Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

[1]  L. Lanfranco,et al.  Unique and common traits in mycorrhizal symbioses , 2020, Nature Reviews Microbiology.

[2]  A. Kohler,et al.  Mycorrhizal effector PaMiSSP10b alters polyamine biosynthesis in Eucalyptus root cells and promotes root colonization. , 2020, The New phytologist.

[3]  A. Kohler,et al.  The small secreted effector protein MiSSP7.6 of Laccaria bicolor is required for the establishment of ectomycorrhizal symbiosis. , 2020, Environmental microbiology.

[4]  P. Kennedy,et al.  Functional convergence in the decomposition of fungal necromass in soil and wood. , 2019, FEMS microbiology ecology.

[5]  C. Mathé,et al.  In silico definition of new ligninolytic peroxidase sub-classes in fungi and putative relation to fungal life style , 2019, Scientific Reports.

[6]  S. Frey Mycorrhizal Fungi as Mediators of Soil Organic Matter Dynamics , 2019, Annual Review of Ecology, Evolution, and Systematics.

[7]  L. Tedersoo,et al.  Mycorrhizal types differ in ecophysiology and alter plant nutrition and soil processes , 2019, Biological reviews of the Cambridge Philosophical Society.

[8]  B. Henrissat,et al.  Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae. , 2019, The New phytologist.

[9]  A. Classen,et al.  Exploring the role of ectomycorrhizal fungi in soil carbon dynamics. , 2019, The New phytologist.

[10]  Juying Yan,et al.  Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi , 2019, Proceedings of the National Academy of Sciences.

[11]  B. Henrissat,et al.  Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina. , 2019, The New phytologist.

[12]  D. Hibbett,et al.  Megaphylogeny resolves global patterns of mushroom evolution , 2019, Nature Ecology & Evolution.

[13]  J. Stajich,et al.  Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota. , 2019, The New phytologist.

[14]  L. Saint-Andre,et al.  First evidences that the ectomycorrhizal fungus Paxillus involutus mobilizes nitrogen and carbon from saprotrophic fungus necromass , 2018, Environmental microbiology.

[15]  Emmanuel Paradis,et al.  ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R , 2018, Bioinform..

[16]  C. Troein,et al.  The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen , 2018, The ISME Journal.

[17]  D. Hibbett,et al.  Contemporaneous radiations of fungi and plants linked to symbiosis , 2018, Nature Communications.

[18]  George E Anasontzis,et al.  The ectomycorrhizal basidiomycete Laccaria bicolor releases a secreted β-1,4 endoglucanase that plays a key role in symbiosis development. , 2018, The New phytologist.

[19]  L. Tedersoo,et al.  Evolutionary history of mycorrhizal symbioses and global host plant diversity. , 2018, The New phytologist.

[20]  M. Selosse,et al.  The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics. , 2018, The New phytologist.

[21]  J. Poulain,et al.  Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle , 2018, Nature Ecology & Evolution.

[22]  R. Vilgalys,et al.  Correction: Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus , 2018, PLoS genetics.

[23]  B. Henrissat,et al.  Rapid Divergence of Genome Architectures Following the Origin of an Ectomycorrhizal Symbiosis in the Genus Amanita , 2018, Molecular biology and evolution.

[24]  B. Henrissat,et al.  Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists. , 2018, The New phytologist.

[25]  Takaki Maekawa,et al.  Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen , 2018, BMC Genomics.

[26]  C. Peterson,et al.  Fenton reaction facilitates organic nitrogen acquisition by an ectomycorrhizal fungus , 2018, The New phytologist.

[27]  D. Zak,et al.  Ectomycorrhizal fungi and the enzymatic liberation of nitrogen from soil organic matter: why evolutionary history matters. , 2018, The New phytologist.

[28]  L. Nagy,et al.  Complex multicellularity in fungi: evolutionary convergence, single origin, or both? , 2018, Biological reviews of the Cambridge Philosophical Society.

[29]  Virginie Puech-Pagès,et al.  Laccaria bicolor MiSSP8 is a small-secreted protein decisive for the establishment of the ectomycorrhizal symbiosis , 2017, bioRxiv.

[30]  Sean Doyle,et al.  Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria , 2017, Nature Ecology & Evolution.

[31]  David K. Smith,et al.  ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data , 2017 .

[32]  L. Tedersoo,et al.  Evolution of ectomycorrhizal symbiosis in plants , 2017 .

[33]  L. Tedersoo,et al.  Ectomycorrhizal Fungal Lineages: Detection of Four New Groups and Notes on Consistent Recognition of Ectomycorrhizal Taxa in High-Throughput Sequencing Studies , 2017 .

[34]  Francis Martin,et al.  Unearthing the roots of ectomycorrhizal symbioses , 2016, Nature Reviews Microbiology.

[35]  R. Vilgalys,et al.  Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus , 2016, PLoS genetics.

[36]  B. Henrissat,et al.  Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum , 2016, Nature Communications.

[37]  M. Schatz,et al.  Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.

[38]  J. Grimwood,et al.  Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles , 2016, PLoS genetics.

[39]  D. Hibbett,et al.  Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities. , 2016, Molecular biology and evolution.

[40]  Scott T. Bates,et al.  FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild , 2016 .

[41]  D. Hibbett,et al.  Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors , 2015, The New phytologist.

[42]  F. Martin,et al.  Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins , 2015, Front. Microbiol..

[43]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[44]  B. Lindahl,et al.  Ectomycorrhizal fungi - potential organic matter decomposers, yet not saprotrophs. , 2015, The New phytologist.

[45]  M. V. D. van der Heijden,et al.  Mycorrhizal ecology and evolution : the past , the present , and the future , 2015 .

[46]  Bernard Henrissat,et al.  Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists , 2015, Nature Genetics.

[47]  R. Henrik Nilsson,et al.  Global diversity and geography of soil fungi , 2014, Science.

[48]  D. Hibbett,et al.  Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts , 2014, Nature Communications.

[49]  F. Martin,et al.  Ectomycorrhizal Cortinarius species participate in enzymatic oxidation of humus in northern forest ecosystems. , 2014, The New phytologist.

[50]  Jens Kattge,et al.  A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms , 2014, Nature Communications.

[51]  S. Grayston,et al.  Specificity of plant-microbe interactions in the tree mycorrhizosphere biome and consequences for soil C cycling , 2014, Front. Microbiol..

[52]  J. Morrell-Falvey,et al.  Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genes , 2014, Proceedings of the National Academy of Sciences.

[53]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[54]  Inna Dubchak,et al.  MycoCosm portal: gearing up for 1000 fungal genomes , 2013, Nucleic Acids Res..

[55]  Pedro M. Coutinho,et al.  The carbohydrate-active enzymes database (CAZy) in 2013 , 2013, Nucleic Acids Res..

[56]  Yan Zhang,et al.  PATRIC, the bacterial bioinformatics database and analysis resource , 2013, Nucleic Acids Res..

[57]  I. Grigoriev,et al.  Chapter One – Fungal Genomics: Sequencing and Annotation , 2014 .

[58]  Ari Löytynoja,et al.  Phylogeny-aware alignment with PRANK. , 2014, Methods in molecular biology.

[59]  C. Troein,et al.  Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus , 2013, The ISME Journal.

[60]  O. Ovaskainen,et al.  Roots and Associated Fungi Drive Long-Term Carbon Sequestration in Boreal Forest , 2013, Science.

[61]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[62]  Manolis Kellis,et al.  TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees , 2012, Systematic biology.

[63]  R. Gibbs,et al.  Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology , 2012, PloS one.

[64]  Albee Y. Ling,et al.  The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes , 2012, Science.

[65]  M. Schatz,et al.  Hybrid error correction and de novo assembly of single-molecule sequencing reads , 2012, Nature Biotechnology.

[66]  Franck Picard,et al.  High-quality sequence clustering guided by network topology and multiple alignment likelihood , 2012, Bioinform..

[67]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[68]  Cedric E. Ginestet ggplot2: Elegant Graphics for Data Analysis , 2011 .

[69]  A. Gnirke,et al.  High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.

[70]  Bernard Henrissat,et al.  Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis , 2010, Nature.

[71]  T. May,et al.  Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages , 2010, Mycorrhiza.

[72]  F. Konietschke,et al.  Simultane Konfidenzintervalle für nichtparametrische relative Kontrasteffekte , 2009 .

[73]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[74]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[75]  Adam P. Arkin,et al.  FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix , 2009, Molecular biology and evolution.

[76]  D. J. Lodge,et al.  Out of the Palaeotropics? Historical biogeography and diversification of the cosmopolitan ectomycorrhizal mushroom family Inocybaceae , 2009 .

[77]  J. Logsdon,et al.  Signs of Sex: What We Know and How We Know It , 2022 .

[78]  Brandi L. Cantarel,et al.  The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics , 2008, Nucleic Acids Res..

[79]  M. Ueda,et al.  Characterization of the carbohydrase productions of an ectomycorrhizal fungus, Tricholoma matsutake , 2008, Mycoscience.

[80]  A. Löytynoja,et al.  Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis , 2008, Science.

[81]  J. Herr,et al.  Ectomycorrhizal fungi and the biotrophy-saprotrophy continuum. , 2008, The New phytologist.

[82]  Y. Van de Peer,et al.  The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis , 2008, Nature.

[83]  Tomislav Domazet-Loso,et al.  A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. , 2007, Trends in genetics : TIG.

[84]  S. Trumbore,et al.  Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest. , 2007, The New phytologist.

[85]  P. Legendre,et al.  vegan : Community Ecology Package. R package version 1.8-5 , 2007 .

[86]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[87]  R. Hanlin,et al.  Perithecial ascomycetes from the 400 million year old Rhynie chert: an example of ancestral polymorphism , 2005 .

[88]  R. Hanlin,et al.  Perithecial ascomycetes from the 400 million year old Rhynie chert: an example of ancestral polymorphism. , 2005, Mycologia.

[89]  Michael J. Sanderson,et al.  R8s: Inferring Absolute Rates of Molecular Evolution, Divergence times in the Absence of a Molecular Clock , 2003, Bioinform..

[90]  Wu-chun Feng,et al.  The design, implementation, and evaluation of mpiBLAST , 2003 .

[91]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[92]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[93]  M. Donoghue,et al.  Fossil mushrooms from Miocene and Cretaceous ambers and the evolution of Homobasidiomycetes. , 1997, American journal of botany.

[94]  B. LePage,et al.  Fossil ectomycorrhizae from the Middle Eocene. , 1997, American journal of botany.

[95]  D. Soltis,et al.  Chloroplast gene sequence data suggest a single origin of the predisposition for symbiotic nitrogen fixation in angiosperms. , 1995, Proceedings of the National Academy of Sciences of the United States of America.