Fedorova ND

References (3)

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 : Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum - van den Berg_2008_Nat.Biotechnol_26_1161
Author(s) : van den Berg MA , Albang R , Albermann K , Badger JH , Daran JM , Driessen AJ , Garcia-Estrada C , Fedorova ND , Harris DM , Heijne WH , Joardar V , Kiel JA , Kovalchuk A , Martin JF , Nierman WC , Nijland JG , Pronk JT , Roubos JA , van der Klei IJ , van Peij NN , Veenhuis M , von Dohren H , Wagner C , Wortman J , Bovenberg RA
Ref : Nat Biotechnol , 26 :1161 , 2008
Abstract : Industrial penicillin production with the filamentous fungus Penicillium chrysogenum is based on an unprecedented effort in microbial strain improvement. To gain more insight into penicillin synthesis, we sequenced the 32.19 Mb genome of P. chrysogenum Wisconsin54-1255 and identified numerous genes responsible for key steps in penicillin production. DNA microarrays were used to compare the transcriptomes of the sequenced strain and a penicillinG high-producing strain, grown in the presence and absence of the side-chain precursor phenylacetic acid. Transcription of genes involved in biosynthesis of valine, cysteine and alpha-aminoadipic acid-precursors for penicillin biosynthesis-as well as of genes encoding microbody proteins, was increased in the high-producing strain. Some gene products were shown to be directly controlling beta-lactam output. Many key cellular transport processes involving penicillins and intermediates remain to be characterized at the molecular level. Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven metabolic engineering.
ESTHER : van den Berg_2008_Nat.Biotechnol_26_1161
PubMedSearch : van den Berg_2008_Nat.Biotechnol_26_1161
PubMedID: 18820685
Gene_locus related to this paper: pench-b6gw01 , pench-b6gwp9 , pench-b6gzt9 , pench-b6h2r5 , pench-b6h3c6 , pench-b6h3s3 , pench-b6h6w7 , pench-b6h7m0 , pench-b6h043 , pench-b6h270 , pench-b6h303 , pench-b6hcx0 , pench-b6hfx1 , pench-b6hjt6 , pench-b6hm64 , pench-b6hmg2 , pench-b6hnf2 , pench-b6hnf7 , pench-b6hph0 , pench-b6huc9 , penrw-b6hdc6 , pench-q3v6c9 , pencw-atg15 , pencw-b6gwt5 , pencw-b6gx34 , pencw-b6gzd8 , pencw-b6gzp7 , pencw-b6h2f4 , pencw-b6h2h0 , pencw-b6h2n4 , pencw-b6h3u7 , pencw-b6h4n3 , pencw-b6h4s6 , pencw-b6h5k2 , pencw-b6h6t6 , pencw-b6h7f0 , pencw-b6h7r1 , pencw-b6h8a0 , pencw-b6h8i1 , pencw-b6h828 , pencw-b6ha41 , pencw-b6hat0 , pencw-b6hb79 , pencw-b6hcq8 , pencw-b6hfx7 , pencw-b6hgb0 , pencw-b6hhg8 , pencw-b6hjj1 , pencw-b6hl02 , pencw-b6hmd9 , pencw-b6hmh5 , pencw-b6hmh7 , pencw-b6hpn2 , pencw-b6hpz6 , pencw-b6hqu4 , pencw-b6hs49 , pencw-b6hun6 , pencw-b6hv09 , pencw-cuti1 , pencw-cuti2 , pencw-dapb , pencw-b6had0 , pencw-b6h497 , pencw-b6gw76 , pencw-b6hs05 , pencw-b6h0h6 , penna-a0a1v6yep8 , penrw-b6huu8 , penrw-kex1 , penrw-cbpya , penrw-adrd

Title : Genome sequencing and analysis of Aspergillus oryzae - Machida_2005_Nature_438_1157
Author(s) : Machida M , Asai K , Sano M , Tanaka T , Kumagai T , Terai G , Kusumoto K , Arima T , Akita O , Kashiwagi Y , Abe K , Gomi K , Horiuchi H , Kitamoto K , Kobayashi T , Takeuchi M , Denning DW , Galagan JE , Nierman WC , Yu J , Archer DB , Bennett JW , Bhatnagar D , Cleveland TE , Fedorova ND , Gotoh O , Horikawa H , Hosoyama A , Ichinomiya M , Igarashi R , Iwashita K , Juvvadi PR , Kato M , Kato Y , Kin T , Kokubun A , Maeda H , Maeyama N , Maruyama J , Nagasaki H , Nakajima T , Oda K , Okada K , Paulsen I , Sakamoto K , Sawano T , Takahashi M , Takase K , Terabayashi Y , Wortman JR , Yamada O , Yamagata Y , Anazawa H , Hata Y , Koide Y , Komori T , Koyama Y , Minetoki T , Suharnan S , Tanaka A , Isono K , Kuhara S , Ogasawara N , Kikuchi H
Ref : Nature , 438 :1157 , 2005
Abstract : The genome of Aspergillus oryzae, a fungus important for the production of traditional fermented foods and beverages in Japan, has been sequenced. The ability to secrete large amounts of proteins and the development of a transformation system have facilitated the use of A. oryzae in modern biotechnology. Although both A. oryzae and Aspergillus flavus belong to the section Flavi of the subgenus Circumdati of Aspergillus, A. oryzae, unlike A. flavus, does not produce aflatoxin, and its long history of use in the food industry has proved its safety. Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans and Aspergillus fumigatus. Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae-specific blocks (lacking synteny with A. nidulans and A. fumigatus) in a mosaic manner throughout the genome of A. oryzae. The blocks of A. oryzae-specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.
ESTHER : Machida_2005_Nature_438_1157
PubMedSearch : Machida_2005_Nature_438_1157
PubMedID: 16372010
Gene_locus related to this paper: aspor-Q2U722 , aspfn-b8mvx2 , aspfn-b8mwk1 , aspfn-b8n1a4 , aspfn-b8n5l3 , aspfn-b8n7y0 , aspfn-b8n829 , aspfn-b8ncj5 , aspfn-b8nhj9 , aspfn-b8njx6 , aspfn-b8nsk2 , aspfu-q4wj61 , aspor-axe1 , aspor-CPI , aspor-cutas , aspor-cuti2 , aspor-DPPIV , aspor-faec , aspor-MDLB , aspor-ppme1 , aspor-q2tw11 , aspor-q2tw16 , aspor-q2tw28 , aspor-q2twc4 , aspor-q2twg0 , aspor-q2twj3 , aspor-q2twv2 , aspor-q2twv4 , aspor-q2tx21 , aspor-q2txq8 , aspor-q2tya1 , aspor-q2tyh6 , aspor-q2tyn9 , aspor-q2typ0 , aspor-q2tyq4 , aspor-q2tyv8 , aspor-q2tz03 , aspor-q2tzh3 , aspor-q2tzr5 , aspor-q2tzv9 , aspor-q2u0k7 , aspor-q2u0q2 , aspor-q2u0r6 , aspor-q2u1a5 , aspor-q2u1a6 , aspor-q2u1k0 , aspor-q2u1k8 , aspor-q2u1m8 , aspor-q2u2a1 , aspor-q2u2a4 , aspor-q2u3a3 , aspor-q2u3a6 , aspor-q2u3k5 , aspor-q2u3l6 , aspor-q2u4a0 , aspor-q2u4e0 , aspor-q2u4f6 , aspor-q2u4g6 , aspor-q2u4h9 , aspor-q2u4w9 , aspor-q2u4y8 , aspor-q2u5f5 , aspor-q2u5n3 , aspor-q2u5y8 , aspor-q2u6h7 , aspor-q2u6j5 , aspor-q2u6m8 , aspor-q2u6m9 , aspor-q2u6n6 , aspor-q2u7i2 , aspor-q2u7v0 , aspor-q2u8j8 , aspor-q2u8r1 , aspor-q2u8r4 , aspor-q2u8t5 , aspor-q2u8z3 , aspor-q2u9a1 , aspor-q2u9n5 , aspor-q2u144 , aspor-q2u161 , aspor-q2u185 , aspor-q2u199 , aspor-q2u212 , aspor-q2u331 , aspor-q2u348 , aspor-q2u400 , aspor-q2u453 , aspor-q2u489 , aspor-q2u704 , aspor-q2u728 , aspor-q2u798 , aspor-q2u822 , aspor-q2u854 , aspor-q2u875 , aspor-q2u908 , aspor-q2ua10 , aspor-q2ua48 , aspor-q2uab6 , aspor-q2uak9 , aspor-q2uaq4 , aspor-q2ub32 , aspor-q2ub76 , aspor-q2uba1 , aspor-q2ubd6 , aspor-q2ubm2 , aspor-q2ubr2 , aspor-q2uc28 , aspor-q2uc65 , aspor-q2uc77 , aspor-q2uc98 , aspor-q2uck0 , aspor-q2ucy7 , aspor-q2ud03 , aspor-q2ud06 , aspor-q2ud08 , aspor-q2ud23 , aspor-q2udn5 , aspor-q2udr0 , aspor-q2uec1 , aspor-q2uef3 , aspor-q2uf10 , aspor-q2uf27 , aspor-q2uf48 , aspor-q2ufd8 , aspor-q2ufe5 , aspor-q2ufm4 , aspor-q2ufr3 , aspor-q2ufz8 , aspor-q2ug78 , aspor-q2ugd6 , aspor-q2uge1 , aspor-q2ugg7 , aspor-q2ugi2 , aspor-q2ugl2 , aspor-q2ugy9 , aspor-q2uh24 , aspor-q2uh73 , aspor-q2uhe4 , aspor-q2uhf0 , aspor-q2uhj6 , aspor-q2uhn1 , aspor-q2uhq0 , aspor-q2ui56 , aspor-q2uib2 , aspor-q2uib5 , aspor-q2uie9 , aspor-q2uih1 , aspor-q2uii1 , aspor-q2uik9 , aspor-q2uiq0 , aspor-q2uiu1 , aspor-q2uix9 , aspor-q2uiy5 , aspor-q2uiz4 , aspor-q2uj89 , aspor-q2uja2 , aspor-q2uju3 , aspor-q2uk31 , aspor-q2uk42 , aspor-q2ukb6 , aspor-q2ukq7 , aspor-q2ul81 , aspor-q2uli9 , aspor-q2ulr2 , aspor-q2ulv7 , aspor-q2umf3 , aspor-q2umv2 , aspor-q2umx6 , aspor-q2unw5 , aspor-q2up23 , aspor-q2up89 , aspor-q2upe6 , aspor-q2upi1 , aspor-q2upl1 , aspor-q2upw4 , aspor-q2uq56 , aspor-q2uqb4 , aspor-q2uqm7 , aspor-q2ur58 , aspor-q2ur64 , aspor-q2ur80 , aspor-q2ur83 , aspor-q2ure7 , aspor-q2urf3 , aspor-q2urg5 , aspor-q2urq0 , aspor-q2urt4 , aspor-q2uru5 , aspor-q2usi0 , aspor-q2usp7 , aspor-q2usq8 , aspor-q2usv6 , aspor-q2uta5 , aspor-q2uu89 , aspor-q2uub4 , aspor-q2uux8 , aspor-q2uv29 , aspor-TGLA , aspor-q2ue03 , aspor-q2uj83 , aspno-a0a0l1j1c9