Ram AF

References (4)

Title : Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus - de Vries_2017_Genome.Biol_18_28
Author(s) : de Vries RP , Riley R , Wiebenga A , Aguilar-Osorio G , Amillis S , Uchima CA , Anderluh G , Asadollahi M , Askin M , Barry K , Battaglia E , Bayram O , Benocci T , Braus-Stromeyer SA , Caldana C , Canovas D , Cerqueira GC , Chen F , Chen W , Choi C , Clum A , Dos Santos RA , Damasio AR , Diallinas G , Emri T , Fekete E , Flipphi M , Freyberg S , Gallo A , Gournas C , Habgood R , Hainaut M , Harispe ML , Henrissat B , Hilden KS , Hope R , Hossain A , Karabika E , Karaffa L , Karanyi Z , Krasevec N , Kuo A , Kusch H , LaButti K , Lagendijk EL , Lapidus A , Levasseur A , Lindquist E , Lipzen A , Logrieco AF , Maccabe A , Makela MR , Malavazi I , Melin P , Meyer V , Mielnichuk N , Miskei M , Molnar AP , Mule G , Ngan CY , Orejas M , Orosz E , Ouedraogo JP , Overkamp KM , Park HS , Perrone G , Piumi F , Punt PJ , Ram AF , Ramon A , Rauscher S , Record E , Riano-Pachon DM , Robert V , Rohrig J , Ruller R , Salamov A , Salih NS , Samson RA , Sandor E , Sanguinetti M , Schutze T , Sepcic K , Shelest E , Sherlock G , Sophianopoulou V , Squina FM , Sun H , Susca A , Todd RB , Tsang A , Unkles SE , van de Wiele N , van Rossen-Uffink D , Oliveira JV , Vesth TC , Visser J , Yu JH , Zhou M , Andersen MR , Archer DB , Baker SE , Benoit I , Brakhage AA , Braus GH , Fischer R , Frisvad JC , Goldman GH , Houbraken J , Oakley B , Pocsi I , Scazzocchio C , Seiboth B , vanKuyk PA , Wortman J , Dyer PS , Grigoriev IV
Ref : Genome Biol , 18 :28 , 2017
Abstract : BACKGROUND: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS: We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. CONCLUSIONS: Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.
ESTHER : de Vries_2017_Genome.Biol_18_28
PubMedSearch : de Vries_2017_Genome.Biol_18_28
PubMedID: 28196534
Gene_locus related to this paper: asptu-a0a1l9nhd0 , aspve-a0a1l9pxx8 , aspve-a0a1l9q4m3 , aspwe-a0a1l9s133 , 9euro-a0a1l9t3v9 , aspwe-a0a1l9rcx6 , aspna-g3y5a6 , aspgl-a0a1l9v4d3 , 9euro-a0a1l9sa36 , aspsb-a0a319eji6 , aspve-a0a1l9px96 , 9euro-a0a1l9tay1 , aspgl-a0a1l9vbc0 , aspc5-a0a1r3rh65 , 9euro-a0a2v5i956 , aspwe-a0a1l9rpp6 , aspna-g3xpw9 , aspve-a0a1l9plv1 , 9euro-a0a1l9tk47 , aspve-a0a1l9pde9 , aspve-a0a1l9pz72 , aspwe-a0a1l9rde6 , 9euro-a0a1l9tdb5 , aspkw-g7xq95 , aspbc-a0a1l9u6h4 , aspbc-a0a1l9u2l4 , asptc-a0a1l9mx83 , aspgl-a0a1l9ve90 , aspve-a0a1l9pvz9 , 9euro-a0a1l9tdh3 , aspc5-a0a1r3rmn9 , aspwe-a0a1l9rlq2 , asptc-a0a1l9nby7 , aspng-a0a100i8t9 , aspc5-a0a1r3rem6 , aspbc-a0a1l9uy89 , aspa1-anee , aspa1-aneh , aspa1-acrc , aspbc-alba , aspa1-acui

Title : The 2008 update of the Aspergillus nidulans genome annotation: a community effort - Wortman_2009_Fungal.Genet.Biol_46 Suppl 1_S2
Author(s) : Wortman JR , Gilsenan JM , Joardar V , Deegan J , Clutterbuck J , Andersen MR , Archer D , Bencina M , Braus G , Coutinho P , von Dohren H , Doonan J , Driessen AJ , Durek P , Espeso E , Fekete E , Flipphi M , Estrada CG , Geysens S , Goldman G , de Groot PW , Hansen K , Harris SD , Heinekamp T , Helmstaedt K , Henrissat B , Hofmann G , Homan T , Horio T , Horiuchi H , James S , Jones M , Karaffa L , Karanyi Z , Kato M , Keller N , Kelly DE , Kiel JA , Kim JM , van der Klei IJ , Klis FM , Kovalchuk A , Krasevec N , Kubicek CP , Liu B , Maccabe A , Meyer V , Mirabito P , Miskei M , Mos M , Mullins J , Nelson DR , Nielsen J , Oakley BR , Osmani SA , Pakula T , Paszewski A , Paulsen I , Pilsyk S , Pocsi I , Punt PJ , Ram AF , Ren Q , Robellet X , Robson G , Seiboth B , van Solingen P , Specht T , Sun J , Taheri-Talesh N , Takeshita N , Ussery D , vanKuyk PA , Visser H , van de Vondervoort PJ , de Vries RP , Walton J , Xiang X , Xiong Y , Zeng AP , Brandt BW , Cornell MJ , van den Hondel CA , Visser J , Oliver SG , Turner G
Ref : Fungal Genet Biol , 46 Suppl 1 :S2 , 2009
Abstract : The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology.
ESTHER : Wortman_2009_Fungal.Genet.Biol_46 Suppl 1_S2
PubMedSearch : Wortman_2009_Fungal.Genet.Biol_46 Suppl 1_S2
PubMedID: 19146970
Gene_locus related to this paper: emeni-axe1 , emeni-c8v4m7 , emeni-faec , emeni-ppme1 , emeni-q5ara9 , emeni-q5arf0 , emeni-q5as30 , emeni-q5ase8 , emeni-q5av79 , emeni-q5aw09 , emeni-q5awc3 , emeni-q5awc7 , emeni-q5awu9 , emeni-q5aww4 , emeni-q5ax50 , emeni-q5ay37 , emeni-q5ay57 , emeni-q5ay59 , emeni-q5ayk9 , emeni-q5ays5 , emeni-q5az32 , emeni-q5az91 , emeni-q5az97 , emeni-q5azp1 , emeni-q5b0i6 , emeni-q5b1h2 , emeni-q5b2a9 , emeni-q5b2p7 , emeni-q5b3d2 , emeni-q5b4q7 , emeni-q5b5u7 , emeni-q5b5y4 , emeni-q5b9e7 , emeni-q5b9i0 , emeni-q5b364 , emeni-q5b446 , emeni-q5b938 , emeni-q5ba78 , emeni-q5bcd1 , emeni-q5bcd2 , emeni-q5bde7 , emeni-q5bdr0 , emeni-q5bf92 , emeni-q7si80 , emeni-q5bdv9 , emeni-c8vu15 , 9euro-a0a3d8t644 , emeni-q5b719 , emeni-q5ax97 , emeni-tdia , emeni-afoc , emeni-dbae

Title : Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88 - Pel_2007_Nat.Biotechnol_25_221
Author(s) : Pel HJ , de Winde JH , Archer DB , Dyer PS , Hofmann G , Schaap PJ , Turner G , de Vries RP , Albang R , Albermann K , Andersen MR , Bendtsen JD , Benen JA , van den Berg M , Breestraat S , Caddick MX , Contreras R , Cornell M , Coutinho PM , Danchin EG , Debets AJ , Dekker P , van Dijck PW , van Dijk A , Dijkhuizen L , Driessen AJ , d'Enfert C , Geysens S , Goosen C , Groot GS , de Groot PW , Guillemette T , Henrissat B , Herweijer M , van den Hombergh JP , van den Hondel CA , van der Heijden RT , van der Kaaij RM , Klis FM , Kools HJ , Kubicek CP , van Kuyk PA , Lauber J , Lu X , van der Maarel MJ , Meulenberg R , Menke H , Mortimer MA , Nielsen J , Oliver SG , Olsthoorn M , Pal K , van Peij NN , Ram AF , Rinas U , Roubos JA , Sagt CM , Schmoll M , Sun J , Ussery D , Varga J , Vervecken W , van de Vondervoort PJ , Wedler H , Wosten HA , Zeng AP , van Ooyen AJ , Visser J , Stam H
Ref : Nat Biotechnol , 25 :221 , 2007
Abstract : The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.
ESTHER : Pel_2007_Nat.Biotechnol_25_221
PubMedSearch : Pel_2007_Nat.Biotechnol_25_221
PubMedID: 17259976
Gene_locus related to this paper: aspna-g3yal2 , aspnc-a2q8r7 , aspnc-a2q814 , aspnc-a2qb93 , aspnc-a2qbd3 , aspnc-a2qbh3 , aspnc-a2qbx7 , aspnc-a2qdj6 , aspnc-a2qe77 , aspnc-a2qf54 , aspnc-a2qfe9 , aspnc-a2qg33 , aspnc-a2qgj6 , aspnc-a2qgm6 , aspnc-a2qh52 , aspnc-a2qh76 , aspnc-a2qh85 , aspnc-a2qhe2 , aspnc-a2qi32 , aspnc-a2qib2 , aspnc-a2qk14 , aspnc-a2ql23 , aspnc-a2ql89 , aspnc-a2ql90 , aspnc-a2qla0 , aspnc-a2qlz0 , aspnc-a2qm14 , aspnc-a2qmk5 , aspnc-a2qms0 , aspnc-a2qn29 , aspnc-a2qn56 , aspnc-a2qn70 , aspnc-a2qnw9 , aspnc-a2qr21 , aspnc-a2qs22 , aspnc-a2qt50 , aspnc-a2qti9 , aspnc-a2qtz0 , aspnc-a2quc1 , aspnc-a2qw06 , aspnc-a2qwz6 , aspnc-a2qx92 , aspnc-a2qyf0 , aspnc-a2qys7 , aspnc-a2qz72 , aspnc-a2qzn6 , aspnc-a2qzr0 , aspnc-a2qzs1 , aspnc-a2qzx0 , aspnc-a2qzx4 , aspnc-a2r0p4 , aspnc-a2r0u0 , aspnc-a2r1p3 , aspnc-a2r1r5 , aspnc-a2r2i5 , aspnc-a2r2l0 , aspnc-a2r3s8 , aspnc-a2r4c0 , aspnc-a2r4j8 , aspnc-a2r5r4 , aspnc-a2r6g3 , aspnc-a2r6h5 , aspnc-a2r6h8 , aspnc-a2r7q1 , aspnc-a2r8r3 , aspnc-a2r8z3 , aspnc-a2r9y8 , aspnc-a2r032 , aspnc-a2r040 , aspnc-a2r273 , aspnc-a2r496 , aspnc-a2r502 , aspnc-a2ra07 , aspnc-a2rap4 , aspnc-a2raq2 , aspnc-a2rav1 , aspnc-a5aaf4 , aspnc-a5ab63 , aspnc-a5abc6 , aspnc-a5abe5 , aspnc-a5abe8 , aspnc-a5abf0 , aspnc-a5abh9 , aspnc-a5abk1 , aspnc-a5abt2 , aspnc-a5abz1 , aspnc-atg15 , aspnc-axe1 , aspnc-cuti1 , aspnc-cuti2 , aspnc-faec , aspng-a2q8w0 , aspng-a2qs46 , aspng-a2qst4 , aspng-a2qv27 , aspng-a2qzk9 , aspng-a2r0p8 , aspng-a2r225 , aspng-DAPB , aspng-DPP5 , aspng-faeb , aspni-APSC , aspni-EstA , aspni-FAEA , aspni-PAPA , aspkw-g7y0v7 , aspnc-a2qt47 , aspnc-a2qt66 , aspnc-a2r199 , aspnc-a2r871 , aspnc-a2qbp6 , aspnc-a2qqa1 , aspnc-a2qt70 , aspna-g3y5a6 , aspna-g3xpw9 , aspnc-a2qw57 , aspaw-a0a401kcz4 , aspna-alba , aspnc-kex1 , aspnc-cbpya , aspnc-a2qbg8

Title : Large scale identification of genes involved in cell surface biosynthesis and architecture in Saccharomyces cerevisiae - Lussier_1997_Genetics_147_435
Author(s) : Lussier M , White AM , Sheraton J , di Paolo T , Treadwell J , Southard SB , Horenstein CI , Chen-Weiner J , Ram AF , Kapteyn JC , Roemer TW , Vo DH , Bondoc DC , Hall J , Zhong WW , Sdicu AM , Davies J , Klis FM , Robbins PW , Bussey H
Ref : Genetics , 147 :435 , 1997
Abstract : The sequenced yeast genome offers a unique resource for the analysis of eukaryotic cell function and enables genome-wide screens for genes involved in cellular processes. We have identified genes involved in cell surface assembly by screening transposon-mutagenized cells for altered sensitivity to calcofluor white, followed by supplementary screens to further characterize mutant phenotypes. The mutated genes were directly retrieved from genomic DNA and then matched uniquely to a gene in the yeast genome database. Eighty-two genes with apparent perturbation of the cell surface were identified, with mutations in 65 of them displaying at least one further cell surface phenotype in addition to their modified sensitivity to calcofluor. Fifty of these genes were previously known, 17 encoded proteins whose function could be anticipated through sequence homology or previously recognized phenotypes and 15 genes had no previously known phenotype.
ESTHER : Lussier_1997_Genetics_147_435
PubMedSearch : Lussier_1997_Genetics_147_435
PubMedID: 9335584
Gene_locus related to this paper: yeast-ECM18