Author Report for: Kuo ANo contact information in database for Kuo A
Freyria NJ, Kuo A, Chovatia M, Johnson J, Lipzen A, Barry KW, Grigoriev IV, Lovejoy C Ref: Commun Biol, 5:500, 2022 : PubMed ESTHER: Freyria_2022_Commun.Biol_5_500 PubMedSearch: Freyria 2022 Commun.Biol 5 500 PubMedID: 35614207 Abstract Little is known at the transcriptional level about microbial eukaryotic adaptations to short-term salinity change. Arctic microalgae are exposed to low salinity due to sea-ice melt and higher salinity with brine channel formation during freeze-up. Here, we investigate the transcriptional response of an ice-associated microalgae over salinities from 45 to 8. Our results show a bracketed response of differential gene expression when the cultures were exposed to progressively decreasing salinity. Key genes associated with salinity changes were involved in specific metabolic pathways, transcription factors and regulators, protein kinases, carbohydrate active enzymes, and inorganic ion transporters. The pelagophyte seemed to use a strategy involving overexpression of Na(+)-H(+) antiporters and Na(+) -Pi symporters as salinity decreases, but the K(+) channel complex at higher salinities. Specific adaptation to cold saline arctic conditions was seen with differential expression of several antifreeze proteins, an ice-binding protein and an acyl-esterase involved in cold adaptation. Title: Serial femtosecond and serial synchrotron crystallography can yield data of equivalent quality: A systematic comparison Mehrabi P, Bucker R, Bourenkov G, Ginn HM, von Stetten D, Muller-Werkmeister HM, Kuo A, Morizumi T, Eger BT and Miller RJD <15 more author(s)> Mehrabi P, Bucker R, Bourenkov G, Ginn HM, von Stetten D, Muller-Werkmeister HM, Kuo A, Morizumi T, Eger BT, Ou WL, Oghbaey S, Sarracini A, Besaw JE, Pare-Labrosse O, Meier S, Schikora H, Tellkamp F, Marx A, Sherrell DA, Axford D, Owen RL, Ernst OP, Pai EF, Schulz EC, Miller RJD (- 15) Ref: Sci Adv, 7:, 2021 : PubMed ESTHER: Mehrabi_2021_Sci.Adv_7_eabf1380 PubMedSearch: Mehrabi 2021 Sci.Adv 7 eabf1380 PubMedID: 33731353 Gene_locus related to this paper: rhopa-q6nam1 Abstract For the two proteins myoglobin and fluoroacetate dehalogenase, we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of micron-sized crystals, the same sample delivery device, and the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins, reasonable data statistics can be obtained with approximately 5000 room-temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that the quality of diffraction data obtained from these samples is linked to the properties of the crystals rather than to the radiation source. Therefore, for other systems with similar properties, time-resolved experiments can be conducted at the radiation source that best matches the desired time resolution. Title: Fixed-target serial oscillation crystallography at room temperature Wierman JL, Pare-Labrosse O, Sarracini A, Besaw JE, Cook MJ, Oghbaey S, Daoud H, Mehrabi P, Kriksunov I and Finke AD <7 more author(s)> Wierman JL, Pare-Labrosse O, Sarracini A, Besaw JE, Cook MJ, Oghbaey S, Daoud H, Mehrabi P, Kriksunov I, Kuo A, Schuller DJ, Smith S, Ernst OP, Szebenyi DME, Gruner SM, Miller RJD, Finke AD (- 7) Ref: IUCrJ, 6:305, 2019 : PubMed ESTHER: Wierman_2019_IUCrJ_6_305 PubMedSearch: Wierman 2019 IUCrJ 6 305 PubMedID: 30867928 Gene_locus related to this paper: rhopa-q6nam1 Abstract A fixed-target approach to high-throughput room-temperature serial synchrotron crystallography with oscillation is described. Patterned silicon chips with microwells provide high crystal-loading density with an extremely high hit rate. The microfocus, undulator-fed beamline at CHESS, which has compound refractive optics and a fast-framing detector, was built and optimized for this experiment. The high-throughput oscillation method described here collects 1-5 degrees of data per crystal at room temperature with fast (10 degrees s(-1)) oscillation rates and translation times, giving a crystal-data collection rate of 2.5 Hz. Partial datasets collected by the oscillation method at a storage-ring source provide more complete data per crystal than still images, dramatically lowering the total number of crystals needed for a complete dataset suitable for structure solution and refinement - up to two orders of magnitude fewer being required. Thus, this method is particularly well suited to instances where crystal quantities are low. It is demonstrated, through comparison of first and last oscillation images of two systems, that dose and the effects of radiation damage can be minimized through fast rotation and low angular sweeps for each crystal. Title: Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species Kjaerbolling I, Vesth TC, Frisvad JC, Nybo JL, Theobald S, Kuo A, Bowyer P, Matsuda Y, Mondo S and Andersen MR <17 more 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 (- 17) Ref: Proc Natl Acad Sci U S A, 115:E753, 2018 : PubMed 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 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. Title: Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi Knapp DG, Nemeth JB, Barry K, Hainaut M, Henrissat B, Johnson J, Kuo A, Lim JHP, Lipzen A and Kovacs GM <6 more author(s)> Knapp DG, Nemeth JB, Barry K, Hainaut M, Henrissat B, Johnson J, Kuo A, Lim JHP, Lipzen A, Nolan M, Ohm RA, Tamas L, Grigoriev IV, Spatafora JW, Nagy LG, Kovacs GM (- 6) Ref: Sci Rep, 8:6321, 2018 : PubMed ESTHER: Knapp_2018_Sci.Rep_8_6321 PubMedSearch: Knapp 2018 Sci.Rep 8 6321 PubMedID: 29679020 Gene_locus related to this paper: 9pleo-a0a2v1dn29, 9helo-a0a2v1c5l1, 9pleo-a0a2v1dti3, 9helo-a0a2v1bts1, 9helo-a0a2v1cbe5, 9pleo-a0a2v1cxz2, 9pleo-a0a2v1d1n3, 9pleo-a0a2v1db80, 9pleo-a0a2v1ddg5, 9pleo-a0a2v1dij1, 9pleo-a0a2v1dp20, 9pleo-a0a2v1e6x2, 9pleo-a0a2v1ee64, 9helo-a0a2v1cbn2, 9helo-a0a2v1b581, 9pleo-a0a2v1e5g2, corcc-a0a2t2nt04, 9helo-a0a2v1buk5 Abstract Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle. Title: Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, Barry KW, Cichocki N, Clum A and Perotto S <18 more author(s)> Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, Barry KW, Cichocki N, Clum A, Dockter RB, Hainaut M, Kuo RC, LaButti K, Lindahl BD, Lindquist EA, Lipzen A, Khouja HR, Magnuson J, Murat C, Ohm RA, Singer SW, Spatafora JW, Wang M, Veneault-Fourrey C, Henrissat B, Grigoriev IV, Martin FM, Perotto S (- 18) Ref: New Phytol, 217:1213, 2018 : PubMed ESTHER: Martino_2018_New.Phytol_217_1213 PubMedSearch: Martino 2018 New.Phytol 217 1213 PubMedID: 29315638 Gene_locus related to this paper: amore-a0a2t3axk4, amore-a0a2t3avs4, amore-a0a2t3ay04, amore-a0a2t3aph0 Abstract Some soil fungi in the Leotiomycetes form ericoid mycorrhizal (ERM) symbioses with Ericaceae. In the harsh habitats in which they occur, ERM plant survival relies on nutrient mobilization from soil organic matter (SOM) by their fungal partners. The characterization of the fungal genetic machinery underpinning both the symbiotic lifestyle and SOM degradation is needed to understand ERM symbiosis functioning and evolution, and its impact on soil carbon (C) turnover. We sequenced the genomes of the ERM fungi Meliniomyces bicolor, M. variabilis, Oidiodendron maius and Rhizoscyphus ericae, and compared their gene repertoires with those of fungi with different lifestyles (ecto- and orchid mycorrhiza, endophytes, saprotrophs, pathogens). We also identified fungal transcripts induced in symbiosis. The ERM fungal gene contents for polysaccharide-degrading enzymes, lipases, proteases and enzymes involved in secondary metabolism are closer to those of saprotrophs and pathogens than to those of ectomycorrhizal symbionts. The fungal genes most highly upregulated in symbiosis are those coding for fungal and plant cell wall-degrading enzymes (CWDEs), lipases, proteases, transporters and mycorrhiza-induced small secreted proteins (MiSSPs). The ERM fungal gene repertoire reveals a capacity for a dual saprotrophic and biotrophic lifestyle. This may reflect an incomplete transition from saprotrophy to the mycorrhizal habit, or a versatile life strategy similar to fungal endophytes. Title: Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle Murat C, Payen T, Noel B, Kuo A, Morin E, Chen J, Kohler A, Krizsan K, Balestrini R and Martin FM <40 more author(s)> Murat C, Payen T, Noel B, Kuo A, Morin E, Chen J, Kohler A, Krizsan K, Balestrini R, Da Silva C, Montanini B, Hainaut M, Levati E, Barry KW, Belfiori B, Cichocki N, Clum A, Dockter RB, Fauchery L, Guy J, Iotti M, Le Tacon F, Lindquist EA, Lipzen A, Malagnac F, Mello A, Molinier V, Miyauchi S, Poulain J, Riccioni C, Rubini A, Sitrit Y, Splivallo R, Traeger S, Wang M, Zifcakova L, Wipf D, Zambonelli A, Paolocci F, Nowrousian M, Ottonello S, Baldrian P, Spatafora JW, Henrissat B, Nagy LG, Aury JM, Wincker P, Grigoriev IV, Bonfante P, Martin FM (- 40) Ref: Nat Ecol Evol, 2:1956, 2018 : PubMed ESTHER: Murat_2018_Nat.Ecol.Evol_2_1956 PubMedSearch: Murat 2018 Nat.Ecol.Evol 2 1956 PubMedID: 30420746 Gene_locus related to this paper: 9pezi-a0a3n4l4q5, 9pezi-a0a3n4lpg7 Abstract Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Perigord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) and desert truffle (Terfezia boudieri) to saprotrophic Pezizomycetes. Reconstructed gene duplication/loss histories along a time-calibrated phylogeny of Ascomycetes revealed that Tuberaceae-specific traits may be related to a higher gene diversification rate. Genomic features in Tuber species appear to be very similar, with high transposon content, few genes coding lignocellulose-degrading enzymes, a substantial set of lineage-specific fruiting-body-upregulated genes and high expression of genes involved in volatile organic compound metabolism. Developmental and metabolic pathways expressed in ectomycorrhizae and fruiting bodies of T. magnatum and T. melanosporum are unexpectedly very similar, owing to the fact that they diverged ~100 Ma. Volatile organic compounds from pungent truffle odours are not the products of Tuber-specific gene innovations, but rely on the differential expression of an existing gene repertoire. These genomic resources will help to address fundamental questions in the evolution of the truffle lifestyle and the ecology of fungi that have been praised as food delicacies for centuries. Title: Population genomics of picophytoplankton unveils novel chromosome hypervariability Blanc-Mathieu R, Krasovec M, Hebrard M, Yau S, Desgranges E, Martin J, Schackwitz W, Kuo A, Salin G and Piganeau G <8 more author(s)> Blanc-Mathieu R, Krasovec M, Hebrard M, Yau S, Desgranges E, Martin J, Schackwitz W, Kuo A, Salin G, Donnadieu C, Desdevises Y, Sanchez-Ferandin S, Moreau H, Rivals E, Grigoriev IV, Grimsley N, Eyre-Walker A, Piganeau G (- 8) Ref: Sci Adv, 3:e1700239, 2017 : PubMed ESTHER: Blanc-Mathieu_2017_Sci.Adv_3_e1700239 PubMedSearch: Blanc-Mathieu 2017 Sci.Adv 3 e1700239 PubMedID: 28695208 Gene_locus related to this paper: ostta-q01g03 Abstract Tiny photosynthetic microorganisms that form the picoplankton (between 0.3 and 3 microm in diameter) are at the base of the food web in many marine ecosystems, and their adaptability to environmental change hinges on standing genetic variation. Although the genomic and phenotypic diversity of the bacterial component of the oceans has been intensively studied, little is known about the genomic and phenotypic diversity within each of the diverse eukaryotic species present. We report the level of genomic diversity in a natural population of Ostreococcus tauri (Chlorophyta, Mamiellophyceae), the smallest photosynthetic eukaryote. Contrary to the expectations of clonal evolution or cryptic species, the spectrum of genomic polymorphism observed suggests a large panmictic population (an effective population size of 1.2 x 10(7)) with pervasive evidence of sexual reproduction. De novo assemblies of low-coverage chromosomes reveal two large candidate mating-type loci with suppressed recombination, whose origin may pre-date the speciation events in the class Mamiellophyceae. This high genetic diversity is associated with large phenotypic differences between strains. Strikingly, resistance of isolates to large double-stranded DNA viruses, which abound in their natural environment, is positively correlated with the size of a single hypervariable chromosome, which contains 44 to 156 kb of strain-specific sequences. Our findings highlight the role of viruses in shaping genome diversity in marine picoeukaryotes. Title: Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels Wu W, Davis RW, Tran-Gyamfi MB, Kuo A, LaButti K, Mihaltcheva S, Hundley H, Chovatia M, Lindquist E and Gladden JM <3 more author(s)> Wu W, Davis RW, Tran-Gyamfi MB, Kuo A, LaButti K, Mihaltcheva S, Hundley H, Chovatia M, Lindquist E, Barry K, Grigoriev IV, Henrissat B, Gladden JM (- 3) Ref: Applied Microbiology & Biotechnology, 101:2603, 2017 : PubMed ESTHER: Wu_2017_Appl.Microbiol.Biotechnol_101_2603 PubMedSearch: Wu 2017 Appl.Microbiol.Biotechnol 101 2603 PubMedID: 28078400 Gene_locus related to this paper: 9pezi-a0a1y2u1s8, 9pezi-a0a1y2x077, 9pezi-a0a1y2vv92, 9pezi-a0a1y2txs8, 9pezi-a0a1y2wzb7, 9pezi-a0a1y2ufj7, 9pezi-a0a1y2vvc9, 9pezi-a0a1y2w3w4 Abstract Recently, several endophytic fungi have been demonstrated to produce volatile organic compounds (VOCs) with properties similar to fossil fuels, called "mycodiesel," while growing on lignocellulosic plant and agricultural residues. The fact that endophytes are plant symbionts suggests that some may be able to produce lignocellulolytic enzymes, making them capable of both deconstructing lignocellulose and converting it into mycodiesel, two properties that indicate that these strains may be useful consolidated bioprocessing (CBP) hosts for the biofuel production. In this study, four endophytes Hypoxylon sp. CI4A, Hypoxylon sp. EC38, Hypoxylon sp. CO27, and Daldinia eschscholzii EC12 were selected and evaluated for their CBP potential. Analysis of their genomes indicates that these endophytes have a rich reservoir of biomass-deconstructing carbohydrate-active enzymes (CAZys), which includes enzymes active on both polysaccharides and lignin, as well as terpene synthases (TPSs), enzymes that may produce fuel-like molecules, suggesting that they do indeed have CBP potential. GC-MS analyses of their VOCs when grown on four representative lignocellulosic feedstocks revealed that these endophytes produce a wide spectrum of hydrocarbons, the majority of which are monoterpenes and sesquiterpenes, including some known biofuel candidates. Analysis of their cellulase activity when grown under the same conditions revealed that these endophytes actively produce endoglucanases, exoglucanases, and beta-glucosidases. The richness of CAZymes as well as terpene synthases identified in these four endophytic fungi suggests that they are great candidates to pursue for development into platform CBP organisms. Title: Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M and Grigoriev IV <107 more 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 (- 107) Ref: Genome Biol, 18:28, 2017 : PubMed 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 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. Title: The genome of Xylona heveae provides a window into fungal endophytism Gazis R, Kuo A, Riley R, LaButti K, Lipzen A, Lin J, Amirebrahimi M, Hesse CN, Spatafora JW and Hibbett DS <3 more author(s)> Gazis R, Kuo A, Riley R, LaButti K, Lipzen A, Lin J, Amirebrahimi M, Hesse CN, Spatafora JW, Henrissat B, Hainaut M, Grigoriev IV, Hibbett DS (- 3) Ref: Fungal Biol, 120:26, 2016 : PubMed ESTHER: Gazis_2016_Fungal.Biol_120_26 PubMedSearch: Gazis 2016 Fungal.Biol 120 26 PubMedID: 26693682 Gene_locus related to this paper: 9pezi-a0a165f9w1, 9pezi-a0a165fsb2, 9pezi-a0a165gpf2, 9pezi-a0a164zp96, xylht-a0a165aju9, xylht-a0a165jye6, xylht-a0a165jir4 Abstract Xylona heveae has only been isolated as an endophyte of rubber trees. In an effort to understand the genetic basis of endophytism, we compared the genome contents of X. heveae and 36 other Ascomycota with diverse lifestyles and nutritional modes. We focused on genes that are known to be important in the host-fungus interaction interface and that presumably have a role in determining the lifestyle of a fungus. We used phylogenomic data to infer the higher-level phylogenetic position of the Xylonomycetes, and mined ITS sequences to explore its taxonomic and ecological diversity. The X. heveae genome contains a low number of enzymes needed for plant cell wall degradation, suggesting that Xylona is a highly adapted specialist and likely dependent on its host for survival. The reduced repertoire of carbohydrate active enzymes could reflect an adaptation to intercellulary growth and to the avoidance of the host's immune system, suggesting that Xylona has a strictly endophytic lifestyle. Phylogenomic data resolved the position of Xylonomycetes as sister to Lecanoromycetes and Eurotiomycetes and placed the beetle-endosymbiont Symbiotaphrina as a member of this class. ITS data revealed that Trinosporium is also part of the Xylonomycetes, extending the taxonomic and ecological diversity of this group. Title: Pan genome of the phytoplankton Emiliania underpins its global distribution Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, Maumus F, Mayer C, Miller J, Monier A and Grigoriev IV <27 more author(s)> Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, Maumus F, Mayer C, Miller J, Monier A, Salamov A, Young J, Aguilar M, Claverie JM, Frickenhaus S, Gonzalez K, Herman EK, Lin YC, Napier J, Ogata H, Sarno AF, Shmutz J, Schroeder D, de Vargas C, Verret F, von Dassow P, Valentin K, Van de Peer Y, Wheeler G, Dacks JB, Delwiche CF, Dyhrman ST, Glockner G, John U, Richards T, Worden AZ, Zhang X, Grigoriev IV (- 27) Ref: Nature, 499:209, 2013 : PubMed ESTHER: Read_2013_Nature_499_209 PubMedSearch: Read 2013 Nature 499 209 PubMedID: 23760476 Abstract Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions. Title: Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis Tisserant E, Malbreil M, Kuo A, Kohler A, Symeonidi A, Balestrini R, Charron P, Duensing N, Frei dit Frey N and Martin F <34 more author(s)> Tisserant E, Malbreil M, Kuo A, Kohler A, Symeonidi A, Balestrini R, Charron P, Duensing N, Frei dit Frey N, Gianinazzi-Pearson V, Gilbert LB, Handa Y, Herr JR, Hijri M, Koul R, Kawaguchi M, Krajinski F, Lammers PJ, Masclaux FG, Murat C, Morin E, Ndikumana S, Pagni M, Petitpierre D, Requena N, Rosikiewicz P, Riley R, Saito K, San Clemente H, Shapiro H, van Tuinen D, Becard G, Bonfante P, Paszkowski U, Shachar-Hill YY, Tuskan GA, Young JP, Sanders IR, Henrissat B, Rensing SA, Grigoriev IV, Corradi N, Roux C, Martin F (- 34) Ref: Proc Natl Acad Sci U S A, 110:20117, 2013 : PubMed ESTHER: Tisserant_2013_Proc.Natl.Acad.Sci.U.S.A_110_20117 PubMedSearch: Tisserant 2013 Proc.Natl.Acad.Sci.U.S.A 110 20117 PubMedID: 24277808 Gene_locus related to this paper: rhiid-u9u175, rhiid-u9trg1, rhiid-u9uh96, rhiid-u9ttu4 Abstract The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota. Title: The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation Blanc G, Agarkova I, Grimwood J, Kuo A, Brueggeman A, Dunigan DD, Gurnon J, Ladunga I, Lindquist E and Van Etten JL <11 more author(s)> Blanc G, Agarkova I, Grimwood J, Kuo A, Brueggeman A, Dunigan DD, Gurnon J, Ladunga I, Lindquist E, Lucas S, Pangilinan J, Proschold T, Salamov A, Schmutz J, Weeks D, Yamada T, Lomsadze A, Borodovsky M, Claverie JM, Grigoriev IV, Van Etten JL (- 11) Ref: Genome Biol, 13:R39, 2012 : PubMed ESTHER: Blanc_2012_Genome.Biol_13_R39 PubMedSearch: Blanc 2012 Genome.Biol 13 R39 PubMedID: 22630137 Gene_locus related to this paper: 9chlo-i0z4k0, 9chlo-i0ylt0, cocsc-i0ytb9, cocsc-i0yin5 Abstract BACKGROUND: Little is known about the mechanisms of adaptation of life to the extreme environmental conditions encountered in polar regions. Here we present the genome sequence of a unicellular green alga from the division chlorophyta, Coccomyxa subellipsoidea C-169, which we will hereafter refer to as C-169. This is the first eukaryotic microorganism from a polar environment to have its genome sequenced. Title: Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH and Archibald JM <63 more author(s)> Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, Elias M, Eveleigh RJ, Herman EK, Klute MJ, Nakayama T, Obornik M, Reyes-Prieto A, Armbrust EV, Aves SJ, Beiko RG, Coutinho P, Dacks JB, Durnford DG, Fast NM, Green BR, Grisdale CJ, Hempel F, Henrissat B, Hoppner MP, Ishida K, Kim E, Koreny L, Kroth PG, Liu Y, Malik SB, Maier UG, McRose D, Mock T, Neilson JA, Onodera NT, Poole AM, Pritham EJ, Richards TA, Rocap G, Roy SW, Sarai C, Schaack S, Shirato S, Slamovits CH, Spencer DF, Suzuki S, Worden AZ, Zauner S, Barry K, Bell C, Bharti AK, Crow JA, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden GI, Lane CE, Keeling PJ, Gray MW, Grigoriev IV, Archibald JM (- 63) Ref: Nature, 492:59, 2012 : PubMed ESTHER: Curtis_2012_Nature_492_59 PubMedSearch: Curtis 2012 Nature 492 59 PubMedID: 23201678 Gene_locus related to this paper: guith-l1i9i5, guith-l1k167, guitc-l1jmn9 Abstract Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph. 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 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: Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics Gobler CJ, Berry DL, Dyhrman ST, Wilhelm SW, Salamov A, Lobanov AV, Zhang Y, Collier JL, Wurch LL and Grigoriev IV <23 more author(s)> Gobler CJ, Berry DL, Dyhrman ST, Wilhelm SW, Salamov A, Lobanov AV, Zhang Y, Collier JL, Wurch LL, Kustka AB, Dill BD, Shah M, VerBerkmoes NC, Kuo A, Terry A, Pangilinan J, Lindquist EA, Lucas S, Paulsen IT, Hattenrath-Lehmann TK, Talmage SC, Walker EA, Koch F, Burson AM, Marcoval MA, Tang YZ, Lecleir GR, Coyne KJ, Berg GM, Bertrand EM, Saito MA, Gladyshev VN, Grigoriev IV (- 23) Ref: Proc Natl Acad Sci U S A, 108:4352, 2011 : PubMed ESTHER: Gobler_2011_Proc.Natl.Acad.Sci.U.S.A_108_4352 PubMedSearch: Gobler 2011 Proc.Natl.Acad.Sci.U.S.A 108 4352 PubMedID: 21368207 Gene_locus related to this paper: auran-f0xvq5, auran-f0xwb9, auran-f0y4x4, auran-f0y5a8, auran-f0ycl4, auran-f0ycp7, auran-f0ye99, auran-f0yge8, auran-f0yci9, auran-f0yr72, auran-f0y8q8, auran-f0y7s1 Abstract Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium- and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs. Title: Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum Sucgang R, Kuo A, Tian X, Salerno W, Parikh A, Feasley CL, Dalin E, Tu H, Huang E and Grigoriev IV <31 more author(s)> Sucgang R, Kuo A, Tian X, Salerno W, Parikh A, Feasley CL, Dalin E, Tu H, Huang E, Barry K, Lindquist E, Shapiro H, Bruce D, Schmutz J, Salamov A, Fey P, Gaudet P, Anjard C, Babu MM, Basu S, Bushmanova Y, van der Wel H, Katoh-Kurasawa M, Dinh C, Coutinho PM, Saito T, Elias M, Schaap P, Kay RR, Henrissat B, Eichinger L, Rivero F, Putnam NH, West CM, Loomis WF, Chisholm RL, Shaulsky G, Strassmann JE, Queller DC, Kuspa A, Grigoriev IV (- 31) Ref: Genome Biol, 12:R20, 2011 : PubMed ESTHER: Sucgang_2011_Genome.Biol_12_R20.1 PubMedSearch: Sucgang 2011 Genome.Biol 12 R20.1 PubMedID: 21356102 Gene_locus related to this paper: dicpu-f0z7q0, dicpu-f0z822, dicpu-f0zfi0, dicpu-f0zjs1, dicpu-f0zks4, dicpu-f0zmm3, dicpu-f0zmm8, dicpu-f0zmm9, dicpu-f0zni7, dicpu-f0znl3, dicpu-f0zq90, dicpu-f0zvn5, dicpu-f0zxa4, dicpu-f0zyf9, dicpu-f1a3n5, dicpu-f1a5b4, dicpu-f1a269, dicpu-f1a615, dicpu-f0ztw9, dicpu-f0zri3, dicpu-f0zys7 Abstract BACKGROUND: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. Title: Comparative genomics of xylose-fermenting fungi for enhanced biofuel production Wohlbach DJ, Kuo A, Sato TK, Potts KM, Salamov AA, LaButti KM, Sun H, Clum A, Pangilinan JL and Gasch AP <11 more author(s)> Wohlbach DJ, Kuo A, Sato TK, Potts KM, Salamov AA, LaButti KM, Sun H, Clum A, Pangilinan JL, Lindquist EA, Lucas S, Lapidus A, Jin M, Gunawan C, Balan V, Dale BE, Jeffries TW, Zinkel R, Barry KW, Grigoriev IV, Gasch AP (- 11) Ref: Proc Natl Acad Sci U S A, 108:13212, 2011 : PubMed ESTHER: Wohlbach_2011_Proc.Natl.Acad.Sci.U.S.A_108_13212 PubMedSearch: Wohlbach 2011 Proc.Natl.Acad.Sci.U.S.A 108 13212 PubMedID: 21788494 Gene_locus related to this paper: cantc-g3b3r0, spapn-g3ap60, spapn-g3aif9, cantc-g3axw7 Abstract Cellulosic biomass is an abundant and underused substrate for biofuel production. The inability of many microbes to metabolize the pentose sugars abundant within hemicellulose creates specific challenges for microbial biofuel production from cellulosic material. Although engineered strains of Saccharomyces cerevisiae can use the pentose xylose, the fermentative capacity pales in comparison with glucose, limiting the economic feasibility of industrial fermentations. To better understand xylose utilization for subsequent microbial engineering, we sequenced the genomes of two xylose-fermenting, beetle-associated fungi, Spathaspora passalidarum and Candida tenuis. To identify genes involved in xylose metabolism, we applied a comparative genomic approach across 14 Ascomycete genomes, mapping phenotypes and genotypes onto the fungal phylogeny, and measured genomic expression across five Hemiascomycete species with different xylose-consumption phenotypes. This approach implicated many genes and processes involved in xylose assimilation. Several of these genes significantly improved xylose utilization when engineered into S. cerevisiae, demonstrating the power of comparative methods in rapidly identifying genes for biomass conversion while reflecting on fungal ecology. Title: The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex Blanc G, Duncan G, Agarkova I, Borodovsky M, Gurnon J, Kuo A, Lindquist E, Lucas S, Pangilinan J and Van Etten JL <7 more author(s)> Blanc G, Duncan G, Agarkova I, Borodovsky M, Gurnon J, Kuo A, Lindquist E, Lucas S, Pangilinan J, Polle J, Salamov A, Terry A, Yamada T, Dunigan DD, Grigoriev IV, Claverie JM, Van Etten JL (- 7) Ref: Plant Cell, 22:2943, 2010 : PubMed ESTHER: Blanc_2010_Plant.Cell_22_2943 PubMedSearch: Blanc 2010 Plant.Cell 22 2943 PubMedID: 20852019 Gene_locus related to this paper: chlva-e1z3j3, chlva-e1z3n9, chlva-e1z620, chlva-e1z882, chlva-e1zd56, chlva-e1zdd9, chlva-e1zde0, chlva-e1ze02, chlva-e1zeh7, chlva-e1zhu4, chlva-e1zie3, chlva-e1zii9, chlva-e1zmj6, chlva-e1ztt0, chlva-e1z5k1, chlva-e1ztf4 Abstract Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model system for studying virus/algal interactions. We sequenced its 46-Mb nuclear genome, revealing an expansion of protein families that could have participated in adaptation to symbiosis. NC64A exhibits variations in GC content across its genome that correlate with global expression level, average intron size, and codon usage bias. Although Chlorella species have been assumed to be asexual and nonmotile, the NC64A genome encodes all the known meiosis-specific proteins and a subset of proteins found in flagella. We hypothesize that Chlorella might have retained a flagella-derived structure that could be involved in sexual reproduction. Furthermore, a survey of phytohormone pathways in chlorophyte algae identified algal orthologs of Arabidopsis thaliana genes involved in hormone biosynthesis and signaling, suggesting that these functions were established prior to the evolution of land plants. We show that the ability of Chlorella to produce chitinous cell walls likely resulted from the capture of metabolic genes by horizontal gene transfer from algal viruses, prokaryotes, or fungi. Analysis of the NC64A genome substantially advances our understanding of the green lineage evolution, including the genomic interplay with viruses and symbiosis between eukaryotes. Title: The genome of Naegleria gruberi illuminates early eukaryotic versatility Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, Kuo A, Paredez A, Chapman J and Dawson SC <14 more author(s)> Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, Kuo A, Paredez A, Chapman J, Pham J, Shu S, Neupane R, Cipriano M, Mancuso J, Tu H, Salamov A, Lindquist E, Shapiro H, Lucas S, Grigoriev IV, Cande WZ, Fulton C, Rokhsar DS, Dawson SC (- 14) Ref: Cell, 140:631, 2010 : PubMed ESTHER: Fritz-Laylin_2010_Cell_140_631 PubMedSearch: Fritz-Laylin 2010 Cell 140 631 PubMedID: 20211133 Gene_locus related to this paper: naegr-d2ux86, naegr-d2uyl7, naegr-d2uyn1, naegr-d2uzk6, naegr-d2uzp4, naegr-d2v1m1, naegr-d2v3p5, naegr-d2v5p1, naegr-d2v6f6, naegr-d2v6y9, naegr-d2v8x8, naegr-d2v186, naegr-d2v339, naegr-d2v556, naegr-d2vbq7, naegr-d2vdq6, naegr-d2ve51, naegr-d2vga2, naegr-d2vgm9, naegr-d2vh14, naegr-d2vha2, naegr-d2vj80, naegr-d2vjj7, naegr-d2vl41, naegr-d2vmj5, naegr-d2vms7, naegr-d2vqi5, naegr-d2vr44, naegr-d2vrq2, naegr-d2vs01, naegr-d2vs58, naegr-d2vts5, naegr-d2vu69, naegr-d2vvg8, naegr-d2vxp2, naegr-d2vyl1, naegr-d2vzy5, naegr-d2w0l5, naegr-d2w0v9, naegr-d2w3g8, naegr-d2w3v7, naegr-d2w3v8, naegr-d2vct1 Abstract Genome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules. Title: Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T and Rokhsar DS <18 more author(s)> Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, Pangilinan J, Kapitonov V, Jurka J, Salamov A, Shapiro H, Schmutz J, Grimwood J, Lindquist E, Lucas S, Grigoriev IV, Schmitt R, Kirk D, Rokhsar DS (- 18) Ref: Science, 329:223, 2010 : PubMed ESTHER: Prochnik_2010_Science_329_223 PubMedSearch: Prochnik 2010 Science 329 223 PubMedID: 20616280 Gene_locus related to this paper: volca-d8tmz1, volca-d8tne9, volca-d8tnn6, volca-d8tns6, volca-d8tr92, volca-d8u2d3, volca-d8u5r0, volca-d8u7s7, volca-d8u7s8, volca-d8u9w4, volca-d8u460, volca-d8uab7, volca-d8uai0, volca-d8uev0, volca-d8uhi9, volca-d8uiw9, volca-d8ujv0, volca-d8uf23, volca-d8tmz9, volca-d8u6e0 Abstract The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are well suited for the investigation of the evolution of multicellularity and development. We sequenced the 138-mega-base pair genome of V. carteri and compared its approximately 14,500 predicted proteins to those of its unicellular relative Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similar protein-coding potentials and few species-specific protein-coding gene predictions. Volvox is enriched in volvocine-algal-specific proteins, including those associated with an expanded and highly compartmentalized extracellular matrix. Our analysis shows that increases in organismal complexity can be associated with modifications of lineage-specific proteins rather than large-scale invention of protein-coding capacity. Title: The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ and Vanetten HD <29 more author(s)> Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ, Zhou S, Schwartz DC, Freitag M, Ma LJ, Danchin EG, Henrissat B, Coutinho PM, Nelson DR, Straney D, Napoli CA, Barker BM, Gribskov M, Rep M, Kroken S, Molnar I, Rensing C, Kennell JC, Zamora J, Farman ML, Selker EU, Salamov A, Shapiro H, Pangilinan J, Lindquist E, Lamers C, Grigoriev IV, Geiser DM, Covert SF, Temporini E, Vanetten HD (- 29) Ref: PLoS Genet, 5:e1000618, 2009 : PubMed ESTHER: Coleman_2009_PLoS.Genet_5_E1000618 PubMedSearch: Coleman 2009 PLoS.Genet 5 E1000618 PubMedID: 19714214 Gene_locus related to this paper: fusso-cutas, nech7-c7yh18, nech7-c7yir8, nech7-c7yiz6, nech7-c7yjl4, nech7-c7yjp7, nech7-c7yjq0, nech7-c7ymg9, nech7-c7ymv6, nech7-c7yna5, nech7-c7ynt6, nech7-c7yq59, nech7-c7yq86, nech7-c7yqb0, nech7-c7yqx3, nech7-c7ysz7, nech7-c7ysz8, nech7-c7ytb2, nech7-c7yum7, nech7-c7yvb1, nech7-c7yvb8, nech7-c7yvf1, nech7-c7yvq8, nech7-c7yw21, nech7-c7yx47, nech7-c7yx92, nech7-c7yxe7, nech7-c7yxq5, nech7-c7yxz4, nech7-c7yy47, nech7-c7yyj7, nech7-c7yym7, nech7-c7z0d7, nech7-c7z0s1, nech7-c7z1g9, nech7-c7z1k9, nech7-c7z2k4, nech7-c7z2m9, nech7-c7z2z2, nech7-c7z3z3, nech7-c7z4a4, nech7-c7z5n1, nech7-c7z5y2, nech7-c7z6g5, nech7-c7z7d0, nech7-c7z7w8, nech7-c7z8q7, nech7-c7z9e7, nech7-c7z073, nech7-c7z354, nech7-c7z389, nech7-c7z688, nech7-c7z855, nech7-c7z987, nech7-c7za94, nech7-c7zah0, nech7-c7zb79, nech7-c7zbr8, nech7-c7zcd1, nech7-c7zdx8, nech7-c7ze42, nech7-c7ze84, nech7-c7zed8, nech7-c7zeh0, nech7-c7zes2, nech7-c7zgw2, nech7-c7zha0, nech7-c7zhy2, nech7-c7zi55, nech7-c7zig4, nech7-c7zjg0, nech7-c7zjv2, nech7-c7zk96, nech7-c7zkb5, nech7-c7zkh4, nech7-c7zla9, nech7-c7zld2, nech7-c7zlz1, nech7-c7zm00, nech7-c7zmn4, nech7-c7zmu6, nech7-c7zp06, nech7-c7zp78, nech7-c7zq58, nech7-c7zq86, nech7-c7zqb5, nech7-c7zqk4, nech7-c7zqp9, nech7-c7zr59, nech7-c7zrh2, nech7-c7zrh3, nech7-dapb, nech7-kex1, nech7-c7zgl9, nech7-c7z935, nech7-c7znc0, nech7-c7yiq8, nech7-c7yiq7, nech7-c7zhu0, nech7-c7yw61, nech7-c7yqd3, nech7-c7zkb6, nech7-c7z3b4, nech7-c7ytr4, nech7-c7zgf7, 9hypo-a0a3m2s2j6, nech7-c7yq54, fusv7-cbpya Abstract The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of >50 species known as the "Fusarium solani species complex". Members of this complex have diverse biological properties including the ability to cause disease on >100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6.52 Mb and that the physical size of the genome, 54.43 Mb, and the number of predicted genes, 15,707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin(s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches. Title: The Phaeodactylum genome reveals the evolutionary history of diatom genomes Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F and Grigoriev IV <67 more author(s)> Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A, Fournet J, Haruta M, Huysman MJ, Jenkins BD, Jiroutova K, Jorgensen RE, Joubert Y, Kaplan A, Kroger N, Kroth PG, La Roche J, Lindquist E, Lommer M, Martin-Jezequel V, Lopez PJ, Lucas S, Mangogna M, McGinnis K, Medlin LK, Montsant A, Oudot-Le Secq MP, Napoli C, Obornik M, Parker MS, Petit JL, Porcel BM, Poulsen N, Robison M, Rychlewski L, Rynearson TA, Schmutz J, Shapiro H, Siaut M, Stanley M, Sussman MR, Taylor AR, Vardi A, von Dassow P, Vyverman W, Willis A, Wyrwicz LS, Rokhsar DS, Weissenbach J, Armbrust EV, Green BR, Van de Peer Y, Grigoriev IV (- 67) Ref: Nature, 456:239, 2008 : PubMed ESTHER: Bowler_2008_Nature_456_239 PubMedSearch: Bowler 2008 Nature 456 239 PubMedID: 18923393 Gene_locus related to this paper: phatc-b7fp91, phatc-b7fqd3, phatc-b7frf9, phatc-b7fry8, phatc-b7ftw8, phatc-b7fv70, phatc-b7fw66, phatc-b7g2b2, phatc-b7g5z5, phatc-b7g6f1, phatc-b7g6r8, phatc-b7g957, phatc-b7ga73, phatc-b7gb22, phatc-b7gc60, phatc-b7gdm3, phatc-b7gdq6, phatc-b7ge82, phatc-b7gee0, phatr-b7frs5, phatr-b7g1k3, phatr-b7s4a4, thaps-b8bsy4, thaps-b8cfn8, phatc-b7g635, phatc-b7gaj3, thaps-b8c079 Abstract Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes ( approximately 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans. Title: The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y and Rokhsar D <26 more author(s)> King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, Zuzow R, Dirks W, Good M, Goodstein D, Lemons D, Li W, Lyons JB, Morris A, Nichols S, Richter DJ, Salamov A, Sequencing JG, Bork P, Lim WA, Manning G, Miller WT, McGinnis W, Shapiro H, Tjian R, Grigoriev IV, Rokhsar D (- 26) Ref: Nature, 451:783, 2008 : PubMed ESTHER: King_2008_Nature_451_783 PubMedSearch: King 2008 Nature 451 783 PubMedID: 18273011 Gene_locus related to this paper: monbe-a9up87, monbe-a9uq69, monbe-a9uq70, monbe-a9uqa7, monbe-a9urz6, monbe-a9usu1, monbe-a9usy8, monbe-a9uta2, monbe-a9uu09, monbe-a9uxl2, monbe-a9uy23, monbe-a9uy95, monbe-a9uym3, monbe-a9uyw1, monbe-a9uzc1, monbe-a9v0e1, monbe-a9v2b0, monbe-a9v3a5, monbe-a9v3t2, monbe-a9v4h5, monbe-a9v6i1, monbe-a9v7b2, monbe-a9v7c1, monbe-a9v8k9, monbe-a9v8u8, monbe-a9v9i9, monbe-a9v9k6, monbe-a9v028, monbe-a9v108, monbe-a9v315, monbe-a9v345, monbe-a9v368, monbe-a9v719, monbe-a9v871, monbe-a9vac5, monbe-a9vah5, monbe-a9van7, monbe-a9vbp2, monbe-a9vcn6, monbe-a9vd99, monbe-a9vdj5, monbe-a9vag0 Abstract Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome of the unicellular choanoflagellate Monosiga brevicollis. The genome contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion and signalling protein domains that are otherwise restricted to metazoans. Here we show that the physical linkages among protein domains often differ between M. brevicollis and metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages. The completion of the M. brevicollis genome allows us to reconstruct with increasing resolution the genomic changes that accompanied the origin of metazoans. Title: The Trichoplax genome and the nature of placozoans Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A and Rokhsar DS <11 more author(s)> Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, Signorovitch AY, Moreno MA, Kamm K, Grimwood J, Schmutz J, Shapiro H, Grigoriev IV, Buss LW, Schierwater B, Dellaporta SL, Rokhsar DS (- 11) Ref: Nature, 454:955, 2008 : PubMed ESTHER: Srivastava_2008_Nature_454_955 PubMedSearch: Srivastava 2008 Nature 454 955 PubMedID: 18719581 Gene_locus related to this paper: triad-b3rka6, triad-b3rkc3, triad-b3rkc4, triad-b3rkc5, triad-b3rkr2, triad-b3rks9, triad-b3rkt0, triad-b3rl14, triad-b3rls2, triad-b3rnj7, triad-b3rnw5, triad-b3rrr2, triad-b3rsh1, triad-b3rsh3, triad-b3rty7, triad-b3ru11, triad-b3rur2, triad-b3rut0, triad-b3rvc1, triad-b3rw12, triad-b3rwp0, triad-b3rwr4, triad-b3rxn2, triad-b3ry59, triad-b3s1y9, triad-b3s3d8, triad-b3s3e9, triad-b3s8a0, triad-b3s9x4, triad-b3s445, triad-b3s449, triad-b3s478, triad-b3s705, triad-b3s706, triad-b3s898, triad-b3s899, triad-b3s949, triad-b3s950, triad-b3sa20, triad-b3sa22, triad-b3sa23, triad-b3sa24, triad-b3sa25, triad-b3sa26, triad-b3sa27, triad-b3sa28, triad-b3sa29, triad-b3sa31, triad-b3sa33, triad-b3sa34, triad-b3sa36, triad-b3sb39, triad-b3scd3, triad-b3scg3, triad-b3scg4, triad-b3scr3, triad-b3seb0, triad-b3seb1, triad-b3seu9, triad-b3sf12, triad-b3rt61, triad-b3rt62, triad-b3rj15, triad-b3sdi1 Abstract As arguably the simplest free-living animals, placozoans may represent a primitive metazoan form, yet their biology is poorly understood. Here we report the sequencing and analysis of the approximately 98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole-genome phylogenetic analysis suggests that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome shows conserved gene content, gene structure and synteny in relation to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signalling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages. | |||||||
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