Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota
Abstract
Summary Endogonales (Mucoromycotina), composed of Endogonaceae and Densosporaceae, is the only known non‐Dikarya order with ectomycorrhizal members. They also form mycorrhizal‐like association with some nonspermatophyte plants. It has been recently proposed that Endogonales were among the earliest mycorrhizal partners with land plants. It remains unknown whether Endogonales possess genomes with mycorrhizal‐lifestyle signatures and whether Endogonales originated around the same time as land plants did. We sampled sporocarp tissue from four Endogonaceae collections and performed shotgun genome sequencing. After binning the metagenome data, we assembled and annotated the Endogonaceae genomes. We performed comparative analysis on plant‐cell‐wall‐degrading enzymes ( PCWDE s) and small secreted proteins ( SSP s). We inferred phylogenetic placement of Endogonaceae and estimated the ages of Endogonaceae and Endogonales with expanded taxon sampling. Endogonaceae have large genomes with high repeat content, low diversity of PCWDE s, but without elevated SSP /secretome ratios. Dating analysis estimated that Endogonaceae originated in the Permian–Triassic boundary and Endogonales originated in the mid–late Silurian. Mycoplasma ‐related endobacterium sequences were identified in three Endogonaceae genomes. Endogonaceae genomes possess typical signatures of mycorrhizal lifestyle. The early origin of Endogonales suggests that the mycorrhizal association between Endogonales and plants might have played an important role during themore »
- Authors:
-
[1];
[2];
[4];
[5];
[6];
[7];
[2];
[1]
- Oregon State Univ., Corvallis, OR (United States)
- Michigan State Univ., East Lansing, MI (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
- Univ. of Lorraine, Champenoux (France). Laboratoire d'excellence ARBRE
- Univ. of California, Riverside, CA (United States)
- Univ. of Florida, Gainesville, FL (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Science Foundation (NSF); French National Research Agency; United States Dept. of Agriculture NIFA
- OSTI Identifier:
- 1580402
- Alternate Identifier(s):
- OSTI ID: 1490757
- Grant/Contract Number:
- AC02-05CH11231; DEB‐1441604; DEB‐1441715; DEB‐1441677; DEB-1737898; ANR‐11‐LABX‐0002‐01; MICL02416; DE‐AC02‐05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- New Phytologist
- Additional Journal Information:
- Journal Volume: 222; Journal Issue: 1; Journal ID: ISSN 0028-646X
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; ectomycorrhiza; Endogonaceae; Endogonales; Mucoromycota; Mycoplasma‐related endobacteria (MRE); mycorrhizal; plant‐cell‐wall‐degrading enzymes
Citation Formats
Chang, Ying, Desirò, Alessandro, Na, Hyunsoo, Sandor, Laura, Lipzen, Anna, Clum, Alicia, Barry, Kerrie, Grigoriev, Igor V., Martin, Francis M., Stajich, Jason E., Smith, Matthew E., Bonito, Gregory, and Spatafora, Joseph W. Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota. United States: N. p., 2018.
Web. doi:10.1111/nph.15613.
Chang, Ying, Desirò, Alessandro, Na, Hyunsoo, Sandor, Laura, Lipzen, Anna, Clum, Alicia, Barry, Kerrie, Grigoriev, Igor V., Martin, Francis M., Stajich, Jason E., Smith, Matthew E., Bonito, Gregory, & Spatafora, Joseph W. Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota. United States. https://doi.org/10.1111/nph.15613
Chang, Ying, Desirò, Alessandro, Na, Hyunsoo, Sandor, Laura, Lipzen, Anna, Clum, Alicia, Barry, Kerrie, Grigoriev, Igor V., Martin, Francis M., Stajich, Jason E., Smith, Matthew E., Bonito, Gregory, and Spatafora, Joseph W. Wed .
"Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota". United States. https://doi.org/10.1111/nph.15613. https://www.osti.gov/servlets/purl/1580402.
@article{osti_1580402,
title = {Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota},
author = {Chang, Ying and Desirò, Alessandro and Na, Hyunsoo and Sandor, Laura and Lipzen, Anna and Clum, Alicia and Barry, Kerrie and Grigoriev, Igor V. and Martin, Francis M. and Stajich, Jason E. and Smith, Matthew E. and Bonito, Gregory and Spatafora, Joseph W.},
abstractNote = {Summary Endogonales (Mucoromycotina), composed of Endogonaceae and Densosporaceae, is the only known non‐Dikarya order with ectomycorrhizal members. They also form mycorrhizal‐like association with some nonspermatophyte plants. It has been recently proposed that Endogonales were among the earliest mycorrhizal partners with land plants. It remains unknown whether Endogonales possess genomes with mycorrhizal‐lifestyle signatures and whether Endogonales originated around the same time as land plants did. We sampled sporocarp tissue from four Endogonaceae collections and performed shotgun genome sequencing. After binning the metagenome data, we assembled and annotated the Endogonaceae genomes. We performed comparative analysis on plant‐cell‐wall‐degrading enzymes ( PCWDE s) and small secreted proteins ( SSP s). We inferred phylogenetic placement of Endogonaceae and estimated the ages of Endogonaceae and Endogonales with expanded taxon sampling. Endogonaceae have large genomes with high repeat content, low diversity of PCWDE s, but without elevated SSP /secretome ratios. Dating analysis estimated that Endogonaceae originated in the Permian–Triassic boundary and Endogonales originated in the mid–late Silurian. Mycoplasma ‐related endobacterium sequences were identified in three Endogonaceae genomes. Endogonaceae genomes possess typical signatures of mycorrhizal lifestyle. The early origin of Endogonales suggests that the mycorrhizal association between Endogonales and plants might have played an important role during the colonization of land by plants.},
doi = {10.1111/nph.15613},
journal = {New Phytologist},
number = 1,
volume = 222,
place = {United States},
year = {Wed Nov 28 00:00:00 EST 2018},
month = {Wed Nov 28 00:00:00 EST 2018}
}
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Works referenced in this record:
Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants
journal, May 2015
- Chang, Ying; Wang, Sishuo; Sekimoto, Satoshi
- Genome Biology and Evolution, Vol. 7, Issue 6
Sphaerocreas pubescens is a member of the Mucoromycotina closely related to fungi associated with liverworts and hornworts
journal, May 2014
- Hirose, Dai; Degawa, Yousuke; Yamamoto, Kohei
- Mycoscience, Vol. 55, Issue 3
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
journal, December 2011
- Holt, Carson; Yandell, Mark
- BMC Bioinformatics, Vol. 12, Issue 1
New Phytologist ? an evolving host for mycorrhizal research
journal, April 2007
- Martin, Francis; Slater, Holly
- New Phytologist, Vol. 174, Issue 2
A mycorrhizal revolution
journal, August 2018
- Hoysted, Grace A.; Kowal, Jill; Jacob, Alison
- Current Opinion in Plant Biology, Vol. 44
Fossil fungi with suggested affinities to the Endogonaceae from the Middle Triassic of Antarctica
journal, March 2012
- Krings, M.; Taylor, T. N.; Dotzler, N.
- Mycologia, Vol. 104, Issue 4
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
journal, April 2000
- Castresana, J.
- Molecular Biology and Evolution, Vol. 17, Issue 4
The Origin and Early Evolution of Roots
journal, September 2014
- Kenrick, P.; Strullu-Derrien, C.
- PLANT PHYSIOLOGY, Vol. 166, Issue 2
Mycorrhizal ecology and evolution: the past, the present, and the future
journal, February 2015
- van der Heijden, Marcel G. A.; Martin, Francis M.; Selosse, Marc-André
- New Phytologist, Vol. 205, Issue 4
The dawn of symbiosis between plants and fungi
journal, February 2011
- Bidartondo, Martin I.; Read, David J.; Trappe, James M.
- Biology Letters, Vol. 7, Issue 4
Phylogenetic analysis of the genus Modicella reveals an independent evolutionary origin of sporocarp-forming fungi in the Mortierellales
journal, December 2013
- Smith, Matthew E.; Gryganskyi, Andrii; Bonito, Gregory
- Fungal Genetics and Biology, Vol. 61
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
journal, November 2007
- Cantarel, B. L.; Korf, I.; Robb, S. M. C.
- Genome Research, Vol. 18, Issue 1
The land flora: a phototroph-fungus partnership?
journal, January 1998
- Selosse, M-A; Le Tacon, F.
- Trends in Ecology & Evolution, Vol. 13, Issue 1
Taxonomy, culture and mycorrhizal associations of some zygosporic Endogonaceae
journal, March 1990
- Warcup, J. H.
- Mycological Research, Vol. 94, Issue 2
Mycoplasma-related endobacteria within Mortierellomycotina fungi: diversity, distribution and functional insights into their lifestyle
journal, February 2018
- Desirò, Alessandro; Hao, Zhen; Liber, Julian A.
- The ISME Journal, Vol. 12, Issue 7
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
journal, June 2015
- Simão, Felipe A.; Waterhouse, Robert M.; Ioannidis, Panagiotis
- Bioinformatics, Vol. 31, Issue 19
Symbiotic options for the conquest of land
journal, August 2015
- Field, Katie J.; Pressel, Silvia; Duckett, Jeffrey G.
- Trends in Ecology & Evolution, Vol. 30, Issue 8
Repbase Update, a database of repetitive elements in eukaryotic genomes
journal, June 2015
- Bao, Weidong; Kojima, Kenji K.; Kohany, Oleksiy
- Mobile DNA, Vol. 6, Issue 1
The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, reveals alternative adaptations to obligate intracellular parasitism
journal, November 2017
- Quandt, C. Alisha; Beaudet, Denis; Corsaro, Daniele
- eLife, Vol. 6
The diversity of fungal genome
journal, April 2015
- Mohanta, Tapan Kumar; Bae, Hanhong
- Biological Procedures Online, Vol. 17, Issue 1
Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum
journal, September 2016
- Peter, Martina; Kohler, Annegret; Ohm, Robin A.
- Nature Communications, Vol. 7, Issue 1
Endogone pisiformis : axenic culture and associations with Sphagnum, Pinus sylvestris, Allium cepa , and Allium porrum
journal, March 1983
- Berch, S. M.; Fortin, J. A.
- Canadian Journal of Botany, Vol. 61, Issue 3
WoLF PSORT: protein localization predictor
journal, May 2007
- Horton, P.; Park, K. -J.; Obayashi, T.
- Nucleic Acids Research, Vol. 35, Issue Web Server
dbCAN: a web resource for automated carbohydrate-active enzyme annotation
journal, May 2012
- Yin, Yanbin; Mao, Xizeng; Yang, Jincai
- Nucleic Acids Research, Vol. 40, Issue W1
Full-length transcriptome assembly from RNA-Seq data without a reference genome
journal, May 2011
- Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran
- Nature Biotechnology, Vol. 29, Issue 7
Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi
journal, December 2017
- Beaudet, Denis; Chen, Eric C. H.; Mathieu, Stephanie
- DNA Research, Vol. 25, Issue 2
Reconsidering mutualistic plant–fungal interactions through the lens of effector biology
journal, August 2015
- Plett, Jonathan M.; Martin, Francis
- Current Opinion in Plant Biology, Vol. 26
The Truffle Microbiome: Species and Geography Effects on Bacteria Associated with Fruiting Bodies of Hypogeous Pezizales
journal, March 2016
- Benucci, Gian Maria Niccolò; Bonito, Gregory M.
- Microbial Ecology, Vol. 72, Issue 1
A new genus, Planticonsortium (Mucoromycotina), and new combination (P. tenue), for the fine root endophyte, Glomus tenue (basionym Rhizophagus tenuis)
journal, January 2018
- Walker, Christopher; Gollotte, Armelle; Redecker, Dirk
- Mycorrhiza, Vol. 28, Issue 3
Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis
journal, July 2010
- Bonfante, Paola; Genre, Andrea
- Nature Communications, Vol. 1, Issue 1
Fast and sensitive protein alignment using DIAMOND
journal, November 2014
- Buchfink, Benjamin; Xie, Chao; Huson, Daniel H.
- Nature Methods, Vol. 12, Issue 1
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
journal, January 2013
- Katoh, K.; Standley, D. M.
- Molecular Biology and Evolution, Vol. 30, Issue 4
Search and clustering orders of magnitude faster than BLAST
journal, August 2010
- Edgar, Robert C.
- Bioinformatics, Vol. 26, Issue 19, p. 2460-2461
Metagenome sequence of E laphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria -rich microbiome
journal, April 2015
- Quandt, C. Alisha; Kohler, Annegret; Hesse, Cedar N.
- Environmental Microbiology, Vol. 17, Issue 8
Kingdom-Wide Analysis of Fungal Small Secreted Proteins (SSPs) Reveals their Potential Role in Host Association
journal, February 2016
- Kim, Ki-Tae; Jeon, Jongbum; Choi, Jaeyoung
- Frontiers in Plant Science, Vol. 7
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
journal, April 2014
- Bouckaert, Remco; Heled, Joseph; Kühnert, Denise
- PLoS Computational Biology, Vol. 10, Issue 4
Evolutionary Stability in a 400-Million-Year-Old Heritable Facultative Mutualism: Evolution in Glomeromycota-Glomeribacter Symbiosis
journal, March 2012
- Mondo, Stephen J.; Toomer, Kevin H.; Morton, Joseph B.
- Evolution, Vol. 66, Issue 8
The origin of land plants: A matter of mycotrophism
journal, March 1975
- Pirozynski, K. A.; Malloch, D. W.
- Biosystems, Vol. 6, Issue 3
First detection of Endogone ectomycorrhizas in natural oak forests
journal, November 2016
- Yamamoto, Kohei; Endo, Naoki; Degawa, Yousuke
- Mycorrhiza, Vol. 27, Issue 3
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
journal, January 2003
- Sanderson, M. J.
- Bioinformatics, Vol. 19, Issue 2
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014
- Stamatakis, Alexandros
- Bioinformatics, Vol. 30, Issue 9
The two-speed genomes of filamentous pathogens: waltz with plants
journal, December 2015
- Dong, Suomeng; Raffaele, Sylvain; Kamoun, Sophien
- Current Opinion in Genetics & Development, Vol. 35
Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota
journal, May 2015
- Naito, Mizue; Morton, Joseph B.; Pawlowska, Teresa E.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 25
Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
journal, September 2017
- López-Escardó, David; Grau-Bové, Xavier; Guillaumet-Adkins, Amy
- Scientific Reports, Vol. 7, Issue 1
Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis
journal, November 2013
- Tisserant, E.; Malbreil, M.; Kuo, A.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 50
Fungal symbioses in hornworts: a chequered history
journal, May 2013
- Desirò, Alessandro; Duckett, Jeffrey G.; Pressel, Silvia
- Proceedings of the Royal Society B: Biological Sciences, Vol. 280, Issue 1759
Fungal associations in Horneophyton ligneri from the Rhynie Chert ( c . 407 million year old) closely resemble those in extant lower land plants: novel insights into ancestral plant-fungus symbioses
journal, April 2014
- Strullu-Derrien, Christine; Kenrick, Paul; Pressel, Silvia
- New Phytologist, Vol. 203, Issue 3
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
journal, May 2012
- Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry
- Journal of Computational Biology, Vol. 19, Issue 5
How Many Bootstrap Replicates Are Necessary?
journal, March 2010
- Pattengale, Nicholas D.; Alipour, Masoud; Bininda-Emonds, Olaf R. P.
- Journal of Computational Biology, Vol. 17, Issue 3
Multigene phylogeny of Endogonales, an early diverging lineage offungi associated with plants
journal, October 2017
- Desirò, Alessandro; Rimington, William R.; Jacob, Alison
- IMA Fungus, Vol. 8, Issue 2
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists
journal, February 2015
- Kohler, Annegret; Kuo, Alan; Nagy, Laszlo G.
- Nature Genetics, Vol. 47, Issue 4
UniProt: the Universal Protein knowledgebase
journal, January 2004
- Apweiler, R.
- Nucleic Acids Research, Vol. 32, Issue 90001
Accelerated Profile HMM Searches
journal, October 2011
- Eddy, Sean R.
- PLoS Computational Biology, Vol. 7, Issue 10
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
journal, June 2009
- Capella-Gutierrez, S.; Silla-Martinez, J. M.; Gabaldon, T.
- Bioinformatics, Vol. 25, Issue 15
Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria
journal, May 2017
- Martin, Francis M.; Uroz, Stéphane; Barker, David G.
- Science, Vol. 356, Issue 6340
Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins
journal, November 2015
- Pellegrin, Clement; Morin, Emmanuelle; Martin, Francis M.
- Frontiers in Microbiology, Vol. 6
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
journal, September 2015
- Truong, Duy Tin; Franzosa, Eric A.; Tickle, Timothy L.
- Nature Methods, Vol. 12, Issue 10
First evidence of mutualism between ancient plant lineages (Haplomitriopsida liverworts) and Mucoromycotina fungi and its response to simulated Palaeozoic changes in atmospheric CO 2
journal, September 2014
- Field, Katie J.; Rimington, William R.; Bidartondo, Martin I.
- New Phytologist, Vol. 205, Issue 2
PATRIC, the bacterial bioinformatics database and analysis resource
journal, November 2013
- Wattam, Alice R.; Abraham, David; Dalay, Oral
- Nucleic Acids Research, Vol. 42, Issue D1
Fungal associations of basal vascular plants: reopening a closed book?
journal, December 2014
- Rimington, William R.; Pressel, Silvia; Duckett, Jeffrey G.
- New Phytologist, Vol. 205, Issue 4
Black truffle - associated bacterial communities during the development and maturation of T uber melanosporum ascocarps and putative functional roles
journal, November 2013
- Antony-Babu, Sanjay; Deveau, Aurélie; Van Nostrand, Joy D.
- Environmental Microbiology, Vol. 16, Issue 9
Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage
journal, March 2016
- Mosier, Annika C.; Miller, Christopher S.; Frischkorn, Kyle R.
- Frontiers in Microbiology, Vol. 7
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
‘Candidatus Moeniiplasma glomeromycotorum’, an endobacterium of arbuscular mycorrhizal fungi
journal, May 2017
- Naito, Mizue; Desirò, Alessandro; González, Jonathan B.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 67, Issue 5, p. 1177-1184
Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics
journal, January 2017
- Sedlar, Karel; Kupkova, Kristyna; Provaznik, Ivo
- Computational and Structural Biotechnology Journal, Vol. 15
Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association
journal, May 2015
- Torres-Cortés, Gloria; Ghignone, Stefano; Bonfante, Paola
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 25
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen
journal, January 2001
- Krogh, Anders; Larsson, Björn; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 305, Issue 3
De novo identification of repeat families in large genomes
journal, June 2005
- Price, A. L.; Jones, N. C.; Pevzner, P. A.
- Bioinformatics, Vol. 21, Issue Suppl 1
Predicting Subcellular Localization of Proteins Based on their N-terminal Amino Acid Sequence
journal, July 2000
- Emanuelsson, Olof; Nielsen, Henrik; Brunak, Søren
- Journal of Molecular Biology, Vol. 300, Issue 4
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
journal, January 2008
- Ellinghaus, David; Kurtz, Stefan; Willhoeft, Ute
- BMC Bioinformatics, Vol. 9, Issue 1
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
journal, February 2012
- Ronquist, Fredrik; Teslenko, Maxim; van der Mark, Paul
- Systematic Biology, Vol. 61, Issue 3
Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees
journal, September 2012
- Stolzer, Maureen; Lai, Han; Xu, Minli
- Bioinformatics, Vol. 28, Issue 18
The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics
journal, March 2018
- Strullu-Derrien, Christine; Selosse, Marc-André; Kenrick, Paul
- New Phytologist, Vol. 220, Issue 4
Evolutionary history of mycorrhizal symbioses and global host plant diversity
journal, January 2018
- Brundrett, Mark C.; Tedersoo, Leho
- New Phytologist, Vol. 220, Issue 4
Endogone , one of the oldest plant-associated fungi, host unique Mollicutes-related endobacteria
journal, October 2014
- Desirò, Alessandro; Faccio, Antonella; Kaech, Andres
- New Phytologist, Vol. 205, Issue 4
Fine endophytes ( Glomus tenue ) are related to Mucoromycotina, not Glomeromycota
journal, October 2016
- Orchard, Suzanne; Hilton, Sally; Bending, Gary D.
- New Phytologist, Vol. 213, Issue 2
A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data
journal, September 2016
- Spatafora, Joseph W.; Chang, Ying; Benny, Gerald L.
- Mycologia, Vol. 108, Issue 5
Dating divergences in the Fungal Tree of Life: review and new analyses
journal, November 2006
- Taylor, J. W.; Berbee, M. L.
- Mycologia, Vol. 98, Issue 6
Morphology and phylogeny of four Endogone species and Sphaerocreas pubescens collected in Japan
journal, September 2015
- Yamamoto, Kohei; Degawa, Yousuke; Hirose, Dai
- Mycological Progress, Vol. 14, Issue 10
Bifiguratus adelaidae , gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats
journal, May 2017
- Torres-Cruz, Terry J.; Billingsley Tobias, Terri L.; Almatruk, Maryam
- Mycologia, Vol. 109, Issue 3
Bacterial Endosymbionts: Master Modulators of Fungal Phenotypes
journal, October 2017
- Araldi-Brondolo, Sarah J.; Spraker, Joseph; Shaffer, Justin P.
- Microbiology Spectrum, Vol. 5, Issue 5
Who lives in a fungus? The diversity, origins and functions of fungal endobacteria living in Mucoromycota
journal, April 2017
- Bonfante, Paola; Desirò, Alessandro
- The ISME Journal, Vol. 11, Issue 8
VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data
journal, January 2015
- Laczny, Cedric C.; Sternal, Tomasz; Plugaru, Valentin
- Microbiome, Vol. 3, Issue 1
jModelTest 2: more models, new heuristics and parallel computing
journal, July 2012
- Darriba, Diego; Taboada, Guillermo L.; Doallo, Ramón
- Nature Methods, Vol. 9, Issue 8
Unearthing the roots of ectomycorrhizal symbioses
journal, October 2016
- Martin, Francis; Kohler, Annegret; Murat, Claude
- Nature Reviews Microbiology, Vol. 14, Issue 12