 , nasvi-k7j7l1

Title : Draft genome sequence of the oilseed species Ricinus communis - Chan_2010_Nat.Biotechnol_28_951
Author(s) : Chan AP , Crabtree J , Zhao Q , Lorenzi H , Orvis J , Puiu D , Melake-Berhan A , Jones KM , Redman J , Chen G , Cahoon EB , Gedil M , Stanke M , Haas BJ , Wortman JR , Fraser-Liggett CM , Ravel J , Rabinowicz PD
Ref : Nat Biotechnol , 28 :951 , 2010
Abstract : Castor bean (Ricinus communis) is an oilseed crop that belongs to the spurge (Euphorbiaceae) family, which comprises approximately 6,300 species that include cassava (Manihot esculenta), rubber tree (Hevea brasiliensis) and physic nut (Jatropha curcas). It is primarily of economic interest as a source of castor oil, used for the production of high-quality lubricants because of its high proportion of the unusual fatty acid ricinoleic acid. However, castor bean genomics is also relevant to biosecurity as the seeds contain high levels of ricin, a highly toxic, ribosome-inactivating protein. Here we report the draft genome sequence of castor bean (4.6-fold coverage), the first for a member of the Euphorbiaceae. Whereas most of the key genes involved in oil synthesis and turnover are single copy, the number of members of the ricin gene family is larger than previously thought. Comparative genomics analysis suggests the presence of an ancient hexaploidization event that is conserved across the dicotyledonous lineage.
ESTHER : Chan_2010_Nat.Biotechnol_28_951
PubMedSearch : Chan_2010_Nat.Biotechnol_28_951
PubMedID: 20729833
Gene_locus related to this paper: ricco-b9r7h7 , ricco-b9re31 , ricco-b9rgi7 , ricco-b9riy7 , ricco-b9rlg6 , ricco-b9rm64 , ricco-b9rsg5 , ricco-b9rtk6 , ricco-b9rtt3 , ricco-b9ry83 , ricco-b9s8p2 , ricco-b9s817 , ricco-b9sby7 , ricco-b9scn1 , ricco-b9scn2 , ricco-b9scn3 , ricco-b9scn5 , ricco-b9ssj7 , ricco-b9ssj8 , ricco-b9sx01 , ricco-b9szu0 , ricco-b9t4l4 , ricco-b9t5x2 , ricco-b9tb84 , ricco-b9rkb0 , ricco-b9rru1 , ricco-b9rdy5 , ricco-b9tey4 , ricco-b9sfw5 , ricco-b9sjw6 , ricco-b9shs6 , ricco-b9rsl2 , ricco-b9r7f8 , ricco-b9rne4 , ricco-b9r8z8 , ricco-b9rf65 , ricco-b9rjk8 , ricco-b9sip5 , ricco-b9t3r4

Title : The genome of the blood fluke Schistosoma mansoni - Berriman_2009_Nature_460_352
Author(s) : Berriman M , Haas BJ , LoVerde PT , Wilson RA , Dillon GP , Cerqueira GC , Mashiyama ST , Al-Lazikani B , Andrade LF , Ashton PD , Aslett MA , Bartholomeu DC , Blandin G , Caffrey CR , Coghlan A , Coulson R , Day TA , Delcher A , DeMarco R , Djikeng A , Eyre T , Gamble JA , Ghedin E , Gu Y , Hertz-Fowler C , Hirai H , Hirai Y , Houston R , Ivens A , Johnston DA , Lacerda D , Macedo CD , McVeigh P , Ning Z , Oliveira G , Overington JP , Parkhill J , Pertea M , Pierce RJ , Protasio AV , Quail MA , Rajandream MA , Rogers J , Sajid M , Salzberg SL , Stanke M , Tivey AR , White O , Williams DL , Wortman J , Wu W , Zamanian M , Zerlotini A , Fraser-Liggett CM , Barrell BG , El-Sayed NM
Ref : Nature , 460 :352 , 2009
Abstract : Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.
ESTHER : Berriman_2009_Nature_460_352
PubMedSearch : Berriman_2009_Nature_460_352
PubMedID: 19606141
Gene_locus related to this paper: schma-ACHE1 , schma-ACHE2 , schma-c4qb79 , schma-c4qmk4 , schma-g4v9h7 , schma-BCHE , schma-g4vmf3

Title : The genome of the model beetle and pest Tribolium castaneum - Richards_2008_Nature_452_949
Author(s) : Richards S , Gibbs RA , Weinstock GM , Brown SJ , Denell R , Beeman RW , Gibbs R , Bucher G , Friedrich M , Grimmelikhuijzen CJ , Klingler M , Lorenzen M , Roth S , Schroder R , Tautz D , Zdobnov EM , Muzny D , Attaway T , Bell S , Buhay CJ , Chandrabose MN , Chavez D , Clerk-Blankenburg KP , Cree A , Dao M , Davis C , Chacko J , Dinh H , Dugan-Rocha S , Fowler G , Garner TT , Garnes J , Gnirke A , Hawes A , Hernandez J , Hines S , Holder M , Hume J , Jhangiani SN , Joshi V , Khan ZM , Jackson L , Kovar C , Kowis A , Lee S , Lewis LR , Margolis J , Morgan M , Nazareth LV , Nguyen N , Okwuonu G , Parker D , Ruiz SJ , Santibanez J , Savard J , Scherer SE , Schneider B , Sodergren E , Vattahil S , Villasana D , White CS , Wright R , Park Y , Lord J , Oppert B , Brown S , Wang L , Weinstock G , Liu Y , Worley K , Elsik CG , Reese JT , Elhaik E , Landan G , Graur D , Arensburger P , Atkinson P , Beidler J , Demuth JP , Drury DW , Du YZ , Fujiwara H , Maselli V , Osanai M , Robertson HM , Tu Z , Wang JJ , Wang S , Song H , Zhang L , Werner D , Stanke M , Morgenstern B , Solovyev V , Kosarev P , Brown G , Chen HC , Ermolaeva O , Hlavina W , Kapustin Y , Kiryutin B , Kitts P , Maglott D , Pruitt K , Sapojnikov V , Souvorov A , Mackey AJ , Waterhouse RM , Wyder S , Kriventseva EV , Kadowaki T , Bork P , Aranda M , Bao R , Beermann A , Berns N , Bolognesi R , Bonneton F , Bopp D , Butts T , Chaumot A , Denell RE , Ferrier DE , Gordon CM , Jindra M , Lan Q , Lattorff HM , Laudet V , von Levetsow C , Liu Z , Lutz R , Lynch JA , da Fonseca RN , Posnien N , Reuter R , Schinko JB , Schmitt C , Schoppmeier M , Shippy TD , Simonnet F , Marques-Souza H , Tomoyasu Y , Trauner J , Van der Zee M , Vervoort M , Wittkopp N , Wimmer EA , Yang X , Jones AK , Sattelle DB , Ebert PR , Nelson D , Scott JG , Muthukrishnan S , Kramer KJ , Arakane Y , Zhu Q , Hogenkamp D , Dixit R , Jiang H , Zou Z , Marshall J , Elpidina E , Vinokurov K , Oppert C , Evans J , Lu Z , Zhao P , Sumathipala N , Altincicek B , Vilcinskas A , Williams M , Hultmark D , Hetru C , Hauser F , Cazzamali G , Williamson M , Li B , Tanaka Y , Predel R , Neupert S , Schachtner J , Verleyen P , Raible F , Walden KK , Angeli S , Foret S , Schuetz S , Maleszka R , Miller SC , Grossmann D
Ref : Nature , 452 :949 , 2008
Abstract : Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
ESTHER : Richards_2008_Nature_452_949
PubMedSearch : Richards_2008_Nature_452_949
PubMedID: 18362917
Gene_locus related to this paper: trica-ACHE1 , trica-ACHE2 , trica-d2a0g9 , trica-d2a0h0 , trica-d2a0w9 , trica-d2a0x0 , trica-d2a0x1 , trica-d2a0x3 , trica-d2a0x4.1 , trica-d2a0x4.2 , trica-d2a0x6 , trica-d2a2b8 , trica-d2a2h1 , trica-d2a3c3 , trica-d2a3g9 , trica-d2a5y5 , trica-d2a309 , trica-d2a514 , trica-d2a515 , trica-d2a516 , trica-d2a577 , trica-d2a578 , trica-d6w6x8 , trica-d6w7f9 , trica-d6w7h2 , trica-d6w8e7 , trica-d6w9c0 , trica-d6w855 , trica-d6wac8 , trica-d6wan4 , trica-d6wd50 , trica-d6wd73 , trica-d6wd74 , trica-A0A139WM97 , trica-d6wfu3 , trica-d6wgl2 , trica-d6wj57 , trica-d6wj59 , trica-d6wjs3 , trica-d6wl31 , trica-d6wnv1 , trica-d6wpl0 , trica-d6wqd6 , trica-d6wqr4 , trica-d6ws52 , trica-d6wsm0 , trica-d6wu38 , trica-d6wu39 , trica-d6wu40 , trica-d6wu41 , trica-d6wu44 , trica-d6wvk5 , trica-d6wvz7 , trica-d6wwu9 , trica-d6wwv0 , trica-d6wxz0 , trica-d6wyy1 , trica-d6wyy2 , trica-d6x0z2 , trica-d6x0z5 , trica-d6x0z6 , trica-d6x4b2 , trica-d6x4e8 , trica-d6x4e9 , trica-d6x197 , trica-d7eip7 , trica-d7eld3 , trica-d7us45 , trica-q5wm43 , trica-q5zex9 , trica-d6wie5 , trica-d6w7t0 , trica-d6x4h0 , trica-d6x4h1 , trica-a0a139wae8 , trica-a0a139wc96 , trica-d6x325 , trica-d2a4s2 , trica-d6wvw8

Title : Genome sequence of Aedes aegypti, a major arbovirus vector - Nene_2007_Science_316_1718
Author(s) : Nene V , Wortman JR , Lawson D , Haas B , Kodira C , Tu ZJ , Loftus B , Xi Z , Megy K , Grabherr M , Ren Q , Zdobnov EM , Lobo NF , Campbell KS , Brown SE , Bonaldo MF , Zhu J , Sinkins SP , Hogenkamp DG , Amedeo P , Arensburger P , Atkinson PW , Bidwell S , Biedler J , Birney E , Bruggner RV , Costas J , Coy MR , Crabtree J , Crawford M , Debruyn B , Decaprio D , Eiglmeier K , Eisenstadt E , El-Dorry H , Gelbart WM , Gomes SL , Hammond M , Hannick LI , Hogan JR , Holmes MH , Jaffe D , Johnston JS , Kennedy RC , Koo H , Kravitz S , Kriventseva EV , Kulp D , LaButti K , Lee E , Li S , Lovin DD , Mao C , Mauceli E , Menck CF , Miller JR , Montgomery P , Mori A , Nascimento AL , Naveira HF , Nusbaum C , O'Leary S , Orvis J , Pertea M , Quesneville H , Reidenbach KR , Rogers YH , Roth CW , Schneider JR , Schatz M , Shumway M , Stanke M , Stinson EO , Tubio JM , Vanzee JP , Verjovski-Almeida S , Werner D , White O , Wyder S , Zeng Q , Zhao Q , Zhao Y , Hill CA , Raikhel AS , Soares MB , Knudson DL , Lee NH , Galagan J , Salzberg SL , Paulsen IT , Dimopoulos G , Collins FH , Birren B , Fraser-Liggett CM , Severson DW
Ref : Science , 316 :1718 , 2007
Abstract : We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.
ESTHER : Nene_2007_Science_316_1718
PubMedSearch : Nene_2007_Science_316_1718
PubMedID: 17510324
Gene_locus related to this paper: aedae-ACHE , aedae-ACHE1 , aedae-glita , aedae-q0iea6 , aedae-q0iev6 , aedae-q0ifn6 , aedae-q0ifn8 , aedae-q0ifn9 , aedae-q0ifp0 , aedae-q0ig41 , aedae-q1dgl0 , aedae-q1dh03 , aedae-q1dh19 , aedae-q1hqe6 , aedae-Q8ITU8 , aedae-Q8MMJ6 , aedae-Q8T9V6 , aedae-q16e91 , aedae-q16f04 , aedae-q16f25 , aedae-q16f26 , aedae-q16f28 , aedae-q16f29 , aedae-q16f30 , aedae-q16gq5 , aedae-q16iq5 , aedae-q16je0 , aedae-q16je1 , aedae-q16je2 , aedae-q16ks8 , aedae-q16lf2 , aedae-q16lv6 , aedae-q16m61 , aedae-q16mc1 , aedae-q16mc6 , aedae-q16mc7 , aedae-q16md1 , aedae-q16ms7 , aedae-q16nk5 , aedae-q16rl5 , aedae-q16rz9 , aedae-q16si8 , aedae-q16t49 , aedae-q16wf1 , aedae-q16x18 , aedae-q16xp8 , aedae-q16xu6 , aedae-q16xw5 , aedae-q16xw6 , aedae-q16y04 , aedae-q16y05 , aedae-q16y06 , aedae-q16y07 , aedae-q16y39 , aedae-q16y40 , aedae-q16yg4 , aedae-q16z03 , aedae-q17aa7 , aedae-q17av1 , aedae-q17av2 , aedae-q17av3 , aedae-q17av4 , aedae-q17b28 , aedae-q17b29 , aedae-q17b30 , aedae-q17b31 , aedae-q17b32 , aedae-q17bm3 , aedae-q17bm4 , aedae-q17bv7 , aedae-q17c44 , aedae-q17cz1 , aedae-q17d32 , aedae-q17g39 , aedae-q17g40 , aedae-q17g41 , aedae-q17g42 , aedae-q17g43 , aedae-q17g44 , aedae-q17gb8 , aedae-q17gr3 , aedae-q17if7 , aedae-q17if9 , aedae-q17ig1 , aedae-q17ig2 , aedae-q17is4 , aedae-q17l09 , aedae-q17m26 , aedae-q17mg9 , aedae-q17mv4 , aedae-q17mv5 , aedae-q17mv6 , aedae-q17mv7 , aedae-q17mw8 , aedae-q17mw9 , aedae-q17nw5 , aedae-q17nx5 , aedae-q17pa4 , aedae-q17q69 , aedae-q170k7 , aedae-q171y4 , aedae-q172e0 , aedae-q176i8 , aedae-q176j0 , aedae-q177k1 , aedae-q177k2 , aedae-q177l9 , aedae-j9hic3 , aedae-q179r9 , aedae-u483 , aedae-j9hj23 , aedae-q17d68 , aedae-q177c7 , aedae-q0ifp1 , aedae-a0a1s4fx83 , aedae-a0a1s4g2m0 , aedae-q1hr49

Title : Draft genome of the filarial nematode parasite Brugia malayi - Ghedin_2007_Science_317_1756
Author(s) : Ghedin E , Wang S , Spiro D , Caler E , Zhao Q , Crabtree J , Allen JE , Delcher AL , Guiliano DB , Miranda-Saavedra D , Angiuoli SV , Creasy T , Amedeo P , Haas B , El-Sayed NM , Wortman JR , Feldblyum T , Tallon L , Schatz M , Shumway M , Koo H , Salzberg SL , Schobel S , Pertea M , Pop M , White O , Barton GJ , Carlow CK , Crawford MJ , Daub J , Dimmic MW , Estes CF , Foster JM , Ganatra M , Gregory WF , Johnson NM , Jin J , Komuniecki R , Korf I , Kumar S , Laney S , Li BW , Li W , Lindblom TH , Lustigman S , Ma D , Maina CV , Martin DM , McCarter JP , McReynolds L , Mitreva M , Nutman TB , Parkinson J , Peregrin-Alvarez JM , Poole C , Ren Q , Saunders L , Sluder AE , Smith K , Stanke M , Unnasch TR , Ware J , Wei AD , Weil G , Williams DJ , Zhang Y , Williams SA , Fraser-Liggett C , Slatko B , Blaxter ML , Scott AL
Ref : Science , 317 :1756 , 2007
Abstract : Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the approximately 90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict approximately 11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during approximately 350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design.
ESTHER : Ghedin_2007_Science_317_1756
PubMedSearch : Ghedin_2007_Science_317_1756
PubMedID: 17885136
Gene_locus related to this paper: bruma-a8ndk6 , bruma-a8njt8 , bruma-a8nl88 , bruma-a8npi4 , bruma-a8npi6 , bruma-a8p6g9 , bruma-a8pah3 , bruma-a8pc38 , bruma-a8pek5 , bruma-a8piq4 , bruma-a8pnw8 , bruma-a8psu4 , bruma-a8pte1 , bruma-a8q606 , bruma-a8q632 , bruma-a8q937 , bruma-a8qav5 , bruma-a8qbd9 , bruma-a8qgj6 , bruma-a8qh78 , bruma-a8q143 , bruma-a0a024mej5 , bruma-a0a0k0jju9 , bruma-a0a0i9n517