Baker SE

References (16)

Title : Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species - Kjaerbolling_2018_Proc.Natl.Acad.Sci.U.S.A_115_E753
Author(s) : Kjaerbolling I , Vesth TC , Frisvad JC , Nybo JL , Theobald S , Kuo A , Bowyer P , Matsuda Y , Mondo S , Lyhne EK , Kogle ME , Clum A , Lipzen A , Salamov A , Ngan CY , Daum C , Chiniquy J , Barry K , LaButti K , Haridas S , Simmons BA , Magnuson JK , Mortensen UH , Larsen TO , Grigoriev IV , Baker SE , Andersen MR
Ref : Proc Natl Acad Sci U S A , 115 :E753 , 2018
Abstract : The fungal genus of Aspergillus is highly interesting, containing everything from industrial cell factories, model organisms, and human pathogens. In particular, this group has a prolific production of bioactive secondary metabolites (SMs). In this work, four diverse Aspergillus species (A. campestris, A. novofumigatus, A. ochraceoroseus, and A. steynii) have been whole-genome PacBio sequenced to provide genetic references in three Aspergillus sections. A. taichungensis and A. candidus also were sequenced for SM elucidation. Thirteen Aspergillus genomes were analyzed with comparative genomics to determine phylogeny and genetic diversity, showing that each presented genome contains 15-27% genes not found in other sequenced Aspergilli. In particular, A. novofumigatus was compared with the pathogenic species A. fumigatus This suggests that A. novofumigatus can produce most of the same allergens, virulence, and pathogenicity factors as A. fumigatus, suggesting that A. novofumigatus could be as pathogenic as A. fumigatus Furthermore, SMs were linked to gene clusters based on biological and chemical knowledge and analysis, genome sequences, and predictive algorithms. We thus identify putative SM clusters for aflatoxin, chlorflavonin, and ochrindol in A. ochraceoroseus, A. campestris, and A. steynii, respectively, and novofumigatonin, ent-cycloechinulin, and epi-aszonalenins in A. novofumigatus Our study delivers six fungal genomes, showing the large diversity found in the Aspergillus genus; highlights the potential for discovery of beneficial or harmful SMs; and supports reports of A. novofumigatus pathogenicity. It also shows how biological, biochemical, and genomic information can be combined to identify genes involved in the biosynthesis of specific SMs.
ESTHER : Kjaerbolling_2018_Proc.Natl.Acad.Sci.U.S.A_115_E753
PubMedSearch : Kjaerbolling_2018_Proc.Natl.Acad.Sci.U.S.A_115_E753
PubMedID: 29317534
Gene_locus related to this paper: 9euro-a0a0f8xhh7 , 9euro-a0a2t5ll04 , aspn1-nvfd

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 : Genome Sequence and Annotation of Trichoderma parareesei, the Ancestor of the Cellulase Producer Trichoderma reesei - Yang_2015_Genome.Announc_3_e00885
Author(s) : Yang D , Pomraning K , Kopchinskiy A , Karimi Aghcheh R , Atanasova L , Chenthamara K , Baker SE , Zhang R , Shen Q , Freitag M , Kubicek CP , Druzhinina IS
Ref : Genome Announc , 3 :e00885 , 2015
Abstract : The filamentous fungus Trichoderma parareesei is the asexually reproducing ancestor of Trichoderma reesei, the holomorphic industrial producer of cellulase and hemicellulase. Here, we present the genome sequence of the T. parareesei type strain CBS 125925, which contains genes for 9,318 proteins.
ESTHER : Yang_2015_Genome.Announc_3_e00885
PubMedSearch : Yang_2015_Genome.Announc_3_e00885
PubMedID: 26272569
Gene_locus related to this paper: hypjr-a0a024s1s9

Title : Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot\/brown-rot paradigm for wood decay fungi - Riley_2014_Proc.Natl.Acad.Sci.U.S.A_111_9923
Author(s) : Riley R , Salamov AA , Brown DW , Nagy LG , Floudas D , Held BW , Levasseur A , Lombard V , Morin E , Otillar R , Lindquist EA , Sun H , LaButti KM , Schmutz J , Jabbour D , Luo H , Baker SE , Pisabarro AG , Walton JD , Blanchette RA , Henrissat B , Martin F , Cullen D , Hibbett DS , Grigoriev IV
Ref : Proc Natl Acad Sci U S A , 111 :9923 , 2014
Abstract : Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white-rot/brown-rot classification paradigm, we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically informed principal-components analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white-rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown-rot fungi. Our results suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.
ESTHER : Riley_2014_Proc.Natl.Acad.Sci.U.S.A_111_9923
PubMedSearch : Riley_2014_Proc.Natl.Acad.Sci.U.S.A_111_9923
PubMedID: 24958869
Gene_locus related to this paper: pleos-a0a067nlj6 , 9agar-a0a067t0n0 , 9agar-a0a067sha0 , 9homo-a0a067pav0 , pleos-a0a067n337 , 9homo-a0a067pz82 , 9homo-a0a067m7p7 , pleos-a0a067p245 , 9homo-a0a067lrz6 , 9homo-a0a067m4r5 , 9homo-a0a067mr63 , 9homo-a0a067mrq8 , 9agar-a0a067t4j6 , 9homo-a0a067pdz2 , 9homo-a0a067q2n9 , 9agar-a0a067tsx5 , 9homo-a0a067mfq5 , 9homo-a0a067qc90 , pleos-a0a067p113 , 9homo-a0a067pwi6 , 9agar-a0a067s6d7 , 9agar-a0a067tie7 , pleos-a0a067ngc3 , 9agar-a0a067st69 , 9agar-a0a067t6h9 , 9agar-a0a067tj80 , pleos-a0a067npl2 , 9agar-a0a067sm07 , 9agar-a0a067tar9 , 9agar-a0a067tid6 , 9agar-a0a067u335 , pleos-a0a067ndv5 , pleos-a0a067nqw6 , 9homo-a0a067pkj2 , 9agar-a0a067t683 , 9homo-a0a067mgl1 , 9agar-a0a067sg35 , 9homo-a0a067q7g6 , 9agar-a0a067tub0 , 9agar-a0a067t8f5 , 9agar-a0a067tj19 , 9homo-a0a067pyu9 , 9agar-a0a067tjp8 , 9agar-a0a067sjg9 , 9agar-a0a067u0h4 , pleos-a0a067nxe9 , 9agar-a0a067sqt2 , 9agar-a0a067tgx3 , 9homo-a0a067psv8 , 9agar-a0a067sq58 , 9homo-a0a067m4m0 , 9agar-a0a067tqz5 , pleos-a0a067new9 , 9homo-a0a067m9v3 , 9agar-a0a067tlx5 , 9agar-a0a067tfq4 , pleos-a0a067nln4 , pleos-a0a067ndf5 , pleos-a0a067nn26 , pleos-a0a067nfv2 , 9homo-a0a067pnd3 , 9agar-a0a067sw48 , pleos-a0a067neg3 , pleos-a0a067nz51 , pleos-a0a067naf9 , pleos-a0a067nad7 , 9agar-a0a067sxe2 , 9agar-a0a067slu3 , pleos-a0a067n7p8 , pleos-a0a067nl60 , pleos-a0a067ncd0 , 9agar-a0a067th99 , 9agar-a0a067sp22 , pleos-a0a067pbw7 , 9homo-a0a067q916 , 9homo-a0a067pwe5 , galm3-a0a067scb0 , galm3-popa

Title : Comparative genomics analysis of Trichoderma reesei strains - Koike_2013_Ind.Biotechnol_9_352
Author(s) : Koike H , Aerts A , LaButti K , Grigoriev IV , Baker SE
Ref : Ind Biotech , 9 :352 , 2013
Abstract : Trichoderma reesei is a key fungus for industrial production of lignocellulolytic enzymes. The genome sequences of the T. reesei hyper-cellulolytic strain RUT-C30 and its parental strain QM6a were compared at the nucleotide level. Approximately 97% of the 87 genomic-sequence scaffolds of T. reesei QM6a (33Mb) were found to have the corresponding nucleotide in the 182 genome-sequence scaffolds of RUT-C30 (32Mb). There are 455 loci within the QM6 sequence not detected in the RUT-C30 sequence. Regions at the termini of QM6a scaffolds as well as 14 small scaffolds do not have corresponding regions in RUT-C30 genomic scaffolds. Seventy-eight protein-encoding genes are included within these regions. Mutated nucleotide(s) in 2,371 positions, including short insertion/deletions (indels), were detected in the aligned regions. The predicted protein-coding regions of 97 gene models contain mutations, 34 of which were not previously described. Twenty-seven out of 34 newly discovered genes were found to have mutations in the peptide amino acid sequence. This is in addition to 63 genes described in a previous study based on low coverage sequencing of RUT-C30. These newly identified proteins are involved in signal transduction, transcription, RNA processing and modification, and post-translational modification according to their annotations. Similar distributions of eukaryotic orthologous group (KOG) categories between the mutated and all other proteins suggest random mutation. The roles of the mutated genes and potential regulatory regions in the observed phenotype of RUT-C30 remain to be explored in a targeted fashion.
ESTHER : Koike_2013_Ind.Biotechnol_9_352
PubMedSearch : Koike_2013_Ind.Biotechnol_9_352
PubMedID:
Gene_locus related to this paper: hypjr-a0a024s1s9

Title : Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens - Condon_2013_PLoS.Genet_9_e1003233
Author(s) : Condon BJ , Leng Y , Wu D , Bushley KE , Ohm RA , Otillar R , Martin J , Schackwitz W , Grimwood J , MohdZainudin N , Xue C , Wang R , Manning VA , Dhillon B , Tu ZJ , Steffenson BJ , Salamov A , Sun H , Lowry S , LaButti K , Han J , Copeland A , Lindquist E , Barry K , Schmutz J , Baker SE , Ciuffetti LM , Grigoriev IV , Zhong S , Turgeon BG
Ref : PLoS Genet , 9 :e1003233 , 2013
Abstract : The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25x higher than those between inbred lines and 50x lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP-encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.
ESTHER : Condon_2013_PLoS.Genet_9_e1003233
PubMedSearch : Condon_2013_PLoS.Genet_9_e1003233
PubMedID: 23357949
Gene_locus related to this paper: cocsn-m2rnc6 , coch5-m2tnl8 , coch4-n4xap8 , sett2-r0j560 , cocsn-m2thl9 , coch5-m2v1s2 , coch4-n4xzy1 , cocsn-m2sqr3 , cocsn-m2rnk8 , coch4-n4xdv7 , coch5-m2uds0 , coch5-m2um94 , sett2-r0i8c5 , coch4-n4wlc8 , coch4-n4x9p3 , cocsn-m2rh47 , cocsn-m2qz08 , sett2-r0jqq6 , sett2-r0imb6 , coch4-n4x7u3 , cocsn-m2rv02 , cocsn-m2sy95 , coch5-m2ubd5 , cocsn-m2t3d2 , sett2-r0kl84 , sett2-r0jts7 , coch4-n4x2h3 , sett2-r0jxt9 , coch4-n4x7r9 , cocsn-m2sh75 , cocsn-m2t5z2 , coch5-m2ucf6 , sett2-r0k664 , cocsn-m2t3q1 , sett2-r0k4b4 , cocsn-m2t4i1 , coch5-m2th93 , cocsn-m2svm8 , cocsn-m2s6q4 , cocsn-m2s5h5 , coch4-n4xf94 , sett2-r0kdl8 , cocsn-m2qvi9 , sett2-r0kfg6 , cocsn-m2szq4 , sett2-r0j437 , coch4-n4x7j4 , coch5-m2twk3 , coch5-m2usf2 , sett2-r0kjt7 , sett2-r0k7y2 , cocsn-m2th03 , sett2-r0iy92 , sett2-r0kbr9 , sett2-r0k997 , coch5-m2sik6 , sett2-r0jzj5 , cocsn-m2r0j6 , coch4-n4x6a4 , cocsn-m2s7a5 , cocsn-m2sv79 , sett2-r0knx4 , sett2-r0ksh8 , sett2-r0ip86 , cocmi-w6yyy3 , cocsn-m2sqe4 , coch4-n4xzc8 , cocvi-w7eyp1 , cocmi-w6zf65 , cocvi-w7er28 , cocca-w6yw25 , cocvi-w7e2g6 , cocmi-w6z7k5 , cocca-w6ys73 , cocca-w6ydq2 , cocca-w6y7i5 , cocmi-w6yyr0 , cocca-w6yh47 , cocmi-w6zju4 , cocca-w6ynq5 , cocmi-w6zm44 , cocca-w6xx85 , cocmi-w6z011 , cocca-w6yre4 , cocmi-w6z9l3 , cocca-w6yfp7 , cocmi-w6zlc2 , cocca-w6yar2 , cocmi-w6yjr7 , cocca-w6yhs1 , cocca-w6xux8 , cocmi-w6z9s8 , cocca-w6yq27 , cocmi-w6zqk9 , cocca-w6xq19 , cocca-w6y1r6 , cocca-w6ygj2 , cocmi-w6zgn4 , cocca-w6ybh2 , cocmi-w6z710 , cocca-w6yk86 , cocmi-w6zjz2 , cocmi-w6z7f2 , cocca-w6xn57 , cocca-w6ybq4 , cocmi-w6yxn5 , cocmi-w6zf08 , cocsn-m2rtg8 , cocmi-w6zuj7 , cocca-w6xtb2 , cocca-w6yk97 , coch5-m2t2x3 , cocmi-w6z646 , cocsn-m2sze4 , sett2-r0kjg6 , cocmi-w6yrn5 , sett2-r0k5q0 , cocvi-w7ezb7 , sett2-r0jtm1 , cocmi-w6ywa1 , cocsn-m2t3e8 , coch5-m2ulw5 , coch5-m2urw9 , sett2-r0knn5 , cocmi-w6ysb2 , cocvi-w7eag7 , cocca-w6y1v2 , sett2-r0i9k2 , coch5-m2uul8 , cocsn-m2sl21

Title : Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88 - Andersen_2011_Genome.Res_21_885
Author(s) : Andersen MR , Salazar MP , Schaap PJ , van de Vondervoort PJ , Culley D , Thykaer J , Frisvad JC , Nielsen KF , Albang R , Albermann K , Berka RM , Braus GH , Braus-Stromeyer SA , Corrochano LM , Dai Z , van Dijck PW , Hofmann G , Lasure LL , Magnuson JK , Menke H , Meijer M , Meijer SL , Nielsen JB , Nielsen ML , van Ooyen AJ , Pel HJ , Poulsen L , Samson RA , Stam H , Tsang A , van den Brink JM , Atkins A , Aerts A , Shapiro H , Pangilinan J , Salamov A , Lou Y , Lindquist E , Lucas S , Grimwood J , Grigoriev IV , Kubicek CP , Martinez D , van Peij NN , Roubos JA , Nielsen J , Baker SE
Ref : Genome Res , 21 :885 , 2011
Abstract : The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.
ESTHER : Andersen_2011_Genome.Res_21_885
PubMedSearch : Andersen_2011_Genome.Res_21_885
PubMedID: 21543515
Gene_locus related to this paper: aspna-g3y4g9 , aspna-g3yal2 , aspna-g3ycq2 , aspnc-a2qbh3 , aspnc-a2qe77 , aspnc-a2qf54 , aspnc-a2qfe9 , aspnc-a2qg33 , aspnc-a2qh76 , aspnc-a2qhe2 , aspnc-a2qi32 , aspnc-a2ql89 , aspnc-a2ql90 , aspnc-a2qla0 , aspnc-a2qmk5 , aspnc-a2qn56 , aspnc-a2qs22 , aspnc-a2qti9 , aspnc-a2qtz0 , aspnc-a2quc1 , aspnc-a2qx92 , aspnc-a2qyf0 , aspnc-a2qys7 , aspnc-a2qz72 , aspnc-a2qzn6 , aspnc-a2qzr0 , aspnc-a2qzx0 , aspnc-a2qzx4 , aspnc-a2r0p4 , aspnc-a2r1r5 , aspnc-a2r2i5 , aspnc-a2r5r4 , aspnc-a2r6h5 , aspnc-a2r8r3 , aspnc-a2r8z3 , aspnc-a2r273 , aspnc-a2r496 , aspnc-a2r502 , aspnc-a5abe5 , aspnc-a5abe8 , aspnc-a5abh9 , aspnc-a5abk1 , aspnc-axe1 , aspnc-cuti1 , aspnc-cuti2 , aspng-a2qs46 , aspng-a2qv27 , aspni-EstA , aspkw-g7y0v7 , aspnc-a2qt47 , aspnc-a2qt66 , aspna-g3xpq9 , aspnc-a2qqa1 , aspna-g3xsl3 , aspna-g3y5a6 , aspna-g3xpw9 , aspaw-a0a401kpx5 , aspnc-a2qw57 , aspaw-a0a401kcz4 , aspna-alba , aspna-azac

Title : Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma - Kubicek_2011_Genome.Biol_12_R40
Author(s) : Kubicek CP , Herrera-Estrella A , Seidl-Seiboth V , Martinez DA , Druzhinina IS , Thon M , Zeilinger S , Casas-Flores S , Horwitz BA , Mukherjee PK , Mukherjee M , Kredics L , Alcaraz LD , Aerts A , Antal Z , Atanasova L , Cervantes-Badillo MG , Challacombe J , Chertkov O , McCluskey K , Coulpier F , Deshpande N , von Dohren H , Ebbole DJ , Esquivel-Naranjo EU , Fekete E , Flipphi M , Glaser F , Gomez-Rodriguez EY , Gruber S , Han C , Henrissat B , Hermosa R , Hernandez-Onate M , Karaffa L , Kosti I , Le Crom S , Lindquist E , Lucas S , Lubeck M , Lubeck PS , Margeot A , Metz B , Misra M , Nevalainen H , Omann M , Packer N , Perrone G , Uresti-Rivera EE , Salamov A , Schmoll M , Seiboth B , Shapiro H , Sukno S , Tamayo-Ramos JA , Tisch D , Wiest A , Wilkinson HH , Zhang M , Coutinho PM , Kenerley CM , Monte E , Baker SE , Grigoriev IV
Ref : Genome Biol , 12 :R40 , 2011
Abstract : BACKGROUND: Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma.
RESULTS: Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei.
CONCLUSIONS: The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.
ESTHER : Kubicek_2011_Genome.Biol_12_R40
PubMedSearch : Kubicek_2011_Genome.Biol_12_R40
PubMedID: 21501500
Gene_locus related to this paper: hypai-g9nem6 , hypai-g9ng36 , hypai-g9ngu2 , hypai-g9nks5 , hypai-g9nks6 , hypai-g9nqe5 , hypai-g9nqk5 , hypai-g9nrx6 , hypai-g9nsx1 , hypai-g9ntn3 , hypai-g9nzc9 , hypai-g9nzd7 , hypai-g9p1t1 , hypai-g9p1v2 , hypai-g9p2n8 , hypai-g9p4z2 , hypai-g9p878 , hypai-g9pa17 , hypai-g9pbz9 , hypvg-g9mem8 , hypvg-g9mg52 , hypvg-g9mga2 , hypvg-g9mhi3 , hypvg-g9mjc7 , hypvg-g9mk44 , hypvg-g9mms1 , hypvg-g9mnf0 , hypvg-g9mng3 , hypvg-g9mpt0 , hypvg-g9mrp9 , hypvg-g9ms16 , hypvg-g9ms32 , hypvg-g9msv5 , hypvg-g9muh6 , hypvg-g9muk0 , hypvg-g9mwe2 , hypvg-g9my79 , hypvg-g9n0p7 , hypvg-g9n2g3 , hypvg-g9n2g4 , hypvg-g9n4k5 , hypvg-g9n9n0 , hypvg-g9n561 , hypvg-g9n988 , hypvg-g9nb12 , hypvg-g9nb54 , hypvg-g9nbh8 , hypai-g9npz7 , hypai-g9njw6 , hypvg-g9mx08 , hypvg-g9mlt2 , hypai-g9p4j3 , hypvg-g9nbd3 , hypai-g9nxf6 , hypvg-g9n3y9 , hypvg-g9mgs4 , hypai-g9p6m2 , hypvg-g9my62 , hypvg-g9nbv2 , hypvg-g9my22 , hypai-g9p2e2 , hypai-g9p596 , hypai-g9nf87 , hypvg-g9me87 , hypvg-g9ndn9 , hypai-g9niy5 , hypai-g9ntx6 , hypvg-g9n3e7 , hypai-g9nu29 , hypvg-g9n2z0 , hypvg-g9ndf4 , 9hypo-a0a2p4zt82 , hypvg-g9n0g0 , hypvg-g9muj2 , hypvg-g9mud0 , hypai-g9nkx5

Title : The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi - Eastwood_2011_Science_333_762
Author(s) : Eastwood DC , Floudas D , Binder M , Majcherczyk A , Schneider P , Aerts A , Asiegbu FO , Baker SE , Barry K , Bendiksby M , Blumentritt M , Coutinho PM , Cullen D , de Vries RP , Gathman A , Goodell B , Henrissat B , Ihrmark K , Kauserud H , Kohler A , LaButti K , Lapidus A , Lavin JL , Lee YH , Lindquist E , Lilly W , Lucas S , Morin E , Murat C , Oguiza JA , Park J , Pisabarro AG , Riley R , Rosling A , Salamov A , Schmidt O , Schmutz J , Skrede I , Stenlid J , Wiebenga A , Xie X , Kues U , Hibbett DS , Hoffmeister D , Hogberg N , Martin F , Grigoriev IV , Watkinson SC
Ref : Science , 333 :762 , 2011
Abstract : Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry rot" fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.
ESTHER : Eastwood_2011_Science_333_762
PubMedSearch : Eastwood_2011_Science_333_762
PubMedID: 21764756
Gene_locus related to this paper: serl3-f8prj2 , serl3-f8qcc4 , serl9-f8ngp6 , serl9-f8nhd7 , serl9-f8nhq9 , serl9-f8nq77 , serl9-f8nr67 , serl9-f8nrt5 , serl9-f8nvy7.1 , serl9-f8nvy7.2 , serl9-f8nvy8 , serl9-f8nxt0.1 , serl9-f8nxt0.2 , serl9-f8nzr3 , serl9-f8p0f0 , serl9-f8p6v0 , serl9-f8p015 , serl9-f8p018 , serl9-f8p386 , serl9-f8paz8 , serl9-f8pbv1 , serl9-f8pby1 , serl9-f8pc25 , serl9-f8pc39 , serl9-f8nia7 , serl3-f8pju2 , serl9-f8peh1 , serl9-nps3

Title : Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris - Berka_2011_Nat.Biotechnol_29_922
Author(s) : Berka RM , Grigoriev IV , Otillar R , Salamov A , Grimwood J , Reid I , Ishmael N , John T , Darmond C , Moisan MC , Henrissat B , Coutinho PM , Lombard V , Natvig DO , Lindquist E , Schmutz J , Lucas S , Harris P , Powlowski J , Bellemare A , Taylor D , Butler G , de Vries RP , Allijn IE , van den Brink J , Ushinsky S , Storms R , Powell AJ , Paulsen IT , Elbourne LD , Baker SE , Magnuson J , Laboissiere S , Clutterbuck AJ , Martinez D , Wogulis M , de Leon AL , Rey MW , Tsang A
Ref : Nat Biotechnol , 29 :922 , 2011
Abstract : Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics.
ESTHER : Berka_2011_Nat.Biotechnol_29_922
PubMedSearch : Berka_2011_Nat.Biotechnol_29_922
PubMedID: 21964414
Gene_locus related to this paper: thiha-cip2 , thite-g2r8b5 , thite-g2rcm8 , thite-g2r192 , thiha-g2qdy2 , thiha-g2qh51 , thite-g2rae6 , thite-g2r5h0 , thiha-g2qj94 , thiha-g2qnb2 , thite-g2rg14 , myctt-g2q973 , thite-g2qtu3 , myctt-g2qpr0 , thite-g2rhm0 , 9pezi-a0a3s4b069 , myctt-g2qmb4 , thett-g2qur2

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 : Genome sequence of the model mushroom Schizophyllum commune - Ohm_2010_Nat.Biotechnol_28_957
Author(s) : Ohm RA , de Jong JF , Lugones LG , Aerts A , Kothe E , Stajich JE , de Vries RP , Record E , Levasseur A , Baker SE , Bartholomew KA , Coutinho PM , Erdmann S , Fowler TJ , Gathman AC , Lombard V , Henrissat B , Knabe N , Kues U , Lilly WW , Lindquist E , Lucas S , Magnuson JK , Piumi F , Raudaskoski M , Salamov A , Schmutz J , Schwarze FW , vanKuyk PA , Horton JS , Grigoriev IV , Wosten HA
Ref : Nat Biotechnol , 28 :957 , 2010
Abstract : Much remains to be learned about the biology of mushroom-forming fungi, which are an important source of food, secondary metabolites and industrial enzymes. The wood-degrading fungus Schizophyllum commune is both a genetically tractable model for studying mushroom development and a likely source of enzymes capable of efficient degradation of lignocellulosic biomass. Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. One-third of the 471 genes predicted to encode transcription factors are differentially expressed during sexual development of S. commune. Whereas inactivation of one of these, fst4, prevented mushroom formation, inactivation of another, fst3, resulted in more, albeit smaller, mushrooms than in the wild-type fungus. Antisense transcripts may also have a role in the formation of fruiting bodies. Better insight into the mechanisms underlying mushroom formation should affect commercial production of mushrooms and their industrial use for producing enzymes and pharmaceuticals.
ESTHER : Ohm_2010_Nat.Biotechnol_28_957
PubMedSearch : Ohm_2010_Nat.Biotechnol_28_957
PubMedID: 20622885
Gene_locus related to this paper: schcm-d8pqz6 , schcm-d8prj2 , schcm-d8pug6 , schcm-d8pxe8 , schcm-d8pxe9 , schcm-d8pxz1 , schcm-d8q1c7 , schcm-d8q2b4 , schcm-d8q3j1 , schcm-d8q5m5 , schcm-d8q7x7.1 , schcm-d8q7x7.2 , schcm-d8q8y8 , schcm-d8q9n6 , schcm-d8q697 , schcm-d8qip8 , schcm-d8q5s5 , schcm-d8ppb3 , schcm-d8ppb6 , schcm-d8pv73 , schcm-d8pzm1 , schcm-d8q5a7 , schcm-d8qif0

Title : Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion - Martinez_2009_Proc.Natl.Acad.Sci.U.S.A_106_1954
Author(s) : Martinez D , Challacombe J , Morgenstern I , Hibbett D , Schmoll M , Kubicek CP , Ferreira P , Ruiz-Duenas FJ , Martinez AT , Kersten P , Hammel KE , Vanden Wymelenberg A , Gaskell J , Lindquist E , Sabat G , Bondurant SS , Larrondo LF , Canessa P , Vicuna R , Yadav J , Doddapaneni H , Subramanian V , Pisabarro AG , Lavin JL , Oguiza JA , Master E , Henrissat B , Coutinho PM , Harris P , Magnuson JK , Baker SE , Bruno K , Kenealy W , Hoegger PJ , Kues U , Ramaiya P , Lucas S , Salamov A , Shapiro H , Tu H , Chee CL , Misra M , Xie G , Teter S , Yaver D , James T , Mokrejs M , Pospisek M , Grigoriev IV , Brettin T , Rokhsar D , Berka R , Cullen D
Ref : Proc Natl Acad Sci U S A , 106 :1954 , 2009
Abstract : Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative beta-1-4 endoglucanase were expressed at high levels relative to glucose-grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also up-regulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H(2)O(2). These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H(2)O(2) react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons with the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost.
ESTHER : Martinez_2009_Proc.Natl.Acad.Sci.U.S.A_106_1954
PubMedSearch : Martinez_2009_Proc.Natl.Acad.Sci.U.S.A_106_1954
PubMedID: 19193860
Gene_locus related to this paper: pospm-b8p1f3 , pospm-b8p2q7 , pospm-b8p4n0 , pospm-b8p4n9 , pospm-b8p5g9 , pospm-b8p5r9 , pospm-b8p6h2 , pospm-b8p7b1 , pospm-b8p7c4 , pospm-b8p8w7 , pospm-b8p9j1 , pospm-b8p164 , pospm-b8p280 , pospm-b8p423.1 , pospm-b8p423.2 , pospm-b8p858 , pospm-b8pam2 , pospm-b8pam5 , pospm-b8pb68 , pospm-b8pbm3 , pospm-b8pc54 , pospm-b8pc56 , pospm-b8pce4 , pospm-b8pd91 , pospm-b8pdk6 , pospm-b8ph32 , pospm-b8ph43 , pospm-b8phc9 , pospm-b8php7 , pospm-b8phy5 , pospm-b8pjg8 , pospm-b8pji9 , pospm-b8plr5 , pospm-b8pmk3 , pospm-b8pfg0 , pospm-b8pg35 , pospm-b8pa20.1 , pospm-b8pa20.2 , pospm-b8p4g8 , pospm-b8phn6

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 : The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization - Cuomo_2007_Science_317_1400
Author(s) : Cuomo CA , Guldener U , Xu JR , Trail F , Turgeon BG , Di Pietro A , Walton JD , Ma LJ , Baker SE , Rep M , Adam G , Antoniw J , Baldwin T , Calvo S , Chang YL , Decaprio D , Gale LR , Gnerre S , Goswami RS , Hammond-Kosack K , Harris LJ , Hilburn K , Kennell JC , Kroken S , Magnuson JK , Mannhaupt G , Mauceli E , Mewes HW , Mitterbauer R , Muehlbauer G , Munsterkotter M , Nelson D , O'Donnell K , Ouellet T , Qi W , Quesneville H , Roncero MI , Seong KY , Tetko IV , Urban M , Waalwijk C , Ward TJ , Yao J , Birren BW , Kistler HC
Ref : Science , 317 :1400 , 2007
Abstract : We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.
ESTHER : Cuomo_2007_Science_317_1400
PubMedSearch : Cuomo_2007_Science_317_1400
PubMedID: 17823352
Gene_locus related to this paper: fusof-f9fxz4 , 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-ppme1 , gibze-q4huy1 , gibze-i1rg17 , gibze-i1rb76 , gibze-i1s1m7 , gibze-i1s3z6 , gibze-i1rd78 , gibze-i1rgl9 , gibze-i1rjp7 , gibze-i1s1q6 , gibze-i1ri35 , gibze-i1rf76 , gibze-i1rhp3 , gibza-a0a016pda4 , gibza-a0a016pl96 , gibze-i1rjb5 , gibze-i1rkc4 , gibze-a0a1c3ylb1 , gibze-gra11 , gibze-fsl2

Title : Two polyketide synthase-encoding genes are required for biosynthesis of the polyketide virulence factor, T-toxin, by Cochliobolus heterostrophus - Baker_2006_Mol.Plant.Microbe.Interact_19_139
Author(s) : Baker SE , Kroken S , Inderbitzin P , Asvarak T , Li BY , Shi L , Yoder OC , Turgeon BG
Ref : Mol Plant Microbe Interact , 19 :139 , 2006
Abstract : Cochliobolus heterostrophus race T, causal agent of southern corn leaf blight, requires T-toxin (a family of C35 to C49 polyketides) for high virulence on T-cytoplasm maize. Production of T-toxin is controlled by two unlinked loci, Tox1A and Tox1B, carried on 1.2 Mb of DNA not found in race O, a mildly virulent form of the fungus that does not produce T-toxin, or in any other Cochliobolus spp. or closely related fungus. PKS1, a polyketide synthase (PKS)-encoding gene at Tox1A, and DEC1, a decarboxylase-encoding gene at Tox1B, are necessary for T-toxin production. Although there is evidence that additional genes are required for T-toxin production, efforts to clone them have been frustrated because the genes are located in highly repeated, A+T-rich DNA. To overcome this difficulty, ligation specificity-based expression analysis display (LEAD), a comparative amplified fragment length polymorphism/gel fractionation/capillary sequencing procedure, was applied to cDNAs from a near-isogenic pair of race T (Tox1+) and race O (Tox1-) strains. This led to discovery of PKS2, a second PKS-encoding gene that maps at Tox1A and is required for both T-toxin biosynthesis and high virulence to maize. Thus, the carbon chain of each T-toxin family member likely is assembled by action of two PKSs, which produce two polyketides, one of which may act as the starter unit for biosynthesis of the mature T-toxin molecule.
ESTHER : Baker_2006_Mol.Plant.Microbe.Interact_19_139
PubMedSearch : Baker_2006_Mol.Plant.Microbe.Interact_19_139
PubMedID: 16529376
Gene_locus related to this paper: coch4-tox9