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

Armaleo, Daniele; Müller, Olaf; Lutzoni, François; Andrésson, Ólafur S.; Blanc, Guillaume; Bode, Helge B.; Collart, Frank R.; Dal Grande, Francesco; Dietrich, Fred; Grigoriev, Igor V.; Joneson, Suzanne; Kuo, Alan; Larsen, Peter E.; Logsdon, Jr, John M.; Lopez, David; Martin, Francis; May, Susan P.; McDonald, Tami R.; Merchant, Sabeeha S.; Miao, Vivian; Morin, Emmanuelle; Oono, Ryoko; Pellegrini, Matteo; Rubinstein, Nimrod; Sanchez-Puerta, Maria Virginia; Savelkoul, Elizabeth; Schmitt, Imke; Slot, Jason C.; Soanes, Darren; Szövényi, Péter; Talbot, Nicholas J.; Veneault-Fourrey, Claire; Xavier, Basil B.

doi:10.1186/s12864-019-5629-x

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

Journal Article · Tue Jul 23 00:00:00 EDT 2019 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-019-5629-x· OSTI ID:1618576

; Müller, Olaf; Lutzoni, François; Andrésson, Ólafur S.; Blanc, Guillaume; Bode, Helge B.; Collart, Frank R.; Dal Grande, Francesco; Dietrich, Fred; Grigoriev, Igor V.; Joneson, Suzanne; Kuo, Alan; Larsen, Peter E.; Logsdon, Jr, John M.; Lopez, David; Martin, Francis; May, Susan P.; McDonald, Tami R.; Merchant, Sabeeha S.; Miao, Vivian more »

Not Available

View Journal Article

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231; FC02-02ER63421

OSTI ID:: 1618576

Alternate ID(s):: OSTI ID: 1572033

Journal Information:: BMC Genomics, Journal Name: BMC Genomics Journal Issue: 1 Vol. 20; ISSN 1471-2164

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (231)

Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression Mihailovich, Marija; Militti, Cristina; Gabaldón, Toni BioEssays, Vol. 32, Issue 2 https://doi.org/10.1002/bies.200900122	journal	January 2010
Using a meiosis detection toolkit to investigate ancient asexual “scandals” and the evolution of sex Schurko, Andrew M.; Logsdon, John M. BioEssays, Vol. 30, Issue 6 https://doi.org/10.1002/bies.20764	journal	January 2008
Some new and Interesting Species of Trebouxia, a Genus of Lichenized Algae Ahmadjian, Vernon American Journal of Botany, Vol. 47, Issue 8 https://doi.org/10.1002/j.1537-2197.1960.tb07152.x	journal	October 1960
Secretome analysis of differentially induced proteins in rice suspension-cultured cells triggered by rice blast fungus and elicitor Kim, Sun Tae; Kang, Young Hyun; Wang, Yiming PROTEOMICS, Vol. 9, Issue 5 https://doi.org/10.1002/pmic.200800589	journal	March 2009
Structure and function of the symbiosis partners of the lung lichen (Lobaria pulmonaria L. Hoffm.) analyzed by metaproteomics Schneider, Thomas; Schmid, Emanuel; de Castro, João V. PROTEOMICS, Vol. 11, Issue 13 https://doi.org/10.1002/pmic.201000679	journal	May 2011
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen Krogh, Anders; Larsson, Björn; von Heijne, Gunnar Journal of Molecular Biology, Vol. 305, Issue 3 https://doi.org/10.1006/jmbi.2000.4315	journal	January 2001
The Distribution of Group I Introns in Lichen Algae Suggests That Lichenization Facilitates Intron Lateral Transfer Friedl, Thomas; Besendahl, Anja; Pfeiffer, Patrick Molecular Phylogenetics and Evolution, Vol. 14, Issue 3 https://doi.org/10.1006/mpev.1999.0711	journal	March 2000
Carbon-dioxide exchange in lichens: determination of transport and carboxylation characteristics Cowan, I. R.; Lange, O. L.; Green, T. G. A. Planta, Vol. 187, Issue 2 https://doi.org/10.1007/BF00201952	journal	May 1992
Characterisation of inorganic carbon fluxes, carbonic anhydrase(s) and ribulose-1,5-biphosphate carboxylase-oxygenase in the green unicellular alga Coccomyxa: Comparisons with Iow-CO2 cells of Chlamydomonas reinhardtii Palmqvist, Kristin; S�ltemeyer, Dieter; Baldet, Pierre Planta, Vol. 197, Issue 2 https://doi.org/10.1007/BF00202657	journal	September 1995
Moisture content and CO2 exchange of lichens: I. Influence of temperature on moisture-dependent net photosynthesis and dark respiration in Ramalina maciformis Lange, Otto L. Oecologia, Vol. 45, Issue 1 https://doi.org/10.1007/BF00346710	journal	April 1980
15N2 Incorporation and metabolism in the lichen Peltigera aphthosa Willd Rai, A. N.; Rowell, P.; Stewart, W. D. P. Planta, Vol. 152, Issue 6 https://doi.org/10.1007/BF00380825	journal	October 1981
The lichen algaTrebouxia: does it occur free-living? Ahmadjian, Vernon Plant Systematics and Evolution, Vol. 158, Issue 2-4 https://doi.org/10.1007/BF00936348	journal	January 1987
The Significance of Lichens and Their Metabolites Huneck, S. Naturwissenschaften, Vol. 86, Issue 12 https://doi.org/10.1007/s001140050676	journal	December 1999
Evolution of ITS Ribosomal RNA Secondary Structures in Fungal and Algal Symbionts of Selected Species of Cladonia sect. Cladonia (Cladoniaceae, Ascomycotina) Beiggi, Sara; Piercey-Normore, Michele D. Journal of Molecular Evolution, Vol. 64, Issue 5 https://doi.org/10.1007/s00239-006-0115-x	journal	April 2007
Ectomycorrhiza-mediated repression of the high-affinity ammonium importer gene AmAMT2 in Amanita muscaria Willmann, Anita; Weiß, Michael; Nehls, Uwe Current Genetics, Vol. 51, Issue 2 https://doi.org/10.1007/s00294-006-0106-x	journal	October 2006
Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling Ho, Yi-Hsuan; Gasch, Audrey P. Current Genetics, Vol. 61, Issue 4 https://doi.org/10.1007/s00294-015-0491-0	journal	May 2015
Cohesin gene defects may impair sister chromatid alignment and genome stability in Arabidopsis thaliana Schubert, Veit; Weißleder, Andrea; Ali, Hoda Chromosoma, Vol. 118, Issue 5 https://doi.org/10.1007/s00412-009-0220-x	journal	June 2009
The cost of surviving nitrogen excess: energy and protein demand in the lichen Cladonia portentosa as revealed by proteomic analysis Munzi, Silvana; Sheppard, Lucy J.; Leith, Ian D. Planta, Vol. 245, Issue 4 https://doi.org/10.1007/s00425-017-2647-2	journal	January 2017
Biodiversity of lichens, including a world-wide analysis of checklist data based on Takhtajan’s floristic regions Feuerer, Tassilo; Hawksworth, David L. Biodiversity and Conservation, Vol. 16, Issue 1 https://doi.org/10.1007/s10531-006-9142-6	journal	January 2007
Extremotolerance and Resistance of Lichens: Comparative Studies on Five Species Used in Astrobiological Research I. Morphological and Anatomical Characteristics Meeßen, J.; Sánchez, F. J.; Brandt, A. Origins of Life and Evolution of Biospheres, Vol. 43, Issue 3 https://doi.org/10.1007/s11084-013-9337-2	journal	June 2013
New features of desiccation tolerance in the lichen photobiont Trebouxia gelatinosa are revealed by a transcriptomic approach Carniel, Fabio Candotto; Gerdol, Marco; Montagner, Alice Plant Molecular Biology, Vol. 91, Issue 3 https://doi.org/10.1007/s11103-016-0468-5	journal	March 2016
Comparative transcriptome analysis of the lichen-forming fungus Endocarpon pusillum elucidates its drought adaptation mechanisms Wang, YanYan; Zhang, XinYu; Zhou, QiMing Science China Life Sciences, Vol. 58, Issue 1 https://doi.org/10.1007/s11427-014-4760-9	journal	December 2014
Asymmetric Co-evolution in the Lichen Symbiosis Caused by a Limited Capacity for Adaptation in the Photobiont Hill, David J. The Botanical Review, Vol. 75, Issue 3 https://doi.org/10.1007/s12229-009-9028-x	journal	May 2009
Evidence of ancient horizontal gene transfer between fungi and the terrestrial alga Trebouxia Beck, A.; Divakar, P. K.; Zhang, N. Organisms Diversity & Evolution, Vol. 15, Issue 2 https://doi.org/10.1007/s13127-014-0199-x	journal	December 2014
Sizing the fungal and algal genomes of the lichen Cladonia grayi through quantitative PCR Armaleo, Daniele; May, Susan Symbiosis, Vol. 49, Issue 1 https://doi.org/10.1007/s13199-009-0012-3	journal	September 2009
Twenty-five cultures of lichenizing fungi available for experimental studies on symbiotic systems McDonald, Tami R.; Gaya, Ester; Lutzoni, François Symbiosis, Vol. 59, Issue 3 https://doi.org/10.1007/s13199-013-0228-0	journal	March 2013
15N – nitrate uptake and nitrogen exchange in the bionts of the lichen Parmelia sulcata Pavlova, Elena A.; Kuzmin, A. N.; Pozdnyakov, N. V. Symbiosis, Vol. 72, Issue 2 https://doi.org/10.1007/s13199-016-0451-6	journal	September 2016
Genetic diversity of green algal and cyanobacterial photobionts in Nephroma (Peltigerales) Lohtander, Katileena; Oksanen, Ilona; Rikkinen, Jouko The Lichenologist, Vol. 35, Issue 4 https://doi.org/10.1016/S0024-2829(03)00051-3	journal	July 2003
DNA Topoisomerase VI Is Essential for Endoreduplication in Arabidopsis Sugimoto-Shirasu, Keiko; Stacey, Nicola J.; Corsar, Julia Current Biology, Vol. 12, Issue 20 https://doi.org/10.1016/S0960-9822(02)01198-3	journal	October 2002
Slow algae, fast fungi: exceptionally high nucleotide substitution rate differences between lichenized fungi Omphalina and their symbiotic green algae Coccomyxa Zoller, S. Molecular Phylogenetics and Evolution, Vol. 29, Issue 3 https://doi.org/10.1016/S1055-7903(03)00215-X	journal	December 2003
Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock Shalgi, Reut; Hurt, Jessica A.; Lindquist, Susan Cell Reports, Vol. 7, Issue 5 https://doi.org/10.1016/j.celrep.2014.04.044	journal	June 2014
Two Meiotic Crossover Classes Cohabit in Arabidopsis Mercier, Raphaël; Jolivet, Sylvie; Vezon, Daniel Current Biology, Vol. 15, Issue 8 https://doi.org/10.1016/j.cub.2005.02.056	journal	April 2005
Dating the molecular clock in fungi – how close are we? Berbee, Mary L.; Taylor, John W. Fungal Biology Reviews, Vol. 24, Issue 1-2 https://doi.org/10.1016/j.fbr.2010.03.001	journal	February 2010
Mechanisms of ammonium transport, accumulation, and retention in ooyctes and yeast cells expressing Arabidopsis AtAMT1;1 Wood, Craig C.; Porée, Fabien; Dreyer, Ingo FEBS Letters, Vol. 580, Issue 16 https://doi.org/10.1016/j.febslet.2006.06.026	journal	June 2006
Breeding systems in the lichen-forming fungal genus Cladonia Seymour, Fabian A.; Crittenden, Peter D.; Dickinson, Matthew J. Fungal Genetics and Biology, Vol. 42, Issue 6 https://doi.org/10.1016/j.fgb.2005.03.006	journal	June 2005
Characterisation of the mating-type locus in the genus Xanthoria (lichen-forming ascomycetes, Lecanoromycetes) Scherrer, Sandra; Zippler, Undine; Honegger, Rosmarie Fungal Genetics and Biology, Vol. 42, Issue 12 https://doi.org/10.1016/j.fgb.2005.09.002	journal	December 2005
Rock-inhabiting fungi originated during periods of dry climate in the late Devonian and middle Triassic Gueidan, Cécile; Ruibal, Constantino; de Hoog, G. S. Fungal Biology, Vol. 115, Issue 10 https://doi.org/10.1016/j.funbio.2011.04.002	journal	October 2011
Mitochondrial genomes from the lichenized fungi Peltigera membranacea and Peltigera malacea: Features and phylogeny Xavier, Basil Britto; Miao, Vivian P. W.; Jónsson, Zophonías O. Fungal Biology, Vol. 116, Issue 7 https://doi.org/10.1016/j.funbio.2012.04.013	journal	July 2012
Putative identification of the usnic acid biosynthetic gene cluster by de novo whole-genome sequencing of a lichen-forming fungus Abdel-Hameed, Mona; Bertrand, Robert L.; Piercey-Normore, Michele D. Fungal Biology, Vol. 120, Issue 3 https://doi.org/10.1016/j.funbio.2015.10.009	journal	March 2016
Cyphobasidium gen. nov., a new lichen-inhabiting lineage in the Cystobasidiomycetes (Pucciniomycotina, Basidiomycota, Fungi) Millanes, Ana M.; Diederich, Paul; Wedin, Mats Fungal Biology, Vol. 120, Issue 11 https://doi.org/10.1016/j.funbio.2015.12.003	journal	November 2016
Fungal and cyanobacterial gene expression in a lichen symbiosis: Effect of temperature and location Steinhäuser, Sophie S.; Andrésson, Ólafur S.; Pálsson, Arnar Fungal Biology, Vol. 120, Issue 10 https://doi.org/10.1016/j.funbio.2016.07.002	journal	October 2016
No support for occurrence of free-living Cladonia mycobionts in dead wood Tuovinen, Veera; Svensson, Måns; Kubartová, Ariana Fungal Ecology, Vol. 14 https://doi.org/10.1016/j.funeco.2014.12.003	journal	April 2015
Protein Folding Requires Crowd Control in a Simulated Cell Jefferys, Benjamin R.; Kelley, Lawrence A.; Sternberg, Michael J. E. Journal of Molecular Biology, Vol. 397, Issue 5 https://doi.org/10.1016/j.jmb.2010.01.074	journal	April 2010
Widespread Regulation of Translation by Elongation Pausing in Heat Shock Shalgi, Reut; Hurt, Jessica A.; Krykbaeva, Irina Molecular Cell, Vol. 49, Issue 3 https://doi.org/10.1016/j.molcel.2012.11.028	journal	February 2013
The Ribosome as a Hub for Protein Quality Control Pechmann, Sebastian; Willmund, Felix; Frydman, Judith Molecular Cell, Vol. 49, Issue 3 https://doi.org/10.1016/j.molcel.2013.01.020	journal	February 2013
An mRNA-Derived Noncoding RNA Targets and Regulates the Ribosome Pircher, Andreas; Bakowska-Zywicka, Kamilla; Schneider, Lukas Molecular Cell, Vol. 54, Issue 1 https://doi.org/10.1016/j.molcel.2014.02.024	journal	April 2014
Recent progress in discovery and functional analysis of effector proteins of fungal and oomycete plant pathogens Ellis, Jeffrey G.; Rafiqi, Maryam; Gan, Pamela Current Opinion in Plant Biology, Vol. 12, Issue 4 https://doi.org/10.1016/j.pbi.2009.05.004	journal	August 2009
Harnessing ectomycorrhizal genomics for ecological insights Martin, Francis; Nehls, Uwe Current Opinion in Plant Biology, Vol. 12, Issue 4 https://doi.org/10.1016/j.pbi.2009.05.007	journal	August 2009
Broad compatibility in fungal root symbioses Zuccaro, Alga; Lahrmann, Urs; Langen, Gregor Current Opinion in Plant Biology, Vol. 20 https://doi.org/10.1016/j.pbi.2014.05.013	journal	August 2014
Structure and function of SWI/SNF chromatin remodeling complexes and mechanistic implications for transcription Tang, Liling; Nogales, Eva; Ciferri, Claudio Progress in Biophysics and Molecular Biology, Vol. 102, Issue 2-3 https://doi.org/10.1016/j.pbiomolbio.2010.05.001	journal	June 2010
WRKY transcription factors Rushton, Paul J.; Somssich, Imre E.; Ringler, Patricia Trends in Plant Science, Vol. 15, Issue 5 https://doi.org/10.1016/j.tplants.2010.02.006	journal	May 2010
Genomic analysis of the smallest giant virus — Feldmannia sp. virus 158 Schroeder, Declan C.; Park, Yunjung; Yoon, Hong-Mook Virology, Vol. 384, Issue 1 https://doi.org/10.1016/j.virol.2008.10.040	journal	February 2009
Evolutionary genomics of nucleo-cytoplasmic large DNA viruses Iyer, Lakshminarayan M.; Balaji, S.; Koonin, Eugene V. Virus Research, Vol. 117, Issue 1 https://doi.org/10.1016/j.virusres.2006.01.009	journal	April 2006
Evolutionary inferences based on ITS rDNA and actin sequences reveal extensive diversity of the common lichen alga Asterochloris (Trebouxiophyceae, Chlorophyta) Skaloud, Pavel; Peksa, Ondrej Molecular Phylogenetics and Evolution, Vol. 54, Issue 1 https://doi.org/10.1016/j.ympev.2009.09.035	journal	January 2010
Integrating coalescent and phylogenetic approaches to delimit species in the lichen photobiont Trebouxia Sadowska-Deś, Anna D.; Dal Grande, Francesco; Lumbsch, H. Thorsten Molecular Phylogenetics and Evolution, Vol. 76 https://doi.org/10.1016/j.ympev.2014.03.020	journal	July 2014
Observing microscopic phases of lichen life cycles on transparent substrata placed *in situ* Sanders, William B. The Lichenologist, Vol. 37, Issue 5 https://doi.org/10.1017/S0024282905015070	journal	September 2005
The draft genome of the lichen-forming fungus Lasallia hispanica (Frey) Sancho & A. Crespo Dal Grande, Francesco; Meiser, Anjuli; Greshake Tzovaras, Bastian The Lichenologist, Vol. 50, Issue 3 https://doi.org/10.1017/S002428291800021X	journal	May 2018
Myrmecia Reticulata as a Phycobiont and Free-Living—free-Living Trebouxia— The Problem of Stenocybe Septata Tschermak-Woess, E. The Lichenologist, Vol. 10, Issue 1 https://doi.org/10.1017/S0024282978000080	journal	April 1978
Zoosporogenesis In Trebouxia Gelatinosa: Ultrastructure Potential For Zoospore Release And Implications For The Lichen Association Slocum, R. D.; Ahmadjian, V.; Hildreth, K. C. The Lichenologist, Vol. 12, Issue 2 https://doi.org/10.1017/S0024282980000151	journal	June 1980
Sex in the extremes: lichen-forming fungi Seymour, Fabian A.; Crittenden, Peter D.; Dyer, Paul S. Mycologist, Vol. 19, Issue 2 https://doi.org/10.1017/S0269915X05002016	journal	May 2005
Morphological and molecular analysis of early stages in the resynthesis of the lichen Baeomyces rufus Trembley, Marcella L.; Ringli, Christoph; Honegger, Rosmarie Mycological Research, Vol. 106, Issue 7 https://doi.org/10.1017/S0953756202006081	journal	July 2002
War in the world of lichens: parasitism and symbiosis as exemplified by lichens and lichenicolous fungi Richardson, David H. S. Mycological Research, Vol. 103, Issue 6 https://doi.org/10.1017/S0953756298008259	journal	June 1999
Sex and the single lichen Murtagh, G. J.; Dyer, P. S.; Crittenden, P. D. Nature, Vol. 404, Issue 6778 https://doi.org/10.1038/35007142	journal	April 2000
Species-specific structural and functional diversity of bacterial communities in lichen symbioses Grube, Martin; Cardinale, Massimiliano; de Castro, João Vieira The ISME Journal, Vol. 3, Issue 9 https://doi.org/10.1038/ismej.2009.63	journal	June 2009
Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics Grube, Martin; Cernava, Tomislav; Soh, Jung The ISME Journal, Vol. 9, Issue 2 https://doi.org/10.1038/ismej.2014.138	journal	July 2014
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis Martin, F.; Aerts, A.; Ahrén, D. Nature, Vol. 452, Issue 7183 https://doi.org/10.1038/nature06556	journal	March 2008
Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis Martin, Francis; Kohler, Annegret; Murat, Claude Nature, Vol. 464, Issue 7291 https://doi.org/10.1038/nature08867	journal	March 2010
The Ectocarpus genome and the independent evolution of multicellularity in brown algae Cock, J. Mark; Sterck, Lieven; Rouzé, Pierre Nature, Vol. 465, Issue 7298 https://doi.org/10.1038/nature09016	journal	June 2010
Molecular chaperones in protein folding and proteostasis Hartl, F. Ulrich; Bracher, Andreas; Hayer-Hartl, Manajit Nature, Vol. 475, Issue 7356 https://doi.org/10.1038/nature10317	journal	July 2011
Full-length transcriptome assembly from RNA-Seq data without a reference genome Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran Nature Biotechnology, Vol. 29, Issue 7 https://doi.org/10.1038/nbt.1883	journal	May 2011
Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis Bonfante, Paola; Genre, Andrea Nature Communications, Vol. 1, Issue 1 https://doi.org/10.1038/ncomms1046	journal	July 2010
Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum Peter, Martina; Kohler, Annegret; Ohm, Robin A. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms12662	journal	September 2016
SignalP 4.0: discriminating signal peptides from transmembrane regions Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar Nature Methods, Vol. 8, Issue 10 https://doi.org/10.1038/nmeth.1701	journal	September 2011
Locating proteins in the cell using TargetP, SignalP and related tools Emanuelsson, Olof; Brunak, Søren; von Heijne, Gunnar Nature Protocols, Vol. 2, Issue 4 https://doi.org/10.1038/nprot.2007.131	journal	April 2007
Protein structure prediction on the Web: a case study using the Phyre server Kelley, Lawrence A.; Sternberg, Michael J. E. Nature Protocols, Vol. 4, Issue 3 https://doi.org/10.1038/nprot.2009.2	journal	February 2009
Extreme genome reduction in symbiotic bacteria McCutcheon, John P.; Moran, Nancy A. Nature Reviews Microbiology, Vol. 10, Issue 1 https://doi.org/10.1038/nrmicro2670	journal	November 2011
Fructosamine 3-kinase, an enzyme involved in protein deglycation Delpierre, G.; Van Schaftingen, E. Biochemical Society Transactions, Vol. 31, Issue 6 https://doi.org/10.1042/bst0311354	journal	December 2003
Genetic variation within and among populations of the threatened lichen Lobaria pulmonaria in Switzerland and implications for its conservation Zoller, S.; Lutzoni, F.; Scheidegger, C. Molecular Ecology, Vol. 8, Issue 12 https://doi.org/10.1046/j.1365-294x.1999.00820.x	journal	December 1999
Light use efficiency of dry matter gain in five macro‐lichens: relative impact of microclimate conditions and species‐specific traits Palmqvist, K.; Sundberg, B. Plant, Cell & Environment, Vol. 23, Issue 1 https://doi.org/10.1046/j.1365-3040.2000.00529.x	journal	January 2000
Tansley Review No. 117: Carbon economy in lichens Palmqvist, Kristin New Phytologist, Vol. 148, Issue 1 https://doi.org/10.1046/j.1469-8137.2000.00732.x	journal	October 2000
Antioxidants and photoprotection in a lichen as compared with its isolated symbiotic partners Kranner, I.; Cram, W. J.; Zorn, M. Proceedings of the National Academy of Sciences, Vol. 102, Issue 8 https://doi.org/10.1073/pnas.0407716102	journal	February 2005
Ammonium/methylammonium transport (Amt) proteins facilitate diffusion of NH ₃ bidirectionally Soupene, Eric; Lee, Haidy; Kustu, Sydney Proceedings of the National Academy of Sciences, Vol. 99, Issue 6 https://doi.org/10.1073/pnas.062043799	journal	March 2002
Triassic origin and early radiation of multicellular volvocine algae Herron, M. D.; Hackett, J. D.; Aylward, F. O. Proceedings of the National Academy of Sciences, Vol. 106, Issue 9 https://doi.org/10.1073/pnas.0811205106	journal	February 2009
The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases Landry, J.; Sutton, A.; Tafrov, S. T. Proceedings of the National Academy of Sciences, Vol. 97, Issue 11 https://doi.org/10.1073/pnas.110148297	journal	May 2000
Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis Tisserant, E.; Malbreil, M.; Kuo, A. Proceedings of the National Academy of Sciences, Vol. 110, Issue 50 https://doi.org/10.1073/pnas.1313452110	journal	November 2013
Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses Blanc, Guillaume; Gallot-Lavallée, Lucie; Maumus, Florian Proceedings of the National Academy of Sciences, Vol. 112, Issue 38 https://doi.org/10.1073/pnas.1506469112	journal	August 2015
The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift Gaya, Ester; Fernández-Brime, Samantha; Vargas, Reinaldo Proceedings of the National Academy of Sciences, Vol. 112, Issue 37 https://doi.org/10.1073/pnas.1507072112	journal	August 2015
Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production Roth, Melissa S.; Cokus, Shawn J.; Gallaher, Sean D. Proceedings of the National Academy of Sciences, Vol. 114, Issue 21 https://doi.org/10.1073/pnas.1619928114	journal	May 2017
Evolution of the fungal self-fertile reproductive life style from self-sterile ancestors Yun, S. -H.; Berbee, M. L.; Yoder, O. C. Proceedings of the National Academy of Sciences, Vol. 96, Issue 10 https://doi.org/10.1073/pnas.96.10.5592	journal	May 1999
Sgt1p Is a Unique Co-chaperone That Acts as a Client Adaptor to Link Hsp90 to Skp1p Catlett, Michael G.; Kaplan, Kenneth B. Journal of Biological Chemistry, Vol. 281, Issue 44 https://doi.org/10.1074/jbc.M603847200	journal	August 2006
Mutants of the Arabidopsis thaliana Cation/H ⁺ Antiporter AtNHX1 Conferring Increased Salt Tolerance in Yeast : THE ENDOSOME/PREVACUOLAR COMPARTMENT IS A TARGET FOR SALT TOXICITY Hernández, Agustín; Jiang, Xingyu; Cubero, Beatriz Journal of Biological Chemistry, Vol. 284, Issue 21 https://doi.org/10.1074/jbc.M806203200	journal	March 2009
Phylogeny and Molecular Evolution of the Green Algae Leliaert, Frederik; Smith, David R.; Moreau, Hervé Critical Reviews in Plant Sciences, Vol. 31, Issue 1 https://doi.org/10.1080/07352689.2011.615705	journal	January 2012
Revisiting photobiont diversity in the lichen family Verrucariaceae (Ascomycota) Thüs, Holger; Muggia, Lucia; Pérez-Ortega, Sergio European Journal of Phycology, Vol. 46, Issue 4 https://doi.org/10.1080/09670262.2011.629788	journal	November 2011
Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments Talavera, Gerard; Castresana, Jose Systematic Biology, Vol. 56, Issue 4 https://doi.org/10.1080/10635150701472164	journal	August 2007
Proteomic analysis of a eukaryotic cilium Pazour, Gregory J.; Agrin, Nathan; Leszyk, John The Journal of Cell Biology, Vol. 170, Issue 1 https://doi.org/10.1083/jcb.200504008	journal	July 2005
Ammonia Pulses and Metabolic Oscillations Guide Yeast Colony Development Palková, Zdena; Devaux, Frédéric; R̆ic̆icová, Markéta Molecular Biology of the Cell, Vol. 13, Issue 11 https://doi.org/10.1091/mbc.e01-12-0149	journal	November 2002
TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae Welch, Aaron Z.; Gibney, Patrick A.; Botstein, David Molecular Biology of the Cell, Vol. 24, Issue 2 https://doi.org/10.1091/mbc.e12-07-0524	journal	January 2013
HyPhy: hypothesis testing using phylogenies Pond, S. L. K.; Frost, S. D. W.; Muse, S. V. Bioinformatics, Vol. 21, Issue 5 https://doi.org/10.1093/bioinformatics/bti079	journal	October 2004
ProtTest: selection of best-fit models of protein evolution Abascal, F.; Zardoya, R.; Posada, D. Bioinformatics, Vol. 21, Issue 9 https://doi.org/10.1093/bioinformatics/bti263	journal	January 2005
CAFE: a computational tool for the study of gene family evolution De Bie, T.; Cristianini, N.; Demuth, J. P. Bioinformatics, Vol. 22, Issue 10 https://doi.org/10.1093/bioinformatics/btl097	journal	March 2006
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Stamatakis, Alexandros Bioinformatics, Vol. 22, Issue 21 https://doi.org/10.1093/bioinformatics/btl446	journal	August 2006
FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors Park, J.; Park, J.; Jang, S. Bioinformatics, Vol. 24, Issue 7 https://doi.org/10.1093/bioinformatics/btn058	journal	February 2008
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Capella-Gutierrez, S.; Silla-Martinez, J. M.; Gabaldon, T. Bioinformatics, Vol. 25, Issue 15 https://doi.org/10.1093/bioinformatics/btp348	journal	June 2009
Long-term consequences of disturbances on reproductive strategies of the rare epiphytic lichen Lobaria pulmonaria: clonality a gift and a curse Singh, Garima; Dal Grande, Francesco; Werth, Silke FEMS Microbiology Ecology, Vol. 91, Issue 1 https://doi.org/10.1093/femsec/fiu009	journal	December 2014
Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity Lang, Daniel; Weiche, Benjamin; Timmerhaus, Gerrit Genome Biology and Evolution, Vol. 2 https://doi.org/10.1093/gbe/evq032	journal	January 2010
Study of Gene Trafficking between Acanthamoeba and Giant Viruses Suggests an Undiscovered Family of Amoeba-Infecting Viruses Maumus, Florian; Blanc, Guillaume Genome Biology and Evolution, Vol. 8, Issue 11 https://doi.org/10.1093/gbe/evw260	journal	November 2016
Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model Csuros, M.; Miklos, I. Molecular Biology and Evolution, Vol. 26, Issue 9 https://doi.org/10.1093/molbev/msp123	journal	June 2009
An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty Penn, O.; Privman, E.; Landan, G. Molecular Biology and Evolution, Vol. 27, Issue 8 https://doi.org/10.1093/molbev/msq066	journal	March 2010
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods Tamura, K.; Peterson, D.; Peterson, N. Molecular Biology and Evolution, Vol. 28, Issue 10 https://doi.org/10.1093/molbev/msr121	journal	May 2011
Multiple Horizontal Gene Transfers of Ammonium Transporters/Ammonia Permeases from Prokaryotes to Eukaryotes: Toward a New Functional and Evolutionary Classification McDonald, T. R.; Dietrich, F. S.; Lutzoni, F. Molecular Biology and Evolution, Vol. 29, Issue 1 https://doi.org/10.1093/molbev/msr123	journal	June 2011
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A. Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402 https://doi.org/10.1093/nar/25.17.3389	journal	September 1997
An efficient algorithm for large-scale detection of protein families Enright, A. J. Nucleic Acids Research, Vol. 30, Issue 7 https://doi.org/10.1093/nar/30.7.1575	journal	April 2002
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Katoh, K. Nucleic Acids Research, Vol. 30, Issue 14 https://doi.org/10.1093/nar/gkf436	journal	July 2002
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
Eukaryotic genome size databases Gregory, T. R.; Nicol, J. A.; Tamm, H. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl828	journal	January 2007
Assessing the gene space in draft genomes Parra, Genis; Bradnam, Keith; Ning, Zemin Nucleic Acids Research, Vol. 37, Issue 1 https://doi.org/10.1093/nar/gkn916	journal	November 2008
The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources Arnaud, M. B.; Cerqueira, G. C.; Inglis, D. O. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr875	journal	November 2011
The Transporter Classification Database (TCDB): recent advances Saier, Milton H.; Reddy, Vamsee S.; Tsu, Brian V. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1103	journal	November 2015
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters Weber, Tilmann; Blin, Kai; Duddela, Srikanth Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv437	journal	May 2015
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides Tsirigos, Konstantinos D.; Peters, Christoph; Shu, Nanjiang Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv485	journal	May 2015
TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life Elbourne, Liam D. H.; Tetu, Sasha G.; Hassan, Karl A. Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1068	journal	November 2016
Nuclear-encoded rDNA group I introns: origin and phylogenetic relationships of insertion site lineages in the green algae Bhattacharya, D.; Friedl, T.; Damberger, S. Molecular Biology and Evolution, Vol. 13, Issue 7 https://doi.org/10.1093/oxfordjournals.molbev.a025666	journal	September 1996
Widespread Occurrence of Spliceosomal Introns in the rDNA Genes of Ascomycetes Bhattacharya, Debashish; Lutzoni, François; Reeb, Valérie Molecular Biology and Evolution, Vol. 17, Issue 12 https://doi.org/10.1093/oxfordjournals.molbev.a026298	journal	December 2000
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis Castresana, J. Molecular Biology and Evolution, Vol. 17, Issue 4 https://doi.org/10.1093/oxfordjournals.molbev.a026334	journal	April 2000
Responses to Desiccation Stress in Lichens are Different from Those in Their Photobionts Kosugi, M.; Arita, M.; Shizuma, R. Plant and Cell Physiology, Vol. 50, Issue 4 https://doi.org/10.1093/pcp/pcp043	journal	March 2009
A Phylogenetic Estimation of Trophic Transition Networks for Ascomycetous Fungi: Are Lichens Cradles of Symbiotrophic Fungal Diversification? Arnold, A. Elizabeth; Miadlikowska, Jolanta; Higgins, K. Lindsay Systematic Biology, Vol. 58, Issue 3 https://doi.org/10.1093/sysbio/syp001	journal	June 2009
The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits Schoch, Conrad L.; Sung, Gi-Ho; López-Giráldez, Francesc Systematic Biology, Vol. 58, Issue 2 https://doi.org/10.1093/sysbio/syp020	journal	April 2009
Chemical and Biological Approaches for Adapting Proteostasis to Ameliorate Protein Misfolding and Aggregation Diseases-Progress and Prognosis Lindquist, S. L.; Kelly, J. W. Cold Spring Harbor Perspectives in Biology, Vol. 3, Issue 12 https://doi.org/10.1101/cshperspect.a004507	journal	September 2011
Expanding Proteostasis by Membrane Trafficking Networks Hutt, D. M.; Balch, W. E. Cold Spring Harbor Perspectives in Biology, Vol. 5, Issue 7 https://doi.org/10.1101/cshperspect.a013383	journal	February 2013
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training Ter-Hovhannisyan, V.; Lomsadze, A.; Chernoff, Y. O. Genome Research, Vol. 18, Issue 12 https://doi.org/10.1101/gr.081612.108	journal	October 2008
The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes Lespinet, O. Genome Research, Vol. 12, Issue 7 https://doi.org/10.1101/gr.174302	journal	July 2002
Cloning, Expression, and Characterization of Sorbitol Transporters from Developing Sour Cherry Fruit and Leaf Sink Tissues Gao, Zhifang; Maurousset, Laurence; Lemoine, Remi Plant Physiology, Vol. 131, Issue 4 https://doi.org/10.1104/pp.102.016725	journal	March 2003
The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex Blanc, Guillaume; Duncan, Garry; Agarkova, Irina The Plant Cell, Vol. 22, Issue 9 https://doi.org/10.1105/tpc.110.076406	journal	September 2010
The BAF60 Subunit of the SWI/SNF Chromatin-Remodeling Complex Directly Controls the Formation of a Gene Loop at FLOWERING LOCUS C in Arabidopsis Jégu, Teddy; Latrasse, David; Delarue, Marianne The Plant Cell, Vol. 26, Issue 2 https://doi.org/10.1105/tpc.113.114454	journal	February 2014
Metagenome sequence of E laphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria -rich microbiome Quandt, C. Alisha; Kohler, Annegret; Hesse, Cedar N. Environmental Microbiology, Vol. 17, Issue 8 https://doi.org/10.1111/1462-2920.12840	journal	April 2015
Beyond histones - the expanding roles of protein lysine methylation Wu, Zhouran; Connolly, Justin; Biggar, Kyle K. The FEBS Journal, Vol. 284, Issue 17 https://doi.org/10.1111/febs.14056	journal	May 2017
Biotic environments and the maintenance of sex-some evidence from mutualistic symbioses Law, R.; Lewis, D. H. Biological Journal of the Linnean Society, Vol. 20, Issue 3 https://doi.org/10.1111/j.1095-8312.1983.tb01876.x	journal	November 1983
The variety of fungal-algal symbioses, their evolutionary significance, and the nature of lichens Hawksworth, D. L. Botanical Journal of the Linnean Society, Vol. 96, Issue 1 https://doi.org/10.1111/j.1095-8339.1988.tb00623.x	journal	January 1988
The Top 10 fungal pathogens in molecular plant pathology: Top 10 fungal pathogens Dean, Ralph; Van Kan, Jan A. L.; Pretorius, Zacharias A. Molecular Plant Pathology, Vol. 13, Issue 4 https://doi.org/10.1111/j.1364-3703.2011.00783.x	journal	April 2012
Do photobionts influence the ecology of lichens? A case study of environmental preferences in symbiotic green alga Asterochloris (Trebouxiophyceae): DO PHOTOBIONTS INFLUENCE LICHEN ECOLOGY? Peksa, OndŘEj; ŠKaloud, Pavel Molecular Ecology, Vol. 20, Issue 18 https://doi.org/10.1111/j.1365-294X.2011.05168.x	journal	June 2011
Vertical and horizontal photobiont transmission within populations of a lichen symbiosis: DYNAMICS OF A LICHEN SYMBIOSIS Dal Grande, F.; Widmer, I.; Wagner, H. H. Molecular Ecology, Vol. 21, Issue 13 https://doi.org/10.1111/j.1365-294X.2012.05482.x	journal	March 2012
The Arabidopsis ROCK-N-ROLLERS gene encodes a homolog of the yeast ATP-dependent DNA helicase MER3 and is required for normal meiotic crossover formation: Arabidopsis crossover formation requires an MER3 homolog Chen, Changbin; Zhang, Wei; Timofejeva, Ljudmilla The Plant Journal, Vol. 43, Issue 3 https://doi.org/10.1111/j.1365-313X.2005.02461.x	journal	June 2005
Arabidopsis SPO11-2 functions with SPO11-1 in meiotic recombination Stacey, Nicola J.; Kuromori, Takashi; Azumi, Yoshitaka The Plant Journal, Vol. 48, Issue 2 https://doi.org/10.1111/j.1365-313X.2006.02867.x	journal	October 2006
Decoding algal genomes: tracing back the history of photosynthetic life on Earth: Decoding algal genomes Tirichine, Leïla; Bowler, Chris The Plant Journal, Vol. 66, Issue 1 https://doi.org/10.1111/j.1365-313X.2011.04540.x	journal	March 2011
Two Trebouxia algae with different physiological performances are ever-present in lichen thalli of Ramalina farinacea. Coexistence versus Competition?: Successful coexistence of two algae in R. farinacea lichens Casano, Leonardo M.; del Campo, Eva M.; García-Breijo, Francisco J. Environmental Microbiology, Vol. 13, Issue 3 https://doi.org/10.1111/j.1462-2920.2010.02386.x	journal	December 2010
Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome: Prokaryotic communities of the lichen microbiome Hodkinson, Brendan P.; Gottel, Neil R.; Schadt, Christopher W. Environmental Microbiology, Vol. 14, Issue 1 https://doi.org/10.1111/j.1462-2920.2011.02560.x	journal	September 2011
Lichen Physiology. xi. the role of the alga in Determining the Pattern of Carbohydrate Movement Between Lichen Symbionts Richardson, D. H. S.; Hill, D. Jackson; Smith, D. C. New Phytologist, Vol. 67, Issue 3 https://doi.org/10.1111/j.1469-8137.1968.tb05476.x	journal	July 1968
Observations on Free-Living Trebouxia de Puymalyand Pseudotrebouxia Archibald, and Evidence that both Symbionts from Xanthoria Parietina (l.) th. fr. can be Found Free-Living in Nature Bubrick, P.; Galun, Margalith; Frensdorff, A. New Phytologist, Vol. 97, Issue 3 https://doi.org/10.1111/j.1469-8137.1984.tb03611.x	journal	July 1984
The control of the cell cycle in microbial symbionts Hill, D. J. New Phytologist, Vol. 112, Issue 2 https://doi.org/10.1111/j.1469-8137.1989.tb02372.x	journal	June 1989
Carbonic anhydrase(s) associated with lichens: in vivo activities, possible locations and putative roles Palmqvist, Kristin; Badger, Murray R. New Phytologist, Vol. 132, Issue 4 https://doi.org/10.1111/j.1469-8137.1996.tb01881.x	journal	April 1996
Saprotrophy and lichenization as options for the same fungal species on different substrata: environmental plasticity and fungal lifestyles in the Stictis-Conotrema complex Wedin, Mats; Döring, Heidi; Gilenstam, Gunnar New Phytologist, Vol. 164, Issue 3 https://doi.org/10.1111/j.1469-8137.2004.01198.x	journal	September 2004
The lichen-forming ascomycete Evernia mesomorpha associates with multiple genotypes of Trebouxia jamesii Piercey-Normore, Michele D. New Phytologist, Vol. 169, Issue 2 https://doi.org/10.1111/j.1469-8137.2005.01576.x	journal	October 2005
Fungal endophytes: diversity and functional roles Rodriguez, R. J.; White Jr, J. F.; Arnold, A. E. New Phytologist, Vol. 182, Issue 2 https://doi.org/10.1111/j.1469-8137.2009.02773.x	journal	February 2009
Hexose and pentose transport in ascomycetous yeasts: an overview Leandro, Maria José; Fonseca, César; Gonçalves, Paula FEMS Yeast Research, Vol. 9, Issue 4, p. 511-525 https://doi.org/10.1111/j.1567-1364.2009.00509.x	journal	June 2009
Photobiont association and genetic diversity of the optionally lichenized fungus Schizoxylon albescens: Optional lichenization in Schizoxylon albescens Muggia, Lucia; Baloch, Elisabeth; Stabentheiner, Edith FEMS Microbiology Ecology, Vol. 75, Issue 2 https://doi.org/10.1111/j.1574-6941.2010.01002.x	journal	December 2010
Transcription factors in fungi Shelest, Ekaterina FEMS Microbiology Letters, Vol. 286, Issue 2 https://doi.org/10.1111/j.1574-6968.2008.01293.x	journal	September 2008
Sexual reproduction and developmental adaptations in Xanthoria parietina Ott, Sieglinde Nordic Journal of Botany, Vol. 7, Issue 2 https://doi.org/10.1111/j.1756-1051.1987.tb00933.x	journal	April 1987
Algal and Fungal Diversity in Antarctic Lichens Park, Chae Haeng; Kim, Kyung Mo; Elvebakk, Arve Journal of Eukaryotic Microbiology, Vol. 62, Issue 2 https://doi.org/10.1111/jeu.12159	journal	September 2014
Phylogenetic analysis of LSU and SSU rDNA group I introns of lichen photobionts associated with the genera Xanthoria and Xanthomendoza (Teloschistaceae, lichenized Ascomycetes) Nyati, Shyam; Bhattacharya, Debashish; Werth, Silke Journal of Phycology, Vol. 49, Issue 6 https://doi.org/10.1111/jpy.12126	journal	November 2013
Assembling the challenging puzzle of algal biodiversity: species delimitation within the genus Asterochloris (Trebouxiophyceae, Chlorophyta) Škaloud, Pavel; Steinová, Jana; Řídká, Tereza Journal of Phycology, Vol. 51, Issue 3 https://doi.org/10.1111/jpy.12295	journal	May 2015
European phylogeography of the epiphytic lichen fungus Lobaria pulmonaria and its green algal symbiont Widmer, Ivo; Dal Grande, Francesco; Excoffier, Laurent Molecular Ecology, Vol. 21, Issue 23 https://doi.org/10.1111/mec.12051	journal	October 2012
The earliest records of internally stratified cyanobacterial and algal lichens from the Lower Devonian of the Welsh Borderland Honegger, Rosmarie; Edwards, Dianne; Axe, Lindsey New Phytologist, Vol. 197, Issue 1 https://doi.org/10.1111/nph.12009	journal	October 2012
Sebacinales – one thousand and one interactions with land plants Weiß, Michael; Waller, Frank; Zuccaro, Alga New Phytologist, Vol. 211, Issue 1 https://doi.org/10.1111/nph.13977	journal	February 2016
Fungal-algal association patterns in lichen symbiosis linked to macroclimate Singh, Garima; Dal Grande, Francesco; Divakar, Pradeep K. New Phytologist, Vol. 214, Issue 1 https://doi.org/10.1111/nph.14366	journal	December 2016
The response of A sterochloris erici (Ahmadjian) Skaloud et Peksa to desiccation: a proteomic approach : Alga desiccation proteome response Gasulla, Franscico; Jain, Renuka; Barreno, Eva Plant, Cell & Environment, Vol. 36, Issue 7 https://doi.org/10.1111/pce.12065	journal	February 2013
Lichen-Like Symbiosis 600 Million Years Ago Yuan, X. Science, Vol. 308, Issue 5724 https://doi.org/10.1126/science.1111347	journal	May 2005
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions Merchant, S. S.; Prochnik, S. E.; Vallon, O. Science, Vol. 318, Issue 5848, p. 245-250 https://doi.org/10.1126/science.1143609	journal	October 2007
Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri Prochnik, S. E.; Umen, J.; Nedelcu, A. M. Science, Vol. 329, Issue 5988 https://doi.org/10.1126/science.1188800	journal	July 2010
Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote Schonknecht, G.; Chen, W. -H.; Ternes, C. M. Science, Vol. 339, Issue 6124 https://doi.org/10.1126/science.1231707	journal	March 2013
Niche engineering demonstrates a latent capacity for fungal-algal mutualism Hom, Erik F. Y.; Murray, Andrew W. Science, Vol. 345, Issue 6192 https://doi.org/10.1126/science.1253320	journal	July 2014
Basidiomycete yeasts in the cortex of ascomycete macrolichens Spribille, Toby; Tuovinen, Veera; Resl, Philipp Science, Vol. 353, Issue 6298 https://doi.org/10.1126/science.aaf8287	journal	July 2016
Mating types and sexual development in filamentous ascomycetes. Coppin, E.; Debuchy, R.; Arnaise, S. Microbiology and molecular biology reviews : MMBR, Vol. 61, Issue 4 https://doi.org/10.1128/.61.4.411-428.1997	journal	January 1997
Eisosome Ultrastructure and Evolution in Fungi, Microalgae, and Lichens Lee, Jae-Hyeok; Heuser, John E.; Roth, Robyn Eukaryotic Cell, Vol. 14, Issue 10 https://doi.org/10.1128/EC.00106-15	journal	August 2015
DNA Sequence Characterization and Molecular Evolution of MAT1 and MAT2 Mating-Type Loci of the Self-Compatible Ascomycete Mold Neosartorya fischeri Rydholm, C.; Dyer, P. S.; Lutzoni, F. Eukaryotic Cell, Vol. 6, Issue 5 https://doi.org/10.1128/EC.00319-06	journal	March 2007
Comparative Genomics of Chrysochromulina Ericina Virus and Other Microalga-Infecting Large DNA Viruses Highlights Their Intricate Evolutionary Relationship with the Established Mimiviridae Family Gallot-Lavallée, Lucie; Blanc, Guillaume; Claverie, Jean-Michel Journal of Virology, Vol. 91, Issue 14 https://doi.org/10.1128/JVI.00230-17	journal	April 2017
Common Origin of Four Diverse Families of Large Eukaryotic DNA Viruses Iyer, L. M.; Aravind, L.; Koonin, E. V. Journal of Virology, Vol. 75, Issue 23 https://doi.org/10.1128/JVI.75.23.11720-11734.2001	journal	December 2001
The Evolution of Sex: a Perspective from the Fungal Kingdom Lee, S. C.; Ni, M.; Li, W. Microbiology and Molecular Biology Reviews, Vol. 74, Issue 2 https://doi.org/10.1128/MMBR.00005-10	journal	May 2010
Draft Genome Sequence of Cladonia macilenta KoLRI003786, a Lichen-Forming Fungus Producing Biruloquinone Park, S. -Y.; Choi, J.; Kim, J. A. Genome Announcements, Vol. 1, Issue 5 https://doi.org/10.1128/genomeA.00695-13	journal	August 2013
Draft Genome Sequence of Lichen-Forming Fungus Cladonia metacorallifera Strain KoLRI002260 Park, S. -Y.; Choi, J.; Lee, G. -W. Genome Announcements, Vol. 2, Issue 1 https://doi.org/10.1128/genomeA.01065-13	journal	January 2014
Lichenized Fungi and the Evolution of Symbiotic Organization Grube, Martin; Wedin, Mats Microbiology Spectrum, Vol. 4, Issue 6 https://doi.org/10.1128/microbiolspec.FUNK-0011-2016	journal	December 2016
Nitrate uptake by isolated bionts of the lichen Parmelia sulcata Pavlova, E. A.; Maslov, A. I. Russian Journal of Plant Physiology, Vol. 55, Issue 4 https://doi.org/10.1134/S1021443708040079	journal	July 2008
Recognition- and defense-related gene expression at 3 resynthesis stages in lichen symbionts Athukorala, Sarangi N. P.; Piercey-Normore, Michele D. Canadian Journal of Microbiology, Vol. 61, Issue 1 https://doi.org/10.1139/cjm-2014-0470	journal	January 2015
The Genomics of Obligate (and Nonobligate) Biotrophs Spanu, Pietro D. Annual Review of Phytopathology, Vol. 50, Issue 1 https://doi.org/10.1146/annurev-phyto-081211-173024	journal	September 2012
Early Molecular Investigations of Lichen-Forming Symbionts: 1986–2001 DePriest, Paula T. Annual Review of Microbiology, Vol. 58, Issue 1 https://doi.org/10.1146/annurev.micro.58.030603.123730	journal	October 2004
Protein Glycation: A Firm Link to Endothelial Cell Dysfunction Wautier, Jean-Luc; Schmidt, Ann Marie Circulation Research, Vol. 95, Issue 3 https://doi.org/10.1161/01.RES.0000137876.28454.64	journal	August 2004
TransportTP: A two-phase classification approach for membrane transporter prediction and characterization Li, Haiquan; Benedito, Vagner A.; Udvardi, Michael K. BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-418	journal	January 2009
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects Holt, Carson; Yandell, Mark BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-491	journal	December 2011
Gene finding in novel genomes Korf, Ian BMC Bioinformatics, Vol. 5, Issue 1 https://doi.org/10.1186/1471-2105-5-59	journal	May 2004
Subcellular localization of ammonium transporters in Dictyostelium discoideum Kirsten, Janet H.; Xiong, Yanhua; Davis, Carter T. BMC Cell Biology, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2121-9-71	journal	January 2008
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 Junttila, Sini; Rudd, Stephen BMC Genomics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2164-13-575	journal	January 2012
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)* Molnár, István; Lopez, David; Wisecaver, Jennifer H. BMC Genomics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2164-13-576	journal	January 2012
High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporter/ammonia permease gene family McDonald, Tami R.; Mueller, Olaf; Dietrich, Fred S. BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-225	journal	January 2013
Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen Junttila, Sini; Laiho, Asta; Gyenesei, Attila BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-870	journal	January 2013
Genome characteristics reveal the impact of lichenization on lichen-forming fungus Endocarpon pusillum Hedwig (Verrucariales, Ascomycota) Wang, Yan-Yan; Liu, Bin; Zhang, Xin-Yu BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-34	journal	January 2014
Medicago truncatula and Glomus intraradices gene expression in cortical cells harboring arbuscules in the arbuscular mycorrhizal symbiosis Gomez, S. Karen; Javot, Hélène; Deewatthanawong, Prasit BMC Plant Biology, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2229-9-10	journal	January 2009
BowStrap v1.0: Assigning statistical significance to expressed genes using short-read transcriptome data Larsen, Peter E.; Collart, Frank R. BMC Research Notes, Vol. 5, Issue 1 https://doi.org/10.1186/1756-0500-5-275	journal	June 2012
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Langmead, Ben; Trapnell, Cole; Pop, Mihai Genome Biology, Vol. 10, Issue 3 https://doi.org/10.1186/gb-2009-10-3-r25	journal	January 2009
The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation Blanc, Guillaume; Agarkova, Irina; Grimwood, Jane Genome Biology, Vol. 13, Issue 5 https://doi.org/10.1186/gb-2012-13-5-r39	journal	January 2012
Radial spoke proteins of Chlamydomonas flagella Yang, P. Journal of Cell Science, Vol. 119, Issue 6 https://doi.org/10.1242/jcs.02811	journal	February 2006
The Evolution of Fungal Metabolic Pathways Wisecaver, Jennifer H.; Slot, Jason C.; Rokas, Antonis PLoS Genetics, Vol. 10, Issue 12 https://doi.org/10.1371/journal.pgen.1004816	journal	December 2014
Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers Lambing, Christophe; Osman, Kim; Nuntasoontorn, Komsun PLOS Genetics, Vol. 11, Issue 7 https://doi.org/10.1371/journal.pgen.1005372	journal	July 2015
Horizontal Transfer of a Nitrate Assimilation Gene Cluster and Ecological Transitions in Fungi: A Phylogenetic Study Slot, Jason C.; Hibbett, David S. PLoS ONE, Vol. 2, Issue 10 https://doi.org/10.1371/journal.pone.0001097	journal	October 2007
An Expanded Inventory of Conserved Meiotic Genes Provides Evidence for Sex in Trichomonas vaginalis Malik, Shehre-Banoo; Pightling, Arthur W.; Stefaniak, Lauren M. PLoS ONE, Vol. 3, Issue 8 https://doi.org/10.1371/journal.pone.0002879	journal	August 2008
The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome Marcet-Houben, Marina; Gabaldón, Toni PLoS ONE, Vol. 4, Issue 2 https://doi.org/10.1371/journal.pone.0004357	journal	February 2009
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
Tracing the Origin of the Fungal α1 Domain Places Its Ancestor in the HMG-Box Superfamily: Implication for Fungal Mating-Type Evolution Martin, Tom; Lu, Shun-Wen; van Tilbeurgh, Herman PLoS ONE, Vol. 5, Issue 12 https://doi.org/10.1371/journal.pone.0015199	journal	December 2010
Origin and Diversification of Major Clades in Parmelioid Lichens (Parmeliaceae, Ascomycota) during the Paleogene Inferred by Bayesian Analysis Amo de Paz, Guillermo; Cubas, Paloma; Divakar, Pradeep K. PLoS ONE, Vol. 6, Issue 12 https://doi.org/10.1371/journal.pone.0028161	journal	December 2011
Genetic Basis of Self-Incompatibility in the Lichen-Forming Fungus Lobaria pulmonaria and Skewed Frequency Distribution of Mating-Type Idiomorphs: Implications for Conservation Singh, Garima; Dal Grande, Francesco; Cornejo, Carolina PLoS ONE, Vol. 7, Issue 12 https://doi.org/10.1371/journal.pone.0051402	journal	December 2012
Dating the Diversification of the Major Lineages of Ascomycota (Fungi) Prieto, María; Wedin, Mats PLoS ONE, Vol. 8, Issue 6 https://doi.org/10.1371/journal.pone.0065576	journal	June 2013
Characterization of New Polyol/H+ Symporters in Debaryomyces hansenii Pereira, Iliana; Madeira, Ana; Prista, Catarina PLoS ONE, Vol. 9, Issue 2 https://doi.org/10.1371/journal.pone.0088180	journal	February 2014
Photobionts in Lichens: Possible Indicators of Phylogenetic Relationships? Rambold, Gerhard; Friedl, Thomas; Beck, Andreas The Bryologist, Vol. 101, Issue 3 https://doi.org/10.1639/0007-2745(1998)101[392:PILPIO]2.0.CO;2	journal	January 1998
Simon Schwendener (1829–1919) and the Dual Hypothesis of Lichens Honegger, Rosmarie The Bryologist, Vol. 103, Issue 2 https://doi.org/10.1639/0007-2745(2000)103[0307:SSATDH]2.0.CO;2	journal	June 2000
Phylogenetic Species, Reproductive Mode, and Specificity of the Green Alga Trebouxia Forming Lichens with the Fungal Genus Letharia Kroken, Scott; Taylor, John W. The Bryologist, Vol. 103, Issue 4 https://doi.org/10.1639/0007-2745(2000)103[0645:PSRMAS]2.0.CO;2	journal	December 2000
Experimental Lichenology and Microbiology of Lichens: Culture Experiments, Secondary Chemistry of Cultured Mycobionts, Resynthesis, and Thallus Morphogenesis Stocker-Wörgötter, Elfriede The Bryologist, Vol. 104, Issue 4 https://doi.org/10.1639/0007-2745(2001)104[0576:ELAMOL]2.0.CO;2	journal	December 2001
Desiccation-Tolerance in Lichens: A Review Kranner, Ilse; Beckett, Richard; Hochman, Ayala The Bryologist, Vol. 111, Issue 4 https://doi.org/10.1639/0007-2745-111.4.576	journal	December 2008
A Guide to the Algae Occurring as Lichen Symbionts: Isolation, Culture, Cultural Physiology, and Identification Ahmadjian, Vernon Phycologia, Vol. 6, Issue 2-3 https://doi.org/10.2216/i0031-8884-6-2-127.1	journal	April 1967
A cyanolichen from the Lower Devonian Rhynie chert Taylor, Thomas N.; Hass, Hagen; Kerp, Hans American Journal of Botany, Vol. 84, Issue 7 https://doi.org/10.2307/2446290	journal	July 1997
Induction of the Production of Lichen Substances by Non-Metabolites Hamada, Nobuo The Bryologist, Vol. 99, Issue 1 https://doi.org/10.2307/3244440	journal	April 1996
Algal switching among lichen symbioses Piercey-Normore, Michele D.; DePriest, Paula T. American Journal of Botany, Vol. 88, Issue 8 https://doi.org/10.2307/3558457	journal	August 2001
Unravelling the phylogenetic relationships of lichenised fungi in Dothideomyceta Nelsen, M. P.; Lücking, R.; Grube, M. Studies in Mycology, Vol. 64 https://doi.org/10.3114/sim.2009.64.07	journal	January 2009
Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins Pellegrin, Clement; Morin, Emmanuelle; Martin, Francis M. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.01278	journal	November 2015
Understanding nitrate assimilation and its regulation in microalgae Sanz-Luque, Emanuel; Chamizo-Ampudia, Alejandro; Llamas, Angel Frontiers in Plant Science, Vol. 6 https://doi.org/10.3389/fpls.2015.00899	journal	October 2015
“Omics” Tools for Better Understanding the Plant–Endophyte Interactions Kaul, Sanjana; Sharma, Tanwi; K. Dhar, Manoj Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.00955	journal	June 2016
A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window Gallot-Lavallée, Lucie; Blanc, Guillaume Viruses, Vol. 9, Issue 1 https://doi.org/10.3390/v9010017	journal	January 2017
Host and geographic structure of endophytic and endolichenic fungi at a continental scale U'Ren, Jana M.; Lutzoni, François; Miadlikowska, Jolanta American Journal of Botany, Vol. 99, Issue 5 https://doi.org/10.3732/ajb.1100459	journal	May 2012
Green algae and the origin of land plants Lewis, Louise A.; McCourt, Richard M. American Journal of Botany, Vol. 91, Issue 10 https://doi.org/10.3732/ajb.91.10.1535	journal	October 2004
Fungal and algal gene expression in early developmental stages of lichen-symbiosis Joneson, Suzanne; Armaleo, Daniele; Lutzoni, François Mycologia, Vol. 103, Issue 2 https://doi.org/10.3852/10-064	journal	March 2011
Insights from the first putative biosynthetic gene cluster for a lichen depside and depsidone Armaleo, Daniele; Sun, Xiameng; Culberson, Chicita Mycologia, Vol. 103, Issue 4 https://doi.org/10.3852/10-335	journal	July 2011
Autophagy is required for tolerance of drought and salt stress in plants Liu, Yimo; Xiong, Yan; Bassham, Diane C. Autophagy, Vol. 5, Issue 7 https://doi.org/10.4161/auto.5.7.9290	journal	October 2009
Structural biology of the PCI-protein fold Ellisdon, Andrew M.; Stewart, Murray BioArchitecture, Vol. 2, Issue 4 https://doi.org/10.4161/bioa.21131	journal	July 2012

Similar Records

Functional genomics of the saprotrophic-symbiotrophic fungus Rhizidium phycophilum and its algal partner Bracteacoccus sp.: increasing algal biomass through symbiosis

Dataset · Fri Sep 28 00:00:00 EDT 2012 · OSTI ID:1488069

Algal-fungal symbiosis leads to photosynthetic mycelium

Journal Article · Tue Jul 16 00:00:00 EDT 2019 · eLife · OSTI ID:1542666

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

Citation Formats

References (231)

Similar Records

Related Subjects