The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata

The draft genome of the lichen-forming fungus Lasallia hispanica (Frey) Sancho & A. Crespo

(2018) Francesco DAL GRANDE et al.   LICHENOLOGIST

Beyond histones - the expanding roles of protein lysine methylation

(2017) Zhouran Wu et al.   FEBS Journal

Comparative Genomics of Chrysochromulina Ericina Virus and Other Microalga-Infecting Large DNA Viruses Highlights Their Intricate Evolutionary Relationship with the Established Mimiviridae Family

(2017) Lucie Gallot-Lavallée et al.   JOURNAL OF VIROLOGY

The cost of surviving nitrogen excess: energy and protein demand in the lichen Cladonia portentosa as revealed by proteomic analysis

(2017) Silvana Munzi et al.   PLANTA

Chromosome-level genome assembly and transcriptome of the green algaChromochloris zofingiensisilluminates astaxanthin production

(2017) Melissa S. Roth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window

(2017) Lucie Gallot-Lavallée et al.   Viruses-Basel

Fungal and cyanobacterial gene expression in a lichen symbiosis: Effect of temperature and location

(2016) Sophie S. Steinhäuser et al.   Fungal Biology

Cyphobasidium gen. nov., a new lichen-inhabiting lineage in the Cystobasidiomycetes (Pucciniomycotina, Basidiomycota, Fungi)

(2016) Ana M. Millanes et al.   Fungal Biology

Putative identification of the usnic acid biosynthetic gene cluster by de novo whole-genome sequencing of a lichen-forming fungus

(2016) Mona Abdel-Hameed et al.   Fungal Biology

Study of Gene Trafficking betweenAcanthamoebaand Giant Viruses Suggests an Undiscovered Family of Amoeba-Infecting Viruses

(2016) Florian Maumus et al.   Genome Biology and Evolution

Sebacinales - one thousand and one interactions with land plants

(2016) Michael Weiß et al.   NEW PHYTOLOGIST

Fungal-algal association patterns in lichen symbiosis linked to macroclimate

(2016) Garima Singh et al.   NEW PHYTOLOGIST

TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

(2016) Liam D. H. Elbourne et al.   NUCLEIC ACIDS RESEARCH

New features of desiccation tolerance in the lichen photobiont Trebouxia gelatinosa are revealed by a transcriptomic approach

(2016) Fabio Candotto Carniel et al.   PLANT MOLECULAR BIOLOGY

Basidiomycete yeasts in the cortex of ascomycete macrolichens

(2016) Toby Spribille et al.   SCIENCE

15N – nitrate uptake and nitrogen exchange in the bionts of the lichen Parmelia sulcata

(2016) Elena A. Pavlova et al.   SYMBIOSIS

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum

(2016) Martina Peter et al.   Nature Communications

“Omics” Tools for Better Understanding the Plant–Endophyte Interactions

(2016) Sanjana Kaul et al.   Frontiers in Plant Science

Recognition- and defense-related gene expression at 3 resynthesis stages in lichen symbionts

(2015) Sarangi N.P. Athukorala et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling

(2015) Yi-Hsuan Ho et al.   CURRENT GENETICS

Metagenome sequence ofElaphomyces granulatusfrom sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and aProteobacteria-rich microbiome

(2015) C. Alisha Quandt et al.   ENVIRONMENTAL MICROBIOLOGY

Eisosome Ultrastructure and Evolution in Fungi, Microalgae, and Lichens

(2015) Jae-Hyeok Lee et al.   EUKARYOTIC CELL

No support for occurrence of free-living Cladonia mycobionts in dead wood

(2015) Veera Tuovinen et al.   Fungal Ecology

Assembling the challenging puzzle of algal biodiversity: species delimitation within the genusAsterochloris(Trebouxiophyceae, Chlorophyta)

(2015) Pavel Škaloud et al.   JOURNAL OF PHYCOLOGY

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

(2015) Annegret Kohler et al.   NATURE GENETICS

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

(2015) Konstantinos D. Tsirigos et al.   NUCLEIC ACIDS RESEARCH

The Transporter Classification Database (TCDB): recent advances

(2015) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses

(2015) Guillaume Blanc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift

(2015) Ester Gaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers

(2015) Christophe Lambing et al.   PLoS Genetics

Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins

(2015) Clement Pellegrin et al.   Frontiers in Microbiology

Understanding nitrate assimilation and its regulation in microalgae

(2015) Emanuel Sanz-Luque et al.   Frontiers in Plant Science

Genome characteristics reveal the impact of lichenization on lichen-forming fungus Endocarpon pusillum Hedwig (Verrucariales, Ascomycota)

(2014) Yan-Yan Wang et al.   BMC GENOMICS

Broad compatibility in fungal root symbioses

(2014) Alga Zuccaro et al.   CURRENT OPINION IN PLANT BIOLOGY

Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

(2014) Martin Grube et al.   ISME Journal

Algal and Fungal Diversity in Antarctic Lichens

(2014) Chae Haeng Park et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

An mRNA-Derived Noncoding RNA Targets and Regulates the Ribosome

(2014) Andreas Pircher et al.   MOLECULAR CELL

Integrating coalescent and phylogenetic approaches to delimit species in the lichen photobiont Trebouxia

(2014) Anna D. Sadowska-Deś et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evidence of ancient horizontal gene transfer between fungi and the terrestrial alga Trebouxia

(2014) A. Beck et al.   ORGANISMS DIVERSITY & EVOLUTION

The BAF60 Subunit of the SWI/SNF Chromatin-Remodeling Complex Directly Controls the Formation of a Gene Loop at FLOWERING LOCUS C in Arabidopsis

(2014) T. Jegu et al.   PLANT CELL

Characterization of New Polyol/H+ Symporters in Debaryomyces hansenii

(2014) Iliana Pereira et al.   PLoS One

Niche engineering demonstrates a latent capacity for fungal-algal mutualism

(2014) E. F. Y. Hom et al.   SCIENCE

Comparative transcriptome analysis of the lichen-forming fungus Endocarpon pusillum elucidates its drought adaptation mechanisms

(2014) YanYan Wang et al.   Science China-Life Sciences

Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock

(2014) Reut Shalgi et al.   Cell Reports

The Evolution of Fungal Metabolic Pathways

(2014) Jennifer H. Wisecaver et al.   PLoS Genetics

Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen

(2013) Sini Junttila et al.   BMC GENOMICS

High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporter/ammonia permease gene family

(2013) Tami R McDonald et al.   BMC GENOMICS

Phylogenetic analysis of LSU and SSU rDNA group I introns of lichen photobionts associated with the generaXanthoriaandXanthomendoza(Teloschistaceae, lichenized Ascomycetes)

(2013) Shyam Nyati et al.   JOURNAL OF PHYCOLOGY

The Ribosome as a Hub for Protein Quality Control

(2013) Sebastian Pechmann et al.   MOLECULAR CELL

Widespread Regulation of Translation by Elongation Pausing in Heat Shock

(2013) Reut Shalgi et al.   MOLECULAR CELL

Extremotolerance and Resistance of Lichens: Comparative Studies on Five Species Used in Astrobiological Research I. Morphological and Anatomical Characteristics

(2013) J. Meeßen et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

The response ofAsterochloris erici(Ahmadjian) Skaloud et Peksa to desiccation: a proteomic approach

(2013) FRANSCICO GASULLA et al.   PLANT CELL AND ENVIRONMENT

Dating the Diversification of the Major Lineages of Ascomycota (Fungi)

(2013) María Prieto et al.   PLoS One

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

(2013) E. Tisserant et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote

(2013) G. Schonknecht et al.   SCIENCE

Twenty-five cultures of lichenizing fungi available for experimental studies on symbiotic systems

(2013) Tami R. McDonald et al.   SYMBIOSIS

Expanding Proteostasis by Membrane Trafficking Networks

(2013) D. M. Hutt et al.   Cold Spring Harbor Perspectives in Biology

Host and geographic structure of endophytic and endolichenic fungi at a continental scale

(2012) Jana M. U'Ren et al.   AMERICAN JOURNAL OF BOTANY

The Genomics of Obligate (and Nonobligate) Biotrophs

(2012) Pietro D. Spanu   Annual Review of Phytopathology

Characterization of a transcriptome from a non-model organism, Cladonia rangiferina, the grey reindeer lichen, using high-throughput next generation sequencing and EST sequence data

(2012) Sini Junttila et al.   BMC GENOMICS

Bio-crude transcriptomics: Gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa)*

(2012) István Molnár et al.   BMC GENOMICS

Phylogeny and Molecular Evolution of the Green Algae

(2012) Frederik Leliaert et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Mitochondrial genomes from the lichenized fungi Peltigera membranacea and Peltigera malacea: Features and phylogeny

(2012) Basil Britto Xavier et al.   Fungal Biology

TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae

(2012) Aaron Z. Welch et al.   MOLECULAR BIOLOGY OF THE CELL

European phylogeography of the epiphytic lichen fungusLobaria pulmonariaand its green algal symbiont

(2012) Ivo Widmer et al.   MOLECULAR ECOLOGY

Vertical and horizontal photobiont transmission within populations of a lichen symbiosis

(2012) F. DAL GRANDE et al.   MOLECULAR ECOLOGY

The Top 10 fungal pathogens in molecular plant pathology

(2012) RALPH DEAN et al.   MOLECULAR PLANT PATHOLOGY

The earliest records of internally stratified cyanobacterial and algal lichens from the Lower Devonian of the Welsh Borderland

(2012) Rosmarie Honegger et al.   NEW PHYTOLOGIST

Genetic Basis of Self-Incompatibility in the Lichen-Forming Fungus Lobaria pulmonaria and Skewed Frequency Distribution of Mating-Type Idiomorphs: Implications for Conservation

(2012) Garima Singh et al.   PLoS One

The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

(2012) Guillaume Blanc et al.   GENOME BIOLOGY

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

(2011) Brendan P. Hodkinson et al.   ENVIRONMENTAL MICROBIOLOGY

Revisiting photobiont diversity in the lichen family Verrucariaceae (Ascomycota)

(2011) Holger Thüs et al.   EUROPEAN JOURNAL OF PHYCOLOGY

Rock-inhabiting fungi originated during periods of dry climate in the late Devonian and middle Triassic

(2011) Cécile Gueidan et al.   Fungal Biology

Multiple Horizontal Gene Transfers of Ammonium Transporters/Ammonia Permeases from Prokaryotes to Eukaryotes: Toward a New Functional and Evolutionary Classification

(2011) T. R. McDonald et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Do photobionts influence the ecology of lichens? A case study of environmental preferences in symbiotic green alga Asterochloris (Trebouxiophyceae)

(2011) ONDŘEJ PEKSA et al.   MOLECULAR ECOLOGY

Fungal and algal gene expression in early developmental stages of lichen-symbiosis

(2011) Suzanne Joneson et al.   MYCOLOGIA

Insights from the first putative biosynthetic gene cluster for a lichen depside and depsidone

(2011) Daniele Armaleo et al.   MYCOLOGIA

Molecular chaperones in protein folding and proteostasis

(2011) F. Ulrich Hartl et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources

(2011) M. B. Arnaud et al.   NUCLEIC ACIDS RESEARCH

Decoding algal genomes: tracing back the history of photosynthetic life on Earth

(2011) Leïla Tirichine et al.   PLANT JOURNAL

Origin and Diversification of Major Clades in Parmelioid Lichens (Parmeliaceae, Ascomycota) during the Paleogene Inferred by Bayesian Analysis

(2011) Guillermo Amo de Paz et al.   PLoS One

Structure and function of the symbiosis partners of the lung lichen (Lobaria pulmonaria L. Hoffm.) analyzed by metaproteomics

(2011) Thomas Schneider et al.   PROTEOMICS

Chemical and Biological Approaches for Adapting Proteostasis to Ameliorate Protein Misfolding and Aggregation Diseases-Progress and Prognosis

(2011) S. L. Lindquist et al.   Cold Spring Harbor Perspectives in Biology

Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression

(2010) Marija Mihailovich et al.   BIOESSAYS

Two Trebouxia algae with different physiological performances are ever-present in lichen thalli of Ramalina farinacea. Coexistence versus Competition?

(2010) Leonardo M. Casano et al.   ENVIRONMENTAL MICROBIOLOGY

Photobiont association and genetic diversity of the optionally lichenized fungus Schizoxylon albescens

(2010) Lucia Muggia et al.   FEMS MICROBIOLOGY ECOLOGY

Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity

(2010) Daniel Lang et al.   Genome Biology and Evolution

Protein Folding Requires Crowd Control in a Simulated Cell

(2010) Benjamin R. Jefferys et al.   JOURNAL OF MOLECULAR BIOLOGY

The Evolution of Sex: a Perspective from the Fungal Kingdom

(2010) S. C. Lee et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty

(2010) O. Penn et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

(2010) J. Mark Cock et al.   NATURE

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

(2010) Francis Martin et al.   NATURE

TheChlorella variabilisNC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex

(2010) Guillaume Blanc et al.   PLANT CELL

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Tracing the Origin of the Fungal α1 Domain Places Its Ancestor in the HMG-Box Superfamily: Implication for Fungal Mating-Type Evolution

(2010) Tom Martin et al.   PLoS One

Structure and function of SWI/SNF chromatin remodeling complexes and mechanistic implications for transcription

(2010) Liling Tang et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri

(2010) S. E. Prochnik et al.   SCIENCE

Unravelling the phylogenetic relationships of lichenised fungi in Dothideomyceta

(2010) M.P. Nelsen et al.   STUDIES IN MYCOLOGY

WRKY transcription factors

(2010) Paul J. Rushton et al.   TRENDS IN PLANT SCIENCE

Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis

(2010) Paola Bonfante et al.   Nature Communications

Dating the molecular clock in fungi – how close are we?

(2010) Mary L. Berbee et al.   Fungal Biology Reviews

Autophagy is required for tolerance of drought and salt stress in plants

(2009) Yimo Liu et al.   Autophagy

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

TransportTP: A two-phase classification approach for membrane transporter prediction and characterization

(2009) Haiquan Li et al.   BMC BIOINFORMATICS

Medicago truncatula and Glomus intraradices gene expression in cortical cells harboring arbuscules in the arbuscular mycorrhizal symbiosis

(2009) S Karen Gomez et al.   BMC PLANT BIOLOGY

Asymmetric Co-evolution in the Lichen Symbiosis Caused by a Limited Capacity for Adaptation in the Photobiont

(2009) David J. Hill   BOTANICAL REVIEW

Cohesin gene defects may impair sister chromatid alignment and genome stability in Arabidopsis thaliana

(2009) Veit Schubert et al.   CHROMOSOMA

Harnessing ectomycorrhizal genomics for ecological insights

(2009) Francis Martin et al.   CURRENT OPINION IN PLANT BIOLOGY

Recent progress in discovery and functional analysis of effector proteins of fungal and oomycete plant pathogens

(2009) Jeffrey G Ellis et al.   CURRENT OPINION IN PLANT BIOLOGY

Hexose and pentose transport in ascomycetous yeasts: an overview

(2009) Maria José Leandro et al.   FEMS YEAST RESEARCH

Species-specific structural and functional diversity of bacterial communities in lichen symbioses

(2009) Martin Grube et al.   ISME Journal

Mutants of theArabidopsis thalianaCation/H+Antiporter AtNHX1 Conferring Increased Salt Tolerance in Yeast

(2009) Agustín Hernández et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model

(2009) M. Csuros et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary inferences based on ITS rDNA and actin sequences reveal extensive diversity of the common lichen alga Asterochloris (Trebouxiophyceae, Chlorophyta)

(2009) Pavel Skaloud et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

Fungal endophytes: diversity and functional roles

(2009) R. J. Rodriguez et al.   NEW PHYTOLOGIST

Responses to Desiccation Stress in Lichens are Different from Those in Their Photobionts

(2009) M. Kosugi et al.   PLANT AND CELL PHYSIOLOGY

The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome

(2009) Marina Marcet-Houben et al.   PLoS One

Triassic origin and early radiation of multicellular volvocine algae

(2009) M. D. Herron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Secretome analysis of differentially induced proteins in rice suspension-cultured cells triggered by rice blast fungus and elicitor

(2009) Sun Tae Kim et al.   PROTEOMICS

Sizing the fungal and algal genomes of the lichen Cladonia grayi through quantitative PCR

(2009) Daniele Armaleo et al.   SYMBIOSIS

A Phylogenetic Estimation of Trophic Transition Networks for Ascomycetous Fungi: Are Lichens Cradles of Symbiotrophic Fungal Diversification?

(2009) A. Elizabeth Arnold et al.   SYSTEMATIC BIOLOGY

The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits

(2009) Conrad L. Schoch et al.   SYSTEMATIC BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Using a meiosis detection toolkit to investigate ancient asexual “scandals” and the evolution of sex

(2008) Andrew M. Schurko et al.   BIOESSAYS

FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors

(2008) J. Park et al.   BIOINFORMATICS

Subcellular localization of ammonium transporters in Dictyostelium discoideum

(2008) Janet H Kirsten et al.   BMC CELL BIOLOGY

Desiccation-Tolerance in Lichens: A Review

(2008) Ilse Kranner et al.   BRYOLOGIST

Transcription factors in fungi

(2008) Ekaterina Shelest   FEMS MICROBIOLOGY LETTERS

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

(2008) F. Martin et al.   NATURE

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

An Expanded Inventory of Conserved Meiotic Genes Provides Evidence for Sex in Trichomonas vaginalis

(2008) Shehre-Banoo Malik et al.   PLoS One

Nitrate uptake by isolated bionts of the lichen Parmelia sulcata

(2008) E. A. Pavlova et al.   RUSSIAN JOURNAL OF PLANT PHYSIOLOGY

Genomic analysis of the smallest giant virus — Feldmannia sp. virus 158

(2008) Declan C. Schroeder et al.   VIROLOGY