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Author Report for: Aerts A

Title: Comparative genomics analysis of Trichoderma reesei strains
Koike H, Aerts A, LaButti K, Grigoriev IV, Baker SE
Ref: Ind Biotech, 9:352, 2013 : PubMed
Abstract


ESTHER: Koike_2013_Ind.Biotechnol_9_352
PubMedSearch: Koike 2013 Ind.Biotechnol 9 352
Gene_locus related to this paper: hypjr-a0a024s1s9

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.



        

Title: Insights into bilaterian evolution from three spiralian genomes
Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J and Rokhsar DS <16 more author(s)> Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J, Arendt D, Savage R, Osoegawa K, de Jong P, Grimwood J, Chapman JA, Shapiro H, Aerts A, Otillar RP, Terry AY, Boore JL, Grigoriev IV, Lindberg DR, Seaver EC, Weisblat DA, Putnam NH, Rokhsar DS (- 16)
Ref: Nature, 493:526, 2013 : PubMed
Abstract


ESTHER: Simakov_2013_Nature_493_526
PubMedSearch: Simakov 2013 Nature 493 526
PubMedID: 23254933
Gene_locus related to this paper: capte-r7t7t5, capte-r7tx98, capte-r7ua57, capte-r7ua73, capte-ACHE1, capte-ACHE2, capte-ACHE3, capte-ACHE4, helro-ACHE1, helro-ACHE1b, lotgi-ACHE1, lotgi-ACHE2, lotgi-v4aaa2, lotgi-v3zx52, lotgi-v4b4v9, capte-r7tuq9, capte-r7v997, capte-r7vgb9, lotgi-v3zwe9, capte-r7tu45, lotgi-v4bvy3, lotgi-v3zh31, capte-r7uie6, lotgi-v4b898, capte-r7u3w8, capte-r7uxb2, lotgi-v3za62, capte-r7ux79, capte-r7uq81, capte-r7vcc3, capte-r7ts12, capte-r7u1x0, capte-r7uhi1, capte-r7vei7, capte-r7v0v3, lotgi-v4bvi8, lotgi-v3zyd8, capte-r7tzy6, lotgi-v3z9i1, helro-t1fsg3, capte-x1yv75, capte-x2b306, lotgi-v3zcw8, capte-r7thp6, helro-t1fy80, lotgi-v4bky5, capte-r7tsq9, lotgi-v4ali9, lotgi-v4a9f2, lotgi-v3zjj3, helro-t1eej5, helro-t1g9b7, capte-r7tiy1, capte-r7tbl5, helro-t1exa6, lotgi-v4a5l7, helro-t1fm33, capte-r7ud05, capte-r7tql8, capte-r7u5g6, capte-r7u5z3, capte-r7ue07, lotgi-v3zk54, lotgi-v4a4r1, lotgi-v4aw76, lotgi-v4b250, lotgi-v4bbk1, lotgi-v3zq85, lotgi-v4a6s5, lotgi-v4amq2, lotgi-v4aqm2, lotgi-v4crq0, capte-r7tad7, capte-r7vgm6, lotgi-v4agl2, lotgi-v3zur2, lotgi-v4aui4, capte-r7tlv8, lotgi-v3zu07, helro-t1g0w9

Abstract

Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.



        

Title: The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes
Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martinez AT, Otillar R, Spatafora JW and Hibbett DS <61 more author(s)> Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martinez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, Coutinho PM, de Vries RP, Ferreira P, Findley K, Foster B, Gaskell J, Glotzer D, Gorecki P, Heitman J, Hesse C, Hori C, Igarashi K, Jurgens JA, Kallen N, Kersten P, Kohler A, Kues U, Kumar TK, Kuo A, LaButti K, Larrondo LF, Lindquist E, Ling A, Lombard V, Lucas S, Lundell T, Martin R, McLaughlin DJ, Morgenstern I, Morin E, Murat C, Nagy LG, Nolan M, Ohm RA, Patyshakuliyeva A, Rokas A, Ruiz-Duenas FJ, Sabat G, Salamov A, Samejima M, Schmutz J, Slot JC, St John F, Stenlid J, Sun H, Sun S, Syed K, Tsang A, Wiebenga A, Young D, Pisabarro A, Eastwood DC, Martin F, Cullen D, Grigoriev IV, Hibbett DS (- 61)
Ref: Science, 336:1715, 2012 : PubMed
Abstract


ESTHER: Floudas_2012_Science_336_1715
PubMedSearch: Floudas 2012 Science 336 1715
PubMedID: 22745431
Gene_locus related to this paper: aurde-j0d098, aurde-j0dc31, glota-s7rlc1, fompi-s8f7s4, dacsp-m5fpg2, dicsq-r7sm16, dacsp-m5g7q5, dacsp-m5fr12, glota-s7q5w3, fompi-s8f826.1, fompi-s8f826.2, dicsq-r7sy09, glota-s7rt87, dicsq-r7t032, glota-s7rym7, fompi-s8fiv2, dacsp-m5gda3.2, dicsq-r7swi6, dacsp-m5frf2, fompi-s8ebb6, dicsq-r7sln3, dicsq-r7sya6, dacsp-m5g7g1, dicsq-r7syx7, dicsq-r7sx57, dacsp-m5fps7, glota-s7pwi7, dicsq-r7swj6, fompi-s8ejq6, dicsq-r7spc3, glota-s7q258, dacsp-m5ft65, glota-s7q3m7, fompi-s8dkc7, glota-s7q1z1, fompi-s8eqi2, glota-s7q1z8, fompi-s8du50, dacsp-m5gg33, dacsp-m5g3a7, fompi-s8ecd7, fompi-s8dps1, dacsp-m5fwr0, dicsq-r7sub7, glota-s7q8k9, fompi-s8ffc3, dacsp-m5g2f9, fompi-s8ecc2, dacsp-m5g868, fompi-s8f890, dicsq-r7t1a8, fompi-s8ebx4, fompi-s8eb97, glota-s7q222, glota-s7puf0, fompi-s8f6v9, dacsp-m5g0z2, dacsp-m5gdh9, fompi-s8fb37, dacsp-m5fy91, glota-s7q5v6, fompi-s8fl44, dicsq-r7stv9, dicsq-r7szk3, fompi-s8epq9, glota-s7rh56, dacsp-m5gbt1, punst-r7s3x9, punst-r7s0t5, glota-s7q312, glota-s7rhh6, dicsq-r7t117, dicsq-r7slz3

Abstract

Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.



        

Title: Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen
Olson A, Aerts A, Asiegbu F, Belbahri L, Bouzid O, Broberg A, Canback B, Coutinho PM, Cullen D and Stenlid J <43 more author(s)> Olson A, Aerts A, Asiegbu F, Belbahri L, Bouzid O, Broberg A, Canback B, Coutinho PM, Cullen D, Dalman K, Deflorio G, van Diepen LT, Dunand C, Duplessis S, Durling M, Gonthier P, Grimwood J, Fossdal CG, Hansson D, Henrissat B, Hietala A, Himmelstrand K, Hoffmeister D, Hogberg N, James TY, Karlsson M, Kohler A, Kues U, Lee YH, Lin YC, Lind M, Lindquist E, Lombard V, Lucas S, Lunden K, Morin E, Murat C, Park J, Raffaello T, Rouze P, Salamov A, Schmutz J, Solheim H, Stahlberg J, Velez H, de Vries RP, Wiebenga A, Woodward S, Yakovlev I, Garbelotto M, Martin F, Grigoriev IV, Stenlid J (- 43)
Ref: New Phytol, 194:1001, 2012 : PubMed
Abstract


ESTHER: Olson_2012_New.Phytol_194_1001
PubMedSearch: Olson 2012 New.Phytol 194 1001
PubMedID: 22463738
Gene_locus related to this paper: 9homo-w4jrb9, 9homo-w4jsg4, 9homo-w4kds7, 9homo-w4jwl9, 9homo-w4kjy2, 9homo-w4jw43, 9homo-w4ka20, 9homo-w4k8t3, 9homo-w4jz43, 9homo-w4k8q2, 9homo-w4k910, 9homo-w4k6f5, 9homo-w4k6j3, 9homo-w4k8n2, 9homo-w4jrf3, 9homo-w4ke07, 9homo-w4k3i8, 9homo-w4jqh1, 9agam-w4k203, 9agam-w4jpy3, 9agam-w4jn81, 9agam-w4jmz2

Abstract

Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato. We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified. A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production. Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.



        

Title: Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize
Suzuki H, MacDonald J, Syed K, Salamov A, Hori C, Aerts A, Henrissat B, Wiebenga A, vanKuyk PA and Master ER <14 more author(s)> Suzuki H, MacDonald J, Syed K, Salamov A, Hori C, Aerts A, Henrissat B, Wiebenga A, vanKuyk PA, Barry K, Lindquist E, LaButti K, Lapidus A, Lucas S, Coutinho P, Gong Y, Samejima M, Mahadevan R, Abou-Zaid M, de Vries RP, Igarashi K, Yadav JS, Grigoriev IV, Master ER (- 14)
Ref: BMC Genomics, 13:444, 2012 : PubMed
Abstract


ESTHER: Suzuki_2012_BMC.Genomics_13_444
PubMedSearch: Suzuki 2012 BMC.Genomics 13 444
PubMedID: 22937793
Gene_locus related to this paper: phacs-k5whx2, phacs-k5v2s8, phacs-k5v5r2, phacs-k5vyk5, phacs-k5vzf8, phacs-k5wbu9, phacs-k5wc10, phacs-k5wpw0, phacs-k5wzn6, phacs-k5x1t8, phacs-k5x5g6, phacs-k5x5p4

Abstract

BACKGROUND: Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome.
RESULTS: P. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood.
CONCLUSIONS: The P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.



        

Title: Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R and Baker SE <37 more 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 (- 37)
Ref: Genome Res, 21:885, 2011 : PubMed
Abstract


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

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.



        

Title: The ecoresponsive genome of Daphnia pulex
Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ and Boore JL <59 more author(s)> Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Caceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Frohlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kultz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL (- 59)
Ref: Science, 331:555, 2011 : PubMed
Abstract


ESTHER: Colbourne_2011_Science_331_555
PubMedSearch: Colbourne 2011 Science 331 555
PubMedID: 21292972
Gene_locus related to this paper: dappu-e9fut0, dappu-e9fut9, dappu-e9fvw6, dappu-e9fxt4, dappu-e9fyr6, dappu-e9fzg6, dappu-e9g1e2, dappu-e9g1e6, dappu-e9g1e7, dappu-e9g1e8, dappu-e9g1v3, dappu-e9g1z2, dappu-e9gb99, dappu-e9gba0, dappu-e9gcb4, dappu-e9gdv5, dappu-e9gdv7, dappu-e9gi24, dappu-e9gj77, dappu-e9gja7, dappu-e9gmp5, dappu-e9gmr0, dappu-e9gn32, dappu-e9gp76, dappu-e9gp82, dappu-e9gp98, dappu-e9gp99, dappu-e9gvl2, dappu-e9gzn7, dappu-e9h1p4, dappu-e9h2c8, dappu-e9h2c9, dappu-e9h6x9, dappu-e9h6y4, dappu-e9h7w9, dappu-e9h8r4, dappu-e9hd06, dappu-e9hh56, dappu-e9hh57, dappu-e9hh59, dappu-e9hmp4, dappu-e9hp64, dappu-e9hp65, dappu-e9hpy8, dappu-e9htg8, dapul-ACHE1, dapul-ACHE2, dappu-e9gnj1, dappu-e9gu36, dappu-e9hpc4, dappu-e9gb07, dappu-e9glp6, dappu-e9glp5, dappu-e9gjv2, dappu-e9h0c7, dappu-e9g4g2, dappu-e9gw69, dappu-e9h3h9, dappu-e9g545, dappu-e9gw71, dappu-e9gw68, dappu-e9h3e7, dappu-e9gfg9, dappu-e9fvy6, dappu-e9hgt2

Abstract

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.



        

Title: Obligate biotrophy features unraveled by the genomic analysis of rust fungi
Duplessis S, Cuomo CA, Lin YC, Aerts A, Tisserant E, Veneault-Fourrey C, Joly DL, Hacquard S, Amselem J and Martin F <40 more author(s)> Duplessis S, Cuomo CA, Lin YC, Aerts A, Tisserant E, Veneault-Fourrey C, Joly DL, Hacquard S, Amselem J, Cantarel BL, Chiu R, Coutinho PM, Feau N, Field M, Frey P, Gelhaye E, Goldberg J, Grabherr MG, Kodira CD, Kohler A, Kues U, Lindquist EA, Lucas SM, Mago R, Mauceli E, Morin E, Murat C, Pangilinan JL, Park R, Pearson M, Quesneville H, Rouhier N, Sakthikumar S, Salamov AA, Schmutz J, Selles B, Shapiro H, Tanguay P, Tuskan GA, Henrissat B, Van de Peer Y, Rouze P, Ellis JG, Dodds PN, Schein JE, Zhong S, Hamelin RC, Grigoriev IV, Szabo LJ, Martin F (- 40)
Ref: Proc Natl Acad Sci U S A, 108:9166, 2011 : PubMed
Abstract


ESTHER: Duplessis_2011_Proc.Natl.Acad.Sci.U.S.A_108_9166
PubMedSearch: Duplessis 2011 Proc.Natl.Acad.Sci.U.S.A 108 9166
PubMedID: 21536894
Gene_locus related to this paper: pucgt-e3k840, pucgt-e3kaq6, pucgt-e3kw59, pucgt-e3kz16, pucgt-e3l9v6, pucgt-e3l279, pucgt-h6qt25, mellp-f4reh4, mellp-f4rhc8, mellp-f4reh2, mellp-f4r3y0, mellp-f4rz15, mellp-f4rz64, mellp-f4rl14, mellp-f4rz66, mellp-f4s751, mellp-f4s2g6, pucgt-e3l1z7, pucgt-e3l803, pucgt-e3kst2, pucgt-e3kst5, mellp-f4ru03, pucgt-e3l1z8, pucgt-e3ktz7, pucgt-e3jun4, mellp-f4rl65, mellp-f4rz16, mellp-f4ru02, mellp-f4sav4, mellp-f4sav3, mellp-f4s1j0, mellp-f4rkp0, mellp-f4s483, pucgt-e3kzu5, pucgt-h6qtq8, mellp-f4r5l5, pucgt-e3krw7, pucgt-e3l7w5, pucgt-e3k2w6, pucgt-e3kfg2, pucgt-kex1

Abstract

Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart from their hosts. Their lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101-Mb genome of Melampsora larici-populina, the causal agent of poplar leaf rust, and the 89-Mb genome of Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust. We then compared the 16,399 predicted proteins of M. larici-populina with the 17,773 predicted proteins of P. graminis f. sp tritici. Genomic features related to their obligate biotrophic lifestyle include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins, impaired nitrogen and sulfur assimilation pathways, and expanded families of amino acid and oligopeptide membrane transporters. The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cells.



        

Title: The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi
Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K and Watkinson SC <38 more 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 (- 38)
Ref: Science, 333:762, 2011 : PubMed
Abstract


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

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.



        

Title: Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma
Ellison CE, Stajich JE, Jacobson DJ, Natvig DO, Lapidus A, Foster B, Aerts A, Riley R, Lindquist EA and Taylor JW <1 more author(s)> Ellison CE, Stajich JE, Jacobson DJ, Natvig DO, Lapidus A, Foster B, Aerts A, Riley R, Lindquist EA, Grigoriev IV, Taylor JW (- 1)
Ref: Genetics, 189:55, 2011 : PubMed
Abstract


ESTHER: Ellison_2011_Genetics_189_55
PubMedSearch: Ellison 2011 Genetics 189 55
PubMedID: 21750257
Gene_locus related to this paper: neucr-90C4.300, neucr-B19A17.360, neucr-B23G1.090, neucr-NCU00292.1, neucr-NCU02679.1, neucr-NCU04930.1, neucr-NCU06573.1, neucr-NCU08752.1, neucr-NCU09575.1, neucr-NCU10022.1, neucr-q7s1x0, neucr-q7s216, neucr-q7s259, neucr-q7s260, neucr-q7scr4, neut8-f8n463, neut9-g4uk39, neucr-f5hbr2, neut8-f8mcp7, neucr-q7ry64, neucr-FAED, neut8-f8mrh8

Abstract

A large region of suppressed recombination surrounds the sex-determining locus of the self-fertile fungus Neurospora tetrasperma. This region encompasses nearly one-fifth of the N. tetrasperma genome and suppression of recombination is necessary for self-fertility. The similarity of the N. tetrasperma mating chromosome to plant and animal sex chromosomes and its recent origin (<5 MYA), combined with a long history of genetic and cytological research, make this fungus an ideal model for studying the evolutionary consequences of suppressed recombination. Here we compare genome sequences from two N. tetrasperma strains of opposite mating type to determine whether structural rearrangements are associated with the nonrecombining region and to examine the effect of suppressed recombination for the evolution of the genes within it. We find a series of three inversions encompassing the majority of the region of suppressed recombination and provide evidence for two different types of rearrangement mechanisms: the recently proposed mechanism of inversion via staggered single-strand breaks as well as ectopic recombination between transposable elements. In addition, we show that the N. tetrasperma mat a mating-type region appears to be accumulating deleterious substitutions at a faster rate than the other mating type (mat A) and thus may be in the early stages of degeneration.



        

Title: Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis
Goodwin SB, M'Barek S B, Dhillon B, Wittenberg AH, Crane CF, Hane JK, Foster AJ, Van der Lee TA, Grimwood J and Kema GH <47 more author(s)> Goodwin SB, M'Barek S B, Dhillon B, Wittenberg AH, Crane CF, Hane JK, Foster AJ, Van der Lee TA, Grimwood J, Aerts A, Antoniw J, Bailey A, Bluhm B, Bowler J, Bristow J, van der Burgt A, Canto-Canche B, Churchill AC, Conde-Ferraez L, Cools HJ, Coutinho PM, Csukai M, Dehal P, De Wit P, Donzelli B, van de Geest HC, van Ham RC, Hammond-Kosack KE, Henrissat B, Kilian A, Kobayashi AK, Koopmann E, Kourmpetis Y, Kuzniar A, Lindquist E, Lombard V, Maliepaard C, Martins N, Mehrabi R, Nap JP, Ponomarenko A, Rudd JJ, Salamov A, Schmutz J, Schouten HJ, Shapiro H, Stergiopoulos I, Torriani SF, Tu H, de Vries RP, Waalwijk C, Ware SB, Wiebenga A, Zwiers LH, Oliver RP, Grigoriev IV, Kema GH (- 47)
Ref: PLoS Genet, 7:e1002070, 2011 : PubMed
Abstract


ESTHER: Goodwin_2011_PLoS.Genet_7_E1002070
PubMedSearch: Goodwin 2011 PLoS.Genet 7 E1002070
PubMedID: 21695235
Gene_locus related to this paper: zymti-f9wzw8, zymti-f9x2y6, zymti-f9x423, zymti-f9x813, zymti-f9xa54, zymti-f9xb42, zymti-f9xbu5, zymti-f9xcr9, zymti-f9xdr7, zymti-f9xer1, zymti-f9xez8, zymti-f9xfz9, zymti-f9xh29, zymti-f9xhe7, zymti-f9xhr4, zymti-f9xk09, zymti-f9xns5, zymti-f9xiu1, zymti-f9xng3, zymti-f9x4f2, zymti-f9x4s7, zymti-f9xdm8, zymti-f9wwy9, zymti-f9xkf2, zymti-f9xlt3, zymti-f9x0i3, zymti-f9wwa6, zymti-f9wyk7, zymti-f9x3z1, zymti-f9xf16, zymtr-a0a1x7rhi5, zymti-f9xfj3, zymti-pks1

Abstract

The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed "mesosynteny" is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors.



        

Title: Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma
Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA and Grigoriev IV <54 more 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 (- 54)
Ref: Genome Biol, 12:R40, 2011 : PubMed
Abstract


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

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.



        

Title: Genome sequence of the model mushroom Schizophyllum commune
Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A and Wosten HA <22 more 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 (- 22)
Ref: Nat Biotechnol, 28:957, 2010 : PubMed
Abstract


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

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.



        

Title: The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
Martin F, Aerts A, Ahren D, Brun A, Danchin EG, Duchaussoy F, Gibon J, Kohler A, Lindquist E and Grigoriev IV <58 more 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 (- 58)
Ref: Nature, 452:88, 2008 : PubMed
Abstract


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

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.



        

Title: Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis
Jeffries TW, Grigoriev IV, Grimwood J, Laplaza JM, Aerts A, Salamov A, Schmutz J, Lindquist E, Dehal P and Richardson PM <3 more author(s)> Jeffries TW, Grigoriev IV, Grimwood J, Laplaza JM, Aerts A, Salamov A, Schmutz J, Lindquist E, Dehal P, Shapiro H, Jin YS, Passoth V, Richardson PM (- 3)
Ref: Nat Biotechnol, 25:319, 2007 : PubMed
Abstract


ESTHER: Jeffries_2007_Nat.Biotechnol_25_319
PubMedSearch: Jeffries 2007 Nat.Biotechnol 25 319
PubMedID: 17334359
Gene_locus related to this paper: picst-a3geu9, picst-a3gfu2, picst-a3ggh9, picst-a3gha8, picst-a3ghe3, picst-a3gi73, picst-a3lmu3, picst-a3ln06, picst-a3ln59, picst-a3lnv8, picst-a3lp77, picst-a3lqt4, picst-a3lrt0, picst-a3ls15, picst-a3lsj8, picst-a3lu11, picst-a3luu0, picst-a3lv87, picst-a3lvi5, picst-a3lvu9, picst-a3lvv2, picst-a3lwa4, picst-a3lxl2, picst-a3lxs8, picst-a3lyi3, picst-atg15, picst-bna7, picst-a3lyh1, picst-a3lnc5, picst-a3lr32

Abstract

Xylose is a major constituent of plant lignocellulose, and its fermentation is important for the bioconversion of plant biomass to fuels and chemicals. Pichia stipitis is a well-studied, native xylose-fermenting yeast. The mechanism and regulation of xylose metabolism in P. stipitis have been characterized and genes from P. stipitis have been used to engineer xylose metabolism in Saccharomyces cerevisiae. We have sequenced and assembled the complete genome of P. stipitis. The sequence data have revealed unusual aspects of genome organization, numerous genes for bioconversion, a preliminary insight into regulation of central metabolic pathways and several examples of colocalized genes with related functions. The genome sequence provides insight into how P. stipitis regulates its redox balance while very efficiently fermenting xylose under microaerobic conditions.



        

Title: The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation
Palenik B, Grimwood J, Aerts A, Rouze P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E and Grigoriev IV <28 more author(s)> Palenik B, Grimwood J, Aerts A, Rouze P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV (- 28)
Ref: Proc Natl Acad Sci U S A, 104:7705, 2007 : PubMed
Abstract


ESTHER: Palenik_2007_Proc.Natl.Acad.Sci.U.S.A_104_7705
PubMedSearch: Palenik 2007 Proc.Natl.Acad.Sci.U.S.A 104 7705
PubMedID: 17460045
Gene_locus related to this paper: ostlu-a4rrl5, ostlu-a4ruh2, ostlu-a4rut7, ostlu-a4ruy3, ostlu-a4rxn1, ostlu-a4ry37, ostlu-a4s2e6, ostlu-a4s2y4, ostlu-a4s3d7, ostlu-a4s4v4, ostlu-a4s5e4, ostlu-a4s5y6, ostlu-a4s7a8, ostlu-a4s7z5, ostlu-a4s8g3, ostlu-a4s8n8, ostlu-a4s8s1, ostlu-a4s958, ostlu-a4sac2, ostlu-a4saz3, ostlu-a4sbb7, ostlu-a4s6q5, ostlu-a4s1q9, ostlu-a4s8b2, ostlu-a4s262

Abstract

The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.



        

Title: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S and Rokhsar D <100 more author(s)> Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, dePamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (- 100)
Ref: Science, 313:1596, 2006 : PubMed
Abstract


ESTHER: Tuskan_2006_Science_313_1596
PubMedSearch: Tuskan 2006 Science 313 1596
PubMedID: 16973872
Gene_locus related to this paper: burvg-a4jw31, delas-a9c1v9, poptr-a9pfp5, poptr-a9ph43, poptr-a9ph71, poptr-a9pha7, poptr-b9giq0, poptr-b9gjs0, poptr-b9gl72, poptr-b9gmx8, poptr-b9gnp9, poptr-b9gny4, poptr-b9grg2, poptr-b9gsc2, poptr-b9gvp3, poptr-b9gvs3, poptr-b9gwn9, poptr-b9gy32, poptr-b9gyq1, poptr-b9gys8, poptr-b9h0h0, poptr-b9h4j2, poptr-b9h6c2, poptr-b9h6c5, poptr-b9h6l8, poptr-b9h8c9, poptr-b9h301, poptr-b9h579, poptr-b9hbl2, poptr-b9hbw5, poptr-b9hcn9, poptr-b9hee0, poptr-b9hee2, poptr-b9hee5, poptr-b9hee6, poptr-b9hef3, poptr-b9hfa7, poptr-b9hfd3, poptr-b9hfi6, poptr-b9hft8, poptr-b9hg83, poptr-b9hif5, poptr-b9hll5, poptr-b9hmd0, poptr-b9hnv3, poptr-b9hqr6, poptr-b9hqr7, poptr-b9hrv7, poptr-b9hs66, poptr-b9huf0, poptr-b9hur3, poptr-b9hux1, poptr-b9hwp2, poptr-b9hxr7, poptr-b9hyk8, poptr-b9hyx2, poptr-b9i2q8, poptr-b9i5b8, poptr-b9i5j8, poptr-b9i5j9, poptr-b9i5k0, poptr-b9i6b6, poptr-b9i7b7, poptr-b9i9p8, poptr-b9i484, poptr-b9i994, poptr-b9ial3, poptr-b9ial4, poptr-b9ib28, poptr-b9ibr8, poptr-b9id97, poptr-b9idr4, poptr-b9iid9, poptr-b9iip0, poptr-b9ik80, poptr-b9ik90, poptr-b9il63, poptr-b9ink7, poptr-b9iqa0, poptr-b9iqd5, poptr-b9mwf1, poptr-b9mwi8, poptr-b9n0c6, poptr-b9n0n1, poptr-b9n0n4, poptr-b9n0z5, poptr-b9n1t8, poptr-b9n1z3, poptr-b9n3m7, poptr-b9n233, poptr-b9n236, poptr-b9n395, poptr-b9nd33, poptr-b9nd34, poptr-b9ndi6, poptr-b9ndj5, poptr-b9p9i8, poptr-a9pfa7, poptr-b9hdp2, poptr-b9inj0, poptr-b9n5g7, poptr-b9i8q4, poptr-u5g0r4, poptr-u5gf59, poptr-u7e1l9, poptr-b9hj61, poptr-b9hwd0, poptr-u5fz17, poptr-a0a2k2brq1, poptr-a0a2k2b9i6, poptr-a0a2k1x9y8, poptr-a9pch4, poptr-a0a2k1wwt1, poptr-a0a2k1wv10, poptr-a0a2k2a850, poptr-a0a2k2asj6, poptr-a0a2k1x6k1, poptr-u5fv96, poptr-a0a2k2blg2, poptr-a0a2k1xpi3, poptr-a0a2k1xpj0, poptr-a0a2k2b331, poptr-a0a2k2byl7, poptr-b9iek5, poptr-a9pfg4

Abstract

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.



        

Title: Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis
Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D and Boore JL <43 more author(s)> Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL (- 43)
Ref: Science, 313:1261, 2006 : PubMed
Abstract


ESTHER: Tyler_2006_Science_313_1261
PubMedSearch: Tyler 2006 Science 313 1261
PubMedID: 16946064
Gene_locus related to this paper: phyrm-h3ga89, phyrm-h3gbl6.1, phyrm-h3gbl6.2, phyrm-h3gbl7, phyrm-h3gdd4, phyrm-h3gl36, phyrm-h3gq42, phyrm-h3gx86, phyrm-h3gyi2, phyrm-h3gyi3, phyrm-h3gyi4, phyrm-h3h292, phyrm-h3h293, phyrm-h3h967, phyrm-h3hcf9, physp-g4ynp3, physp-g4yut6, physp-g4yut8, physp-g4yw23, physp-g4zis3, physp-g4zqe3, physp-g4zqe4, physp-g4zqf0, physp-g4zqn9, physp-g4zwy9, physp-g5a582, physp-g5a583, physp-g5aav9, phyrm-h3g9e7, physp-g4zwu9, phyrm-h3ggp1, physp-g4ztq5, physp-g4zwu8, physp-g4zwv7, physp-g4zwv6, physp-g4zwv0, physp-g4zwv8, phyrm-h3gp95, phyrm-h3g6r5, physp-g4zwv9, physp-g5a510, phyrm-h3glu3, physp-g5aci1, phyrm-h3h2d0, physp-g4ztb2, physp-g4yg47, phyrm-h3h2c9, physp-g4ztb3, phyrm-h3gvj3, phyrm-h3gy62, physp-g4yg46, physp-g4zdt9, phyrm-h3gdh5, physp-g4zm41, physp-g5abj7, phyrm-h3gz76, physp-g5a425, phyrm-h3h080, physp-g4ytv0, phyrm-h3gcw7

Abstract

Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oomycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oomycete avirulence genes.



        

Title: The DNA sequence and biology of human chromosome 19
Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O and Lucas SM <88 more author(s)> Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, Aerts A, Altherr M, Ashworth L, Bajorek E, Black S, Branscomb E, Caenepeel S, Carrano A, Caoile C, Chan YM, Christensen M, Cleland CA, Copeland A, Dalin E, Dehal P, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Garcia C, Georgescu AM, Glavina T, Gomez M, Gonzales E, Groza M, Hammon N, Hawkins T, Haydu L, Ho I, Huang W, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Larionov V, Leem SH, Lopez F, Lou Y, Lowry S, Malfatti S, Martinez D, McCready P, Medina C, Morgan J, Nelson K, Nolan M, Ovcharenko I, Pitluck S, Pollard M, Popkie AP, Predki P, Quan G, Ramirez L, Rash S, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, She X, Smith D, Slezak T, Solovyev V, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wagner M, Wheeler J, Wu K, Xie G, Yang J, Dubchak I, Furey TS, DeJong P, Dickson M, Gordon D, Eichler EE, Pennacchio LA, Richardson P, Stubbs L, Rokhsar DS, Myers RM, Rubin EM, Lucas SM (- 88)
Ref: Nature, 428:529, 2004 : PubMed
Abstract


ESTHER: Grimwood_2004_Nature_428_529
PubMedSearch: Grimwood 2004 Nature 428 529
PubMedID: 15057824

Abstract

Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.



        

Title: The sequence and analysis of duplication-rich human chromosome 16
Martin J, Han C, Gordon LA, Terry A, Prabhakar S, She X, Xie G, Hellsten U, Chan YM and Pennacchio LA <112 more author(s)> Martin J, Han C, Gordon LA, Terry A, Prabhakar S, She X, Xie G, Hellsten U, Chan YM, Altherr M, Couronne O, Aerts A, Bajorek E, Black S, Blumer H, Branscomb E, Brown NC, Bruno WJ, Buckingham JM, Callen DF, Campbell CS, Campbell ML, Campbell EW, Caoile C, Challacombe JF, Chasteen LA, Chertkov O, Chi HC, Christensen M, Clark LM, Cohn JD, Denys M, Detter JC, Dickson M, Dimitrijevic-Bussod M, Escobar J, Fawcett JJ, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Goodwin LA, Grady DL, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Hildebrand CE, Huang W, Israni S, Jett J, Jewett PB, Kadner K, Kimball H, Kobayashi A, Krawczyk MC, Leyba T, Longmire JL, Lopez F, Lou Y, Lowry S, Ludeman T, Manohar CF, Mark GA, McMurray KL, Meincke LJ, Morgan J, Moyzis RK, Mundt MO, Munk AC, Nandkeshwar RD, Pitluck S, Pollard M, Predki P, Parson-Quintana B, Ramirez L, Rash S, Retterer J, Ricke DO, Robinson DL, Rodriguez A, Salamov A, Saunders EH, Scott D, Shough T, Stallings RL, Stalvey M, Sutherland RD, Tapia R, Tesmer JG, Thayer N, Thompson LS, Tice H, Torney DC, Tran-Gyamfi M, Tsai M, Ulanovsky LE, Ustaszewska A, Vo N, White PS, Williams AL, Wills PL, Wu JR, Wu K, Yang J, DeJong P, Bruce D, Doggett NA, Deaven L, Schmutz J, Grimwood J, Richardson P, Rokhsar DS, Eichler EE, Gilna P, Lucas SM, Myers RM, Rubin EM, Pennacchio LA (- 112)
Ref: Nature, 432:988, 2004 : PubMed
Abstract


ESTHER: Martin_2004_Nature_432_988
PubMedSearch: Martin 2004 Nature 432 988
PubMedID: 15616553
Gene_locus related to this paper: human-CES1, human-CES2, human-CES3, human-CES4A, human-CES5A

Abstract

Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.