Fronick C

References (6)

Title : Genome sequence of Cronobacter sakazakii BAA-894 and comparative genomic hybridization analysis with other Cronobacter species - Kucerova_2010_PLoS.One_5_e9556
Author(s) : Kucerova E , Clifton SW , Xia XQ , Long F , Porwollik S , Fulton L , Fronick C , Minx P , Kyung K , Warren W , Fulton R , Feng D , Wollam A , Shah N , Bhonagiri V , Nash WE , Hallsworth-Pepin K , Wilson RK , McClelland M , Forsythe SJ
Ref : PLoS ONE , 5 :e9556 , 2010
Abstract : BACKGROUND: The genus Cronobacter (formerly called Enterobacter sakazakii) is composed of five species; C. sakazakii, C. malonaticus, C. turicensis, C. muytjensii, and C. dublinensis. The genus includes opportunistic human pathogens, and the first three species have been associated with neonatal infections. The most severe diseases are caused in neonates and include fatal necrotizing enterocolitis and meningitis. The genetic basis of the diversity within the genus is unknown, and few virulence traits have been identified. METHODOLOGY/PRINCIPAL FINDINGS: We report here the first sequence of a member of this genus, C. sakazakii strain BAA-894. The genome of Cronobacter sakazakii strain BAA-894 comprises a 4.4 Mb chromosome (57% GC content) and two plasmids; 31 kb (51% GC) and 131 kb (56% GC). The genome was used to construct a 387,000 probe oligonucleotide tiling DNA microarray covering the whole genome. Comparative genomic hybridization (CGH) was undertaken on five other C. sakazakii strains, and representatives of the four other Cronobacter species. Among 4,382 annotated genes inspected in this study, about 55% of genes were common to all C. sakazakii strains and 43% were common to all Cronobacter strains, with 10-17% absence of genes. CONCLUSIONS/SIGNIFICANCE: CGH highlighted 15 clusters of genes in C. sakazakii BAA-894 that were divergent or absent in more than half of the tested strains; six of these are of probable prophage origin. Putative virulence factors were identified in these prophage and in other variable regions. A number of genes unique to Cronobacter species associated with neonatal infections (C. sakazakii, C. malonaticus and C. turicensis) were identified. These included a copper and silver resistance system known to be linked to invasion of the blood-brain barrier by neonatal meningitic strains of Escherichia coli. In addition, genes encoding for multidrug efflux pumps and adhesins were identified that were unique to C. sakazakii strains from outbreaks in neonatal intensive care units.
ESTHER : Kucerova_2010_PLoS.One_5_e9556
PubMedSearch : Kucerova_2010_PLoS.One_5_e9556
PubMedID: 20221447
Gene_locus related to this paper: cros8-a7men1 , cros8-a7mft0 , 9entr-k7zz64

Title : Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome - Baxter_2010_Science_330_1549
Author(s) : Baxter L , Tripathy S , Ishaque N , Boot N , Cabral A , Kemen E , Thines M , Ah-Fong A , Anderson R , Badejoko W , Bittner-Eddy P , Boore JL , Chibucos MC , Coates M , Dehal P , Delehaunty K , Dong S , Downton P , Dumas B , Fabro G , Fronick C , Fuerstenberg SI , Fulton L , Gaulin E , Govers F , Hughes L , Humphray S , Jiang RH , Judelson H , Kamoun S , Kyung K , Meijer H , Minx P , Morris P , Nelson J , Phuntumart V , Qutob D , Rehmany A , Rougon-Cardoso A , Ryden P , Torto-Alalibo T , Studholme D , Wang Y , Win J , Wood J , Clifton SW , Rogers J , Van den Ackerveken G , Jones JD , McDowell JM , Beynon J , Tyler BM
Ref : Science , 330 :1549 , 2010
Abstract : Many oomycete and fungal plant pathogens are obligate biotrophs, which extract nutrients only from living plant tissue and cannot grow apart from their hosts. Although these pathogens cause substantial crop losses, little is known about the molecular basis or evolution of obligate biotrophy. Here, we report the genome sequence of the oomycete Hyaloperonospora arabidopsidis (Hpa), an obligate biotroph and natural pathogen of Arabidopsis thaliana. In comparison with genomes of related, hemibiotrophic Phytophthora species, the Hpa genome exhibits dramatic reductions in genes encoding (i) RXLR effectors and other secreted pathogenicity proteins, (ii) enzymes for assimilation of inorganic nitrogen and sulfur, and (iii) proteins associated with zoospore formation and motility. These attributes comprise a genomic signature of evolution toward obligate biotrophy.
ESTHER : Baxter_2010_Science_330_1549
PubMedSearch : Baxter_2010_Science_330_1549
PubMedID: 21148394
Gene_locus related to this paper: hyaae-m4b4d8 , hyaae-m4b4e0 , hyaae-m4bkr1 , hyaae-m4bkw7

Title : The B73 maize genome: complexity, diversity, and dynamics - Schnable_2009_Science_326_1112
Author(s) : Schnable PS , Ware D , Fulton RS , Stein JC , Wei F , Pasternak S , Liang C , Zhang J , Fulton L , Graves TA , Minx P , Reily AD , Courtney L , Kruchowski SS , Tomlinson C , Strong C , Delehaunty K , Fronick C , Courtney B , Rock SM , Belter E , Du F , Kim K , Abbott RM , Cotton M , Levy A , Marchetto P , Ochoa K , Jackson SM , Gillam B , Chen W , Yan L , Higginbotham J , Cardenas M , Waligorski J , Applebaum E , Phelps L , Falcone J , Kanchi K , Thane T , Scimone A , Thane N , Henke J , Wang T , Ruppert J , Shah N , Rotter K , Hodges J , Ingenthron E , Cordes M , Kohlberg S , Sgro J , Delgado B , Mead K , Chinwalla A , Leonard S , Crouse K , Collura K , Kudrna D , Currie J , He R , Angelova A , Rajasekar S , Mueller T , Lomeli R , Scara G , Ko A , Delaney K , Wissotski M , Lopez G , Campos D , Braidotti M , Ashley E , Golser W , Kim H , Lee S , Lin J , Dujmic Z , Kim W , Talag J , Zuccolo A , Fan C , Sebastian A , Kramer M , Spiegel L , Nascimento L , Zutavern T , Miller B , Ambroise C , Muller S , Spooner W , Narechania A , Ren L , Wei S , Kumari S , Faga B , Levy MJ , McMahan L , Van Buren P , Vaughn MW , Ying K , Yeh CT , Emrich SJ , Jia Y , Kalyanaraman A , Hsia AP , Barbazuk WB , Baucom RS , Brutnell TP , Carpita NC , Chaparro C , Chia JM , Deragon JM , Estill JC , Fu Y , Jeddeloh JA , Han Y , Lee H , Li P , Lisch DR , Liu S , Liu Z , Nagel DH , McCann MC , SanMiguel P , Myers AM , Nettleton D , Nguyen J , Penning BW , Ponnala L , Schneider KL , Schwartz DC , Sharma A , Soderlund C , Springer NM , Sun Q , Wang H , Waterman M , Westerman R , Wolfgruber TK , Yang L , Yu Y , Zhang L , Zhou S , Zhu Q , Bennetzen JL , Dawe RK , Jiang J , Jiang N , Presting GG , Wessler SR , Aluru S , Martienssen RA , Clifton SW , McCombie WR , Wing RA , Wilson RK
Ref : Science , 326 :1112 , 2009
Abstract : We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.
ESTHER : Schnable_2009_Science_326_1112
PubMedSearch : Schnable_2009_Science_326_1112
PubMedID: 19965430
Gene_locus related to this paper: maize-b4ffc7 , maize-b6u7e1 , maize-c0pcy5 , maize-c0pgf7 , maize-c0pgw1 , maize-c0pfl3 , maize-b4fpr7 , maize-k7vy73 , maize-a0a096swr3 , maize-k7v3i9 , maize-b6u9v9 , maize-a0a3l6e780 , maize-b4fv80 , maize-a0a1d6nse2 , maize-c4j9a1 , maize-k7uba1

Title : Generation and annotation of the DNA sequences of human chromosomes 2 and 4 - Hillier_2005_Nature_434_724
Author(s) : Hillier LW , Graves TA , Fulton RS , Fulton LA , Pepin KH , Minx P , Wagner-McPherson C , Layman D , Wylie K , Sekhon M , Becker MC , Fewell GA , Delehaunty KD , Miner TL , Nash WE , Kremitzki C , Oddy L , Du H , Sun H , Bradshaw-Cordum H , Ali J , Carter J , Cordes M , Harris A , Isak A , Van Brunt A , Nguyen C , Du F , Courtney L , Kalicki J , Ozersky P , Abbott S , Armstrong J , Belter EA , Caruso L , Cedroni M , Cotton M , Davidson T , Desai A , Elliott G , Erb T , Fronick C , Gaige T , Haakenson W , Haglund K , Holmes A , Harkins R , Kim K , Kruchowski SS , Strong CM , Grewal N , Goyea E , Hou S , Levy A , Martinka S , Mead K , McLellan MD , Meyer R , Randall-Maher J , Tomlinson C , Dauphin-Kohlberg S , Kozlowicz-Reilly A , Shah N , Swearengen-Shahid S , Snider J , Strong JT , Thompson J , Yoakum M , Leonard S , Pearman C , Trani L , Radionenko M , Waligorski JE , Wang C , Rock SM , Tin-Wollam AM , Maupin R , Latreille P , Wendl MC , Yang SP , Pohl C , Wallis JW , Spieth J , Bieri TA , Berkowicz N , Nelson JO , Osborne J , Ding L , Sabo A , Shotland Y , Sinha P , Wohldmann PE , Cook LL , Hickenbotham MT , Eldred J , Williams D , Jones TA , She X , Ciccarelli FD , Izaurralde E , Taylor J , Schmutz J , Myers RM , Cox DR , Huang X , McPherson JD , Mardis ER , Clifton SW , Warren WC , Chinwalla AT , Eddy SR , Marra MA , Ovcharenko I , Furey TS , Miller W , Eichler EE , Bork P , Suyama M , Torrents D , Waterston RH , Wilson RK
Ref : Nature , 434 :724 , 2005
Abstract : Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.
ESTHER : Hillier_2005_Nature_434_724
PubMedSearch : Hillier_2005_Nature_434_724
PubMedID: 15815621
Gene_locus related to this paper: human-ABHD1 , human-LDAH , human-ABHD18 , human-KANSL3 , human-PGAP1 , human-PREPL

Title : Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid - McClelland_2004_Nat.Genet_36_1268
Author(s) : McClelland M , Sanderson KE , Clifton SW , Latreille P , Porwollik S , Sabo A , Meyer R , Bieri T , Ozersky P , McLellan M , Harkins CR , Wang C , Nguyen C , Berghoff A , Elliott G , Kohlberg S , Strong C , Du F , Carter J , Kremizki C , Layman D , Leonard S , Sun H , Fulton L , Nash W , Miner T , Minx P , Delehaunty K , Fronick C , Magrini V , Nhan M , Warren W , Florea L , Spieth J , Wilson RK
Ref : Nat Genet , 36 :1268 , 2004
Abstract : Salmonella enterica serovars often have a broad host range, and some cause both gastrointestinal and systemic disease. But the serovars Paratyphi A and Typhi are restricted to humans and cause only systemic disease. It has been estimated that Typhi arose in the last few thousand years. The sequence and microarray analysis of the Paratyphi A genome indicates that it is similar to the Typhi genome but suggests that it has a more recent evolutionary origin. Both genomes have independently accumulated many pseudogenes among their approximately 4,400 protein coding sequences: 173 in Paratyphi A and approximately 210 in Typhi. The recent convergence of these two similar genomes on a similar phenotype is subtly reflected in their genotypes: only 30 genes are degraded in both serovars. Nevertheless, these 30 genes include three known to be important in gastroenteritis, which does not occur in these serovars, and four for Salmonella-translocated effectors, which are normally secreted into host cells to subvert host functions. Loss of function also occurs by mutation in different genes in the same pathway (e.g., in chemotaxis and in the production of fimbriae).
ESTHER : McClelland_2004_Nat.Genet_36_1268
PubMedSearch : McClelland_2004_Nat.Genet_36_1268
PubMedID: 15531882
Gene_locus related to this paper: salen-OPDB , salty-AES , salty-BIOH , salty-DLHH , salty-ENTF , salty-FES , salty-IROD , salty-IROE , salty-P74847 , salty-PLDB , salty-STM2547 , salty-STM4506 , salty-STY1441 , salty-STY2428 , salty-STY3846 , salty-yafa , salty-YBFF , salty-ycfp , salty-YFBB , salty-YHET , salty-YQIA

Title : Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution - Hillier_2004_Nature_432_695
Author(s) : Hillier LW , Miller W , Birney E , Warren W , Hardison RC , Ponting CP , Bork P , Burt DW , Groenen MA , Delany ME , Dodgson JB , Chinwalla AT , Cliften PF , Clifton SW , Delehaunty KD , Fronick C , Fulton RS , Graves TA , Kremitzki C , Layman D , Magrini V , McPherson JD , Miner TL , Minx P , Nash WE , Nhan MN , Nelson JO , Oddy LG , Pohl CS , Randall-Maher J , Smith SM , Wallis JW , Yang SP , Romanov MN , Rondelli CM , Paton B , Smith J , Morrice D , Daniels L , Tempest HG , Robertson L , Masabanda JS , Griffin DK , Vignal A , Fillon V , Jacobbson L , Kerje S , Andersson L , Crooijmans RP , Aerts J , van der Poel JJ , Ellegren H , Caldwell RB , Hubbard SJ , Grafham DV , Kierzek AM , McLaren SR , Overton IM , Arakawa H , Beattie KJ , Bezzubov Y , Boardman PE , Bonfield JK , Croning MD , Davies RM , Francis MD , Humphray SJ , Scott CE , Taylor RG , Tickle C , Brown WR , Rogers J , Buerstedde JM , Wilson SA , Stubbs L , Ovcharenko I , Gordon L , Lucas S , Miller MM , Inoko H , Shiina T , Kaufman J , Salomonsen J , Skjoedt K , Ka-Shu Wong G , Wang J , Liu B , Yu J , Yang H , Nefedov M , Koriabine M , deJong PJ , Goodstadt L , Webber C , Dickens NJ , Letunic I , Suyama M , Torrents D , von Mering C , Zdobnov EM , Makova K , Nekrutenko A , Elnitski L , Eswara P , King DC , Yang S , Tyekucheva S , Radakrishnan A , Harris RS , Chiaromonte F , Taylor J , He J , Rijnkels M , Griffiths-Jones S , Ureta-Vidal A , Hoffman MM , Severin J , Searle SM , Law AS , Speed D , Waddington D , Cheng Z , Tuzun E , Eichler E , Bao Z , Flicek P , Shteynberg DD , Brent MR , Bye JM , Huckle EJ , Chatterji S , Dewey C , Pachter L , Kouranov A , Mourelatos Z , Hatzigeorgiou AG , Paterson AH , Ivarie R , Brandstrom M , Axelsson E , Backstrom N , Berlin S , Webster MT , Pourquie O , Reymond A , Ucla C , Antonarakis SE , Long M , Emerson JJ , Betran E , Dupanloup I , Kaessmann H , Hinrichs AS , Bejerano G , Furey TS , Harte RA , Raney B , Siepel A , Kent WJ , Haussler D , Eyras E , Castelo R , Abril JF , Castellano S , Camara F , Parra G , Guigo R , Bourque G , Tesler G , Pevzner PA , Smit A , Fulton LA , Mardis ER , Wilson RK
Ref : Nature , 432 :695 , 2004
Abstract : We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
ESTHER : Hillier_2004_Nature_432_695
PubMedSearch : Hillier_2004_Nature_432_695
PubMedID: 15592404
Gene_locus related to this paper: chick-a0a1d5pmd9 , chick-b3tzb3 , chick-BCHE , chick-cb043 , chick-d3wgl5 , chick-e1bsm0 , chick-e1bvq6 , chick-e1bwz0 , chick-e1bwz1 , chick-e1byn1 , chick-e1bz81 , chick-e1c0z8 , chick-e1c7p7 , chick-f1nby4 , chick-f1ncz8 , chick-f1ndp3 , chick-f1nep4 , chick-f1nj68 , chick-f1njg6 , chick-f1njk4 , chick-f1njs4 , chick-f1njs5 , chick-f1nk87 , chick-f1nmx9 , chick-f1ntp8 , chick-f1nvg7 , chick-f1nwf2 , chick-f1p1l1 , chick-f1p3j5 , chick-f1p4c6 , chick-f1p508 , chick-fas , chick-h9l0k6 , chick-nlgn1 , chick-NLGN3 , chick-q5f3h8 , chick-q5zhm0 , chick-q5zi81 , chick-q5zij5 , chick-q5zin0 , chick-thyro , chick-f1nrq2 , chick-e1byd4 , chick-e1c2h6 , chick-a0a1d5pk92 , chick-a0a1d5pzg7 , chick-f1nbc2 , chick-f1nf25 , chick-f1nly5 , chick-f1p4h5 , chick-f1nzi7 , chick-f1p5k3 , chick-f1nm35 , chick-a0a1d5pl11 , chick-a0a1d5pj73 , chick-f1nxu6 , chick-a0a1d5nwc0 , chick-e1bxs8 , chick-f1p2g7 , chick-f1nd96