Danchin EG

References (8)

Title : Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea - Amselem_2011_PLoS.Genet_7_e1002230
Author(s) : Amselem J , Cuomo CA , van Kan JA , Viaud M , Benito EP , Couloux A , Coutinho PM , de Vries RP , Dyer PS , Fillinger S , Fournier E , Gout L , Hahn M , Kohn L , Lapalu N , Plummer KM , Pradier JM , Quevillon E , Sharon A , Simon A , ten Have A , Tudzynski B , Tudzynski P , Wincker P , Andrew M , Anthouard V , Beever RE , Beffa R , Benoit I , Bouzid O , Brault B , Chen Z , Choquer M , Collemare J , Cotton P , Danchin EG , Da Silva C , Gautier A , Giraud C , Giraud T , Gonzalez C , Grossetete S , Guldener U , Henrissat B , Howlett BJ , Kodira C , Kretschmer M , Lappartient A , Leroch M , Levis C , Mauceli E , Neuveglise C , Oeser B , Pearson M , Poulain J , Poussereau N , Quesneville H , Rascle C , Schumacher J , Segurens B , Sexton A , Silva E , Sirven C , Soanes DM , Talbot NJ , Templeton M , Yandava C , Yarden O , Zeng Q , Rollins JA , Lebrun MH , Dickman M
Ref : PLoS Genet , 7 :e1002230 , 2011
Abstract : Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
ESTHER : Amselem_2011_PLoS.Genet_7_e1002230
PubMedSearch : Amselem_2011_PLoS.Genet_7_e1002230
PubMedID: 21876677
Gene_locus related to this paper: botci-cutas , botci-q6rki2 , botf4-g2y7k8 , botfb-dapb , botfu-g2xyd8 , botfu-g2ynh8 , scls1-a7e814 , scls1-a7edc9 , scls1-a7edh1 , scls1-a7emm0 , scls1-a7eti8 , scls1-a7eu48 , scls1-a7f208 , scls1-dapb , botf4-g2xqp7 , scls1-a7eqq8 , botf4-g2xqc6 , scls1-a7ebs4 , botf4-g2xn51 , scls1-a7f5m9 , botf4-g2xti4 , botf4-g2xtu7 , botf4-g2yfp1 , scls1-a7f534 , botf4-g2yys3 , scls1-a7erz9 , botf4-g2y037 , botf4-g2y0e1 , scls1-a7f706 , scls1-a7ewt6 , botf4-g2yuj6 , botf1-m7u3d1 , botf1-m7u430 , botf1-m7tei8 , botf1-m7u0w9 , botf1-m7tij6 , botf1-m7u819 , botf1-m7u6d8 , botf1-m7tzd4 , botf1-m7tqd7 , botf1-m7tyz9 , botf1-m7unl9 , botf1-m7u429 , botf1-m7u4s5 , botf1-m7ul92 , botf1-m7tx42 , botf1-m7u9h4 , botf1-m7u187 , botf1-m7uz64 , botf1-m7u4q4 , botf1-m7u2f6 , botf1-m7tt59 , botf1-m7v3h2 , botf1-m7u6c9 , botf1-m7tud9 , botf1-m7u309 , scls1-a7et87 , botf4-g2ylt4 , scls1-a7f5a0 , scls1-a7f900 , botf4-g2yib9 , scls1-a7f3m9 , scls1-a7er46 , botf4-g2y3y4 , botf4-g2xyy5 , botf1-m7uct5 , scls1-a7ea78 , scls1-kex1 , scls1-cbpya , botfb-cbpya , scls1-a7ecx1

Title : Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium - Ma_2010_Nature_464_367
Author(s) : Ma LJ , van der Does HC , Borkovich KA , Coleman JJ , Daboussi MJ , Di Pietro A , Dufresne M , Freitag M , Grabherr M , Henrissat B , Houterman PM , Kang S , Shim WB , Woloshuk C , Xie X , Xu JR , Antoniw J , Baker SE , Bluhm BH , Breakspear A , Brown DW , Butchko RA , Chapman S , Coulson R , Coutinho PM , Danchin EG , Diener A , Gale LR , Gardiner DM , Goff S , Hammond-Kosack KE , Hilburn K , Hua-Van A , Jonkers W , Kazan K , Kodira CD , Koehrsen M , Kumar L , Lee YH , Li L , Manners JM , Miranda-Saavedra D , Mukherjee M , Park G , Park J , Park SY , Proctor RH , Regev A , Ruiz-Roldan MC , Sain D , Sakthikumar S , Sykes S , Schwartz DC , Turgeon BG , Wapinski I , Yoder O , Young S , Zeng Q , Zhou S , Galagan J , Cuomo CA , Kistler HC , Rep M
Ref : Nature , 464 :367 , 2010
Abstract : Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.
ESTHER : Ma_2010_Nature_464_367
PubMedSearch : Ma_2010_Nature_464_367
PubMedID: 20237561
Gene_locus related to this paper: fusox-a0a1d3s5h0 , gibf5-fus2 , fusof-f9f2k2 , fusof-f9f3l6 , fusof-f9f6t8 , fusof-f9f6v2 , fusof-f9f132 , fusof-f9f781 , fusof-f9fd72 , fusof-f9fd90 , fusof-f9fem0 , fusof-f9fhk2 , fusof-f9fj19 , fusof-f9fj20 , fusof-f9fki8 , fusof-f9fmx2 , fusof-f9fnt4 , fusof-f9fpy4 , fusof-f9fvs6 , fusof-f9fwu0 , fusof-f9fxz4 , fusof-f9fzy5 , fusof-f9g2a2 , fusof-f9g3b1 , fusof-f9g5h7 , fusof-f9g6e6 , fusof-f9g6y7 , fusof-f9g7b0 , fusof-f9g797 , fusof-f9g972 , fusof-f9ga50 , fusof-f9gck4 , fusof-f9gd15 , gibze-a8w610 , gibze-b1pdn0 , gibze-i1r9e6 , gibze-i1rda9 , gibze-i1rdk7 , gibze-i1rec8 , gibze-i1rgs0 , gibze-i1rgy0 , gibze-i1rh52 , gibze-i1rhi8 , gibze-i1rig9 , gibze-i1rip5 , gibze-i1rpg6 , gibze-i1rsg2 , gibze-i1rv36 , gibze-i1rxm5 , gibze-i1rxp8 , gibze-i1rxv5 , gibze-i1s1u3 , gibze-i1s3j9 , gibze-i1s6l7 , gibze-i1s8i8 , gibze-i1s9x4 , gibze-q4huy1 , gibze-i1rg17 , fuso4-j9mvr9 , fuso4-j9ngs6 , fuso4-j9niq8 , fuso4-j9nqm2 , gibze-i1rb76 , gibze-i1s1m7 , gibze-i1s3z6 , gibze-i1rd78 , gibze-i1rgl9 , gibze-i1rjp7 , gibze-i1s1q6 , gibze-i1ri35 , gibze-i1rf76 , gibze-i1rhp3 , fusc1-n4uj11 , fusc4-n1s9p6 , gibf5-s0dqr2 , gibm7-w7n1b5 , fusof-f9g6q0 , gibm7-w7n497 , fusox-x0bme4 , gibm7-w7mcf8 , gibm7-w7mak5 , fusox-x0a2c5 , gibm7-w7mum7 , fusox-w9iyc7 , gibm7-w7maw6 , gibm7-w7msi0 , gibm7-w7luf0 , gibm7-w7msa3 , gibm7-w7mna8 , gibm7-w7n8b7 , gibm7-w7n564 , fusox-w9jpi0 , gibm7-w7ngc3 , gibm7-w7m4v6 , gibm7-w7m4v2 , gibm7-w7lt61 , gibm7-w7mly6 , gibm7-w7ncn3 , fusox-w9ibd7 , fusof-f9fnm6 , gibm7-w7n526 , gibza-a0a016pda4 , gibza-a0a016pl96 , gibm7-w7muq1 , fusof-f9gfd3 , gibm7-w7mt52 , gibze-i1rjb5 , gibf5-s0ehu3 , fusox-w9hvf0 , gibze-i1rkc4 , gibm7-w7mv30 , gibze-a0a1c3ylb1 , fuso4-a0a0c4diy4 , gibm7-w7n4n0 , gibze-gra11 , gibze-fsl2 , gibf5-fub4 , gibf5-fub5 , gibf5-fus5 , gibm7-dlh1

Title : The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion - Coleman_2009_PLoS.Genet_5_e1000618
Author(s) : Coleman JJ , Rounsley SD , Rodriguez-Carres M , Kuo A , Wasmann CC , Grimwood J , Schmutz J , Taga M , White GJ , Zhou S , Schwartz DC , Freitag M , Ma LJ , Danchin EG , Henrissat B , Coutinho PM , Nelson DR , Straney D , Napoli CA , Barker BM , Gribskov M , Rep M , Kroken S , Molnar I , Rensing C , Kennell JC , Zamora J , Farman ML , Selker EU , Salamov A , Shapiro H , Pangilinan J , Lindquist E , Lamers C , Grigoriev IV , Geiser DM , Covert SF , Temporini E , Vanetten HD
Ref : PLoS Genet , 5 :e1000618 , 2009
Abstract : The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of >50 species known as the "Fusarium solani species complex". Members of this complex have diverse biological properties including the ability to cause disease on >100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6.52 Mb and that the physical size of the genome, 54.43 Mb, and the number of predicted genes, 15,707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin(s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches.
ESTHER : Coleman_2009_PLoS.Genet_5_e1000618
PubMedSearch : Coleman_2009_PLoS.Genet_5_e1000618
PubMedID: 19714214
Gene_locus related to this paper: fusso-cutas , nech7-c7yh18 , nech7-c7yir8 , nech7-c7yiz6 , nech7-c7yjl4 , nech7-c7yjp7 , nech7-c7yjq0 , nech7-c7ymg9 , nech7-c7ymv6 , nech7-c7yna5 , nech7-c7ynt6 , nech7-c7yq59 , nech7-c7yq86 , nech7-c7yqb0 , nech7-c7yqx3 , nech7-c7ysz7 , nech7-c7ysz8 , nech7-c7ytb2 , nech7-c7yum7 , nech7-c7yvb1 , nech7-c7yvb8 , nech7-c7yvf1 , nech7-c7yvq8 , nech7-c7yw21 , nech7-c7yx47 , nech7-c7yx92 , nech7-c7yxe7 , nech7-c7yxq5 , nech7-c7yxz4 , nech7-c7yy47 , nech7-c7yyj7 , nech7-c7yym7 , nech7-c7z0d7 , nech7-c7z0s1 , nech7-c7z1g9 , nech7-c7z1k9 , nech7-c7z2k4 , nech7-c7z2m9 , nech7-c7z2z2 , nech7-c7z3z3 , nech7-c7z4a4 , nech7-c7z5n1 , nech7-c7z5y2 , nech7-c7z6g5 , nech7-c7z7d0 , nech7-c7z7w8 , nech7-c7z8q7 , nech7-c7z9e7 , nech7-c7z073 , nech7-c7z354 , nech7-c7z389 , nech7-c7z688 , nech7-c7z855 , nech7-c7z987 , nech7-c7za94 , nech7-c7zah0 , nech7-c7zb79 , nech7-c7zbr8 , nech7-c7zcd1 , nech7-c7zdx8 , nech7-c7ze42 , nech7-c7ze84 , nech7-c7zed8 , nech7-c7zeh0 , nech7-c7zes2 , nech7-c7zgw2 , nech7-c7zha0 , nech7-c7zhy2 , nech7-c7zi55 , nech7-c7zig4 , nech7-c7zjg0 , nech7-c7zjv2 , nech7-c7zk96 , nech7-c7zkb5 , nech7-c7zkh4 , nech7-c7zla9 , nech7-c7zld2 , nech7-c7zlz1 , nech7-c7zm00 , nech7-c7zmn4 , nech7-c7zmu6 , nech7-c7zp06 , nech7-c7zp78 , nech7-c7zq58 , nech7-c7zq86 , nech7-c7zqb5 , nech7-c7zqk4 , nech7-c7zqp9 , nech7-c7zr59 , nech7-c7zrh2 , nech7-c7zrh3 , nech7-dapb , nech7-kex1 , nech7-c7zgl9 , nech7-c7z935 , nech7-c7znc0 , nech7-c7yiq8 , nech7-c7yiq7 , nech7-c7zhu0 , nech7-c7yw61 , nech7-c7yqd3 , nech7-c7zkb6 , nech7-c7z3b4 , nech7-c7ytr4 , nech7-c7zgf7 , 9hypo-a0a3m2s2j6 , nech7-c7yq54 , fusv7-cbpya

Title : The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis - Martin_2008_Nature_452_88
Author(s) : Martin F , Aerts A , Ahren D , Brun A , Danchin EG , Duchaussoy F , Gibon J , Kohler A , Lindquist E , Pereda V , Salamov A , Shapiro HJ , Wuyts J , Blaudez D , Buee M , Brokstein P , Canback B , Cohen D , Courty PE , Coutinho PM , Delaruelle C , Detter JC , Deveau A , Difazio S , Duplessis S , Fraissinet-Tachet L , Lucic E , Frey-Klett P , Fourrey C , Feussner I , Gay G , Grimwood J , Hoegger PJ , Jain P , Kilaru S , Labbe J , Lin YC , Legue V , Le Tacon F , Marmeisse R , Melayah D , Montanini B , Muratet M , Nehls U , Niculita-Hirzel H , Oudot-Le Secq MP , Peter M , Quesneville H , Rajashekar B , Reich M , Rouhier N , Schmutz J , Yin T , Chalot M , Henrissat B , Kues U , Lucas S , Van de Peer Y , Podila GK , Polle A , Pukkila PJ , Richardson PM , Rouze P , Sanders IR , Stajich JE , Tunlid A , Tuskan G , Grigoriev IV
Ref : Nature , 452 :88 , 2008
Abstract : Mycorrhizal symbioses--the union of roots and soil fungi--are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains approximately 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
ESTHER : Martin_2008_Nature_452_88
PubMedSearch : Martin_2008_Nature_452_88
PubMedID: 18322534
Gene_locus related to this paper: lacbs-b0cns1 , lacbs-b0cpl4 , lacbs-b0cr62 , lacbs-b0cr66 , lacbs-b0csq9 , lacbs-b0ct56 , lacbs-b0ctt5 , lacbs-b0cuw1 , lacbs-b0cv23 , lacbs-b0cxm7 , lacbs-b0cz37 , lacbs-b0czx3 , lacbs-b0d0z5 , lacbs-b0d4i0 , lacbs-b0d4j3 , lacbs-b0d5n6 , lacbs-b0d8k0 , lacbs-b0d263 , lacbs-b0dhh1 , lacbs-b0dkp6 , lacbs-b0dmr2 , lacbs-b0dmt4 , lacbs-b0dsx5 , lacbs-b0dt05 , lacbs-b0dtw4 , lacbs-b0du88 , lacbs-b0dsl6

Title : The genome sequence of the model ascomycete fungus Podospora anserina - Espagne_2008_Genome.Biol_9_R77
Author(s) : Espagne E , Lespinet O , Malagnac F , Da Silva C , Jaillon O , Porcel BM , Couloux A , Aury JM , Segurens B , Poulain J , Anthouard V , Grossetete S , Khalili H , Coppin E , Dequard-Chablat M , Picard M , Contamine V , Arnaise S , Bourdais A , Berteaux-Lecellier V , Gautheret D , de Vries RP , Battaglia E , Coutinho PM , Danchin EG , Henrissat B , Khoury RE , Sainsard-Chanet A , Boivin A , Pinan-Lucarre B , Sellem CH , Debuchy R , Wincker P , Weissenbach J , Silar P
Ref : Genome Biol , 9 :R77 , 2008
Abstract : BACKGROUND: The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development. RESULTS: We present a 10X draft sequence of P. anserina genome, linked to the sequences of a large expressed sequence tag collection. Similar to higher eukaryotes, the P. anserina transcription/splicing machinery generates numerous non-conventional transcripts. Comparison of the P. anserina genome and orthologous gene set with the one of its close relatives, Neurospora crassa, shows that synteny is poorly conserved, the main result of evolution being gene shuffling in the same chromosome. The P. anserina genome contains fewer repeated sequences and has evolved new genes by duplication since its separation from N. crassa, despite the presence of the repeat induced point mutation mechanism that mutates duplicated sequences. We also provide evidence that frequent gene loss took place in the lineages leading to P. anserina and N. crassa. P. anserina contains a large and highly specialized set of genes involved in utilization of natural carbon sources commonly found in its natural biotope. It includes genes potentially involved in lignin degradation and efficient cellulose breakdown. CONCLUSION: The features of the P. anserina genome indicate a highly dynamic evolution since the divergence of P. anserina and N. crassa, leading to the ability of the former to use specific complex carbon sources that match its needs in its natural biotope.
ESTHER : Espagne_2008_Genome.Biol_9_R77
PubMedSearch : Espagne_2008_Genome.Biol_9_R77
PubMedID: 18460219
Gene_locus related to this paper: podan-b2a8u1 , podan-b2a9c4 , podan-b2a9k6 , podan-b2aa90 , podan-b2ab33 , podan-b2abs0 , podan-b2ac17 , podan-b2ack2 , podan-b2ad07 , podan-b2adj6 , podan-b2adk0 , podan-b2ae59 , podan-b2aee7 , podan-b2af51 , podan-b2afn5 , podan-b2afu6 , podan-b2akq7 , podan-b2aly0 , podan-b2am11 , podan-b2an24 , podan-b2ank1 , podan-b2apa8 , podan-b2api8 , podan-b2apj6 , podan-b2arl9 , podan-b2arz7 , podan-b2ase4 , podan-b2atn0 , podan-b2au46 , podan-b2aun9 , podan-b2av47 , podan-b2ava6 , podan-b2avm3 , podan-b2avu5 , podan-b2avx3 , podan-b2awk8 , podan-b2axk2 , podan-b2axz2 , podan-b2b1p7 , podan-b2b5e4 , podan-b2b6n7 , podan-b2b069 , podan-b2b073 , podan-b2b395 , podan-dapb , podan-b2afr0 , podan-b2a9k8 , podan-b2atb3 , podan-b2aca3 , podan-b2arv3 , podan-b2ank5 , podan-b2ax54 , podan-b2ad56 , podan-b2anm1 , podan-b2aya1 , podan-b2b164 , podan-a0a090d4h4 , podan-a0a090ccl8 , podan-b2b5p4 , podan-b2azp1 , podan-b2af75 , podan-b2alm5 , podan-b2ass5 , podan-b2aez8 , podan-kex1 , podan-cbpya

Title : Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina) - Martinez_2008_Nat.Biotechnol_26_553
Author(s) : Martinez D , Berka RM , Henrissat B , Saloheimo M , Arvas M , Baker SE , Chapman J , Chertkov O , Coutinho PM , Cullen D , Danchin EG , Grigoriev IV , Harris P , Jackson M , Kubicek CP , Han CS , Ho I , Larrondo LF , de Leon AL , Magnuson JK , Merino S , Misra M , Nelson B , Putnam N , Robbertse B , Salamov AA , Schmoll M , Terry A , Thayer N , Westerholm-Parvinen A , Schoch CL , Yao J , Barabote R , Nelson MA , Detter C , Bruce D , Kuske CR , Xie G , Richardson P , Rokhsar DS , Lucas SM , Rubin EM , Dunn-Coleman N , Ward M , Brettin TS
Ref : Nat Biotechnol , 26 :553 , 2008
Abstract : Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.
ESTHER : Martinez_2008_Nat.Biotechnol_26_553
PubMedSearch : Martinez_2008_Nat.Biotechnol_26_553
PubMedID: 18454138
Gene_locus related to this paper: hypjq-g0rh85 , hypjq-cip2 , hypjq-g0r9d1 , hypjq-g0r810 , hypjq-g0rbm4 , hypjq-g0rez4 , hypjq-g0rfr3 , hypjq-g0rg60 , hypjq-g0rij9 , hypjq-g0riu1 , hypjq-g0rl87 , hypjq-g0rlh4 , hypjq-g0rme5 , hypjq-g0rwy5 , hypje-axylest , hypje-q7z9m3 , hypjq-g0r6x2 , hypje-a0a024s1b8 , hypjr-a0a024s1s9 , hypjq-g0rxi5

Title : Biotechnological applications and potential of fungal feruloyl esterases based on prevalence, classification and biochemical diversity - Benoit_2008_Biotechnol.Lett_30_387
Author(s) : Benoit I , Danchin EG , Bleichrodt RJ , de Vries RP
Ref : Biotechnol Lett , 30 :387 , 2008
Abstract : Feruloyl esterases are part of the enzymatic spectrum employed by fungi and other microorganisms to degrade plant polysaccharides. They release ferulic acid and other aromatic acids from these polymeric structures and have received an increasing interest in industrial applications such as in the food, pulp and paper and bio-fuel industries. This review provides an overview of the current knowledge on fungal feruloyl esterases focussing in particular on the differences in substrate specificity, regulation of their production, prevalence of these enzymes in fungal genomes and industrial applications.
ESTHER : Benoit_2008_Biotechnol.Lett_30_387
PubMedSearch : Benoit_2008_Biotechnol.Lett_30_387
PubMedID: 17973091

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