Angiuoli S

References (5)

Title : Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus - Fedorova_2008_PLoS.Genet_4_e1000046
Author(s) : Fedorova ND , Khaldi N , Joardar VS , Maiti R , Amedeo P , Anderson MJ , Crabtree J , Silva JC , Badger JH , Albarraq A , Angiuoli S , Bussey H , Bowyer P , Cotty PJ , Dyer PS , Egan A , Galens K , Fraser-Liggett CM , Haas BJ , Inman JM , Kent R , Lemieux S , Malavazi I , Orvis J , Roemer T , Ronning CM , Sundaram JP , Sutton G , Turner G , Venter JC , White OR , Whitty BR , Youngman P , Wolfe KH , Goldman GH , Wortman JR , Jiang B , Denning DW , Nierman WC
Ref : PLoS Genet , 4 :e1000046 , 2008
Abstract : We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and up to 2% unique genes in each genome. While the core genes are 99.8% identical at the nucleotide level, identity for variable genes can be as low 40%. The most divergent loci appear to contain heterokaryon incompatibility (het) genes associated with fungal programmed cell death such as developmental regulator rosA. Cross-species comparison has revealed that 8.5%, 13.5% and 12.6%, respectively, of A. fumigatus, N. fischeri and A. clavatus genes are species-specific. These genes are significantly smaller in size than core genes, contain fewer exons and exhibit a subtelomeric bias. Most of them cluster together in 13 chromosomal islands, which are enriched for pseudogenes, transposons and other repetitive elements. At least 20% of A. fumigatus-specific genes appear to be functional and involved in carbohydrate and chitin catabolism, transport, detoxification, secondary metabolism and other functions that may facilitate the adaptation to heterogeneous environments such as soil or a mammalian host. Contrary to what was suggested previously, their origin cannot be attributed to horizontal gene transfer (HGT), but instead is likely to involve duplication, diversification and differential gene loss (DDL). The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated "gene dumps" and, perhaps, simultaneously, as "gene factories".
ESTHER : Fedorova_2008_PLoS.Genet_4_e1000046
PubMedSearch : Fedorova_2008_PLoS.Genet_4_e1000046
PubMedID: 18404212
Gene_locus related to this paper: aspcl-a1c4m6 , aspcl-a1c5a7 , aspcl-a1c6w3 , aspcl-a1c8p7 , aspcl-a1c8q9 , aspcl-a1c9k4 , aspcl-a1c759 , aspcl-a1c786 , aspcl-a1c823 , aspcl-a1c859 , aspcl-a1c881 , aspcl-a1c994 , aspcl-a1cag4 , aspcl-a1caj8 , aspcl-a1cas0 , aspcl-a1cc86 , aspcl-a1ccq2 , aspcl-a1cfv7 , aspcl-a1chj6 , aspcl-a1cif4 , aspcl-a1ck14 , aspcl-a1cke4 , aspcl-a1ckq1 , aspcl-a1cli1 , aspcl-a1cln8 , aspcl-a1cm72 , aspcl-a1cns2 , aspcl-a1cpk9 , aspcl-a1cra8 , aspcl-a1crr5 , aspcl-a1crs9 , aspcl-a1cs04 , aspcl-a1cs39 , aspcl-a1cu39 , aspcl-atg15 , aspcl-axe1 , aspcl-cuti1 , aspcl-cuti3 , aspcl-dapb , aspcl-dpp4 , aspcl-dpp5 , aspcl-faeb , aspcl-faec1 , aspcl-faec2 , aspfc-b0xp50 , aspfc-b0xu40 , aspfc-b0xzj6 , aspfc-b0y2h6 , aspfc-b0y962 , aspfc-b0yaj6 , aspfc-dpp5 , aspfu-DPP4 , aspfu-faeb1 , aspfu-faec , aspfu-ppme1 , aspfu-q4w9r3 , aspfu-q4w9t5 , aspfu-q4w9z4 , aspfu-q4wa57 , aspfu-q4wa78 , aspfu-q4wag0 , aspfu-q4wal3 , aspfu-q4wbc5 , aspfu-q4wbj7 , aspfu-q4wdg2 , aspfu-q4wf06 , aspfu-q4wf29 , aspfu-q4wf56 , aspfu-q4wfq9 , aspfu-q4wg73 , aspfu-q4wgm4 , aspfu-q4win2 , aspfu-q4wk31 , aspfu-q4wk44 , aspfu-q4wk90 , aspfu-q4wm12 , aspfu-q4wm84 , aspfu-q4wm86 , aspfu-q4wmr0 , aspfu-q4wny7 , aspfu-q4wp19 , aspfu-q4wpb9 , aspfu-q4wqj8 , aspfu-q4wqv2 , aspfu-q4wrr7 , aspfu-q4wu51 , aspfu-q4wub2 , aspfu-q4wui7 , aspfu-q4wuk8 , aspfu-q4wum3 , aspfu-q4wuw0 , aspfu-q4wvy1 , aspfu-q4ww22 , aspfu-q4wx13 , aspfu-q4wxd0 , aspfu-q4wxe4 , aspfu-q4wxr1 , aspfu-q4wyq5 , aspfu-q4wz16 , aspfu-q4wzd5 , aspfu-q4wzh6 , aspfu-q4x0n6 , aspfu-q4x1n0 , aspfu-q4x1w9 , aspfu-q4x078 , neofi-a1cwa6 , neofi-a1d4m8 , neofi-a1d4p0 , neofi-a1d5p2 , neofi-a1d104 , neofi-a1d380 , neofi-a1d512 , neofi-a1d654 , neofi-a1da18 , neofi-a1dal8 , neofi-a1df46 , neofi-a1dhj0 , neofi-a1di44 , neofi-a1dk35 , neofi-a1dki7 , neofi-a1dkt6 , neofi-a1dn55 , neofi-atg15 , neofi-axe1 , neofi-faeb1 , neofi-faeb2 , neofi-faec , aspcl-a1cd34 , aspcl-a1cd88 , neofi-a1dc66 , aspcl-a1ceh5 , neofi-a1dfr9 , aspfm-a0a084bf80 , aspcl-a1cqb5 , aspcl-a1cs44 , neofi-a1d517 , neofi-a1dbz0 , neofi-a1cuz0 , aspcl-a1c5e8 , neofi-a1d0b8 , aspcl-a1cdf0 , aspcl-a1ccd3 , neofi-a1da82 , neofi-a1d5e6 , aspcl-kex1 , aspcl-cbpya

Title : Comparative genomics of trypanosomatid parasitic protozoa - El-Sayed_2005_Science_309_404
Author(s) : El-Sayed NM , Myler PJ , Blandin G , Berriman M , Crabtree J , Aggarwal G , Caler E , Renauld H , Worthey EA , Hertz-Fowler C , Ghedin E , Peacock C , Bartholomeu DC , Haas BJ , Tran AN , Wortman JR , Alsmark UC , Angiuoli S , Anupama A , Badger J , Bringaud F , Cadag E , Carlton JM , Cerqueira GC , Creasy T , Delcher AL , Djikeng A , Embley TM , Hauser C , Ivens AC , Kummerfeld SK , Pereira-Leal JB , Nilsson D , Peterson J , Salzberg SL , Shallom J , Silva JC , Sundaram J , Westenberger S , White O , Melville SE , Donelson JE , Andersson B , Stuart KD , Hall N
Ref : Science , 309 :404 , 2005
Abstract : A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that-along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions-have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.
ESTHER : El-Sayed_2005_Science_309_404
PubMedSearch : El-Sayed_2005_Science_309_404
PubMedID: 16020724
Gene_locus related to this paper: tryb2-q382c1 , trycr-q4dhv2 , trycr-q4dpt2 , trycr-q4dpy4

Title : Genome sequence of the human malaria parasite Plasmodium falciparum - Gardner_2002_Nature_419_498
Author(s) : Gardner MJ , Hall N , Fung E , White O , Berriman M , Hyman RW , Carlton JM , Pain A , Nelson KE , Bowman S , Paulsen IT , James K , Eisen JA , Rutherford K , Salzberg SL , Craig A , Kyes S , Chan MS , Nene V , Shallom SJ , Suh B , Peterson J , Angiuoli S , Pertea M , Allen J , Selengut J , Haft D , Mather MW , Vaidya AB , Martin DM , Fairlamb AH , Fraunholz MJ , Roos DS , Ralph SA , McFadden GI , Cummings LM , Subramanian GM , Mungall C , Venter JC , Carucci DJ , Hoffman SL , Newbold C , Davis RW , Fraser CM , Barrell B
Ref : Nature , 419 :498 , 2002
Abstract : The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host-parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria.
ESTHER : Gardner_2002_Nature_419_498
PubMedSearch : Gardner_2002_Nature_419_498
PubMedID: 12368864
Gene_locus related to this paper: plaf7-c0h4q4 , plaf7-q8i5y6 , plaf7-q8iik5 , plafa-PF10.0018 , plafa-PF10.0020 , plafa-PF10.0379 , plafa-PF11.0211 , plafa-PF11.0276 , plafa-PF11.0441 , plafa-PF14.0015 , plafa-PF14.0017 , plafa-PF14.0099 , plafa-PF14.0250 , plafa-PF14.0395 , plafa-PF14.0737 , plafa-PF14.0738 , plafa-PFL2530W

Title : Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14 - Gardner_2002_Nature_419_531
Author(s) : Gardner MJ , Shallom SJ , Carlton JM , Salzberg SL , Nene V , Shoaibi A , Ciecko A , Lynn J , Rizzo M , Weaver B , Jarrahi B , Brenner M , Parvizi B , Tallon L , Moazzez A , Granger D , Fujii C , Hansen C , Pederson J , Feldblyum T , Peterson J , Suh B , Angiuoli S , Pertea M , Allen J , Selengut J , White O , Cummings LM , Smith HO , Adams MD , Venter JC , Carucci DJ , Hoffman SL , Fraser CM
Ref : Nature , 419 :531 , 2002
Abstract : The mosquito-borne malaria parasite Plasmodium falciparum kills an estimated 0.7-2.7 million people every year, primarily children in sub-Saharan Africa. Without effective interventions, a variety of factors-including the spread of parasites resistant to antimalarial drugs and the increasing insecticide resistance of mosquitoes-may cause the number of malaria cases to double over the next two decades. To stimulate basic research and facilitate the development of new drugs and vaccines, the genome of Plasmodium falciparum clone 3D7 has been sequenced using a chromosome-by-chromosome shotgun strategy. We report here the nucleotide sequences of chromosomes 10, 11 and 14, and a re-analysis of the chromosome 2 sequence. These chromosomes represent about 35% of the 23-megabase P. falciparum genome.
ESTHER : Gardner_2002_Nature_419_531
PubMedSearch : Gardner_2002_Nature_419_531
PubMedID: 12368868
Gene_locus related to this paper: plafa-MAL3P8.11

Title : Complete genome sequence of a virulent isolate of Streptococcus pneumoniae - Tettelin_2001_Science_293_498
Author(s) : Tettelin H , Nelson KE , Paulsen IT , Eisen JA , Read TD , Peterson S , Heidelberg J , DeBoy RT , Haft DH , Dodson RJ , Durkin AS , Gwinn M , Kolonay JF , Nelson WC , Peterson JD , Umayam LA , White O , Salzberg SL , Lewis MR , Radune D , Holtzapple E , Khouri H , Wolf AM , Utterback TR , Hansen CL , McDonald LA , Feldblyum TV , Angiuoli S , Dickinson T , Hickey EK , Holt IE , Loftus BJ , Yang F , Smith HO , Venter JC , Dougherty BA , Morrison DA , Hollingshead SK , Fraser CM
Ref : Science , 293 :498 , 2001
Abstract : The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines provide a substantial source of carbon and nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several surface-exposed proteins that may serve as potential vaccine candidates were identified. Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity.
ESTHER : Tettelin_2001_Science_293_498
PubMedSearch : Tettelin_2001_Science_293_498
PubMedID: 11463916
Gene_locus related to this paper: strp2-q04l35 , strpj-b8zns7 , strpn-AXE1 , strpn-b2dz20 , strpn-pepx , strpn-SP0614 , strpn-SP0666 , strpn-SP0777 , strpn-SP0902 , strpn-SP1343