van der Heijden M, Klironomos J, Ursic M, Moutoglis P, Streitwolf-Engel R, Boller T, et al. Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature. 1998;74:69–72.
van der Heijden M, Martin F, Selosse M, Sanders I. Mycorrhizal ecology and evolution: the past, the present, and the future. N Phytol. 2015;205:1406–23.
Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, et al. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia. 2016;108:1028–46.
Remy W, Taylor TN, Hass H, Kerp H. Four hundred-million-year-old vesicular arbuscular mycorrhizae. Proc Natl Acad Sci USA. 1994;91:11841–3.
Koch AM, Croll D, Sanders IR. Genetic variability in a population of arbuscular mycorrhizal fungi causes variation in plant growth. Ecol Lett. 2006;9:103–10.
Roger A, Colard A, Angelard C, Sanders IR. Relatedness among arbuscular mycorrhizal fungi drives plant growth and intraspecific fungal coexistence. ISME J. 2013;7:2137–46.
Sanders IR. Sex, plasticity, and biologically significant variation in one Glomeromycotina species. N Phytol. 2018;220:968–70.
Ropars J, Toro KS, Noel J, Pelin A, Charron P, Farinelli L, et al. Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi. Nat Microbiol. 2016;1:16033.
Judson OP, Normark BB. Ancient asexual scandals. Trends Ecol Evol. 1996;11:41–6.
Giovannetti M, Azzolini D, Citernesi AS. Anastomosis formation and nuclear and protoplasmic exchange in arbuscular mycorrhizal fungi. Appl Environ Microbiol. 1999;65:5571–5.
Croll D, Giovannetti M, Koch AM, Sbrana C, Ehinger M, Lammers PJ, et al. Nonself vegetative fusion and genetic exchange in the arbuscular mycorrhizal fungus Glomus intraradices. N Phytol. 2009;181:924–37.
Giovannetti M, Sbrana C, Avio L, Strani P. Patterns of below-ground plant interconnections established by means of arbuscular mycorrhizal networks. N Phytol. 2004;164:175–81.
Pepe A, Giovannetti M, Sbrana C. Different levels of hyphal self-incompatibility modulate interconnectedness of mycorrhizal networks in three arbuscular mycorrhizal fungi within the Glomeraceae. Mycorrhiza. 2016;26:325–32.
Kuhn G, Hijri M, Sanders IR, Walker C. Evidence for the evolution of multiple genomes in arbuscular mycorrhizal fungi. Nature. 2001;619:745–8.
Bever JD, Morton J. Heritable variation and mechanism of inheritance of spore shape within a population of Scutellosporea pellucida, an arbuscular mycorrhi. Am J Bot. 1999;86:1209–16.
Savary R, Masclaux FG, Wyss T, Droh G, Cruz Corella J, Machado AP, et al. A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis. ISME J. 2018;12:17–30.
Halary S, Malik S-B, Lildhar L, Slamovits CH, Hijri M, Corradi N. Conserved meiotic machinery in Glomus spp., a putatively ancient asexual fungal lineage. Genome Biol Evol. 2011;3:950–8.
Tisserant E, Malbreil M, Kuo A, Kohler A, Symeonidi A, et al. Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci. 2013;111:562–3.
Morin E, Miyauchi S, San Clemente H, Chen ECH, Pelin A, Providencia I, et al. Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina. N. Phytol. 2019;222:1584–98.
Croll D, Sanders IR. Recombination in Glomus intraradices, a supposed ancient asexual arbuscular mycorrhizal fungus. BMC Evol Biol. 2009;9:13.
Chen EC, Mathieu S, Hoffrichter A, Sedzielewska-Toro K, Peart M, Pelin A, et al. Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi. Elife. 2018;7:1–17.
Auxier B, Bazzicalupo A. Comment on ‘Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi’. Elife. 2019;8:1–9.
Sprague GF, Jensen R, Herskowitz I. Control of yeast cell type by the mating type locus: positive regulation of the alpha-specific STE3 gene by the MAT alpha 1 product. Cell. 1983;32:409–15.
Gioti A, Mushegian AA, Strandberg R, Stajich JE, Johannesson H. Unidirectional evolutionary transitions in fungal mating systems and the role of transposable elements. Mol Biol Evol. 2012;29:3215–26.
Fraser J, Heitman J. Fungal mating-type loci. Curr Biol. 2003;13:R792–R795.
Gryganskyi AP, Lee SC, Litvintseva AP, Smith ME, Bonito G, Porter TM, et al. Structure, function, and phylogeny of the mating locus in the Rhizopus oryzae complex. PLoS One. 2010;5:1–12.
Lee SC, Corradi N, Byrnes EJ, Torres-Martinez S, Dietrich FS, Keeling PJ, et al. Microsporidia evolved from ancestral sexual fungi. Curr Biol. 2008;18:1675–9.
Idnurm A, Walton FJ, Floyd A, Heitman J. Identification of the sex genes in an early diverged fungus. Nature. 2008;451:193–6.
Lee SC, Ni M, Li W, Shertz C, Heitman J. The evolution of sex: a perspective from the fungal kingdom. Microbiol Mol Biol Rev. 2010;74:298–340.
Tedersoo L, Sánchez-Ramírez S, Kõljalg U, Bahram M, Döring M, Schigel D, et al. High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal Divers. 2018;90:135–59.
Idnurm A. Sex determination in the first-described sexual fungus. Eukaryot Cell. 2011;10:1485–91.
Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, et al. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science. 2000;287:873–80.
Lee SC, Heitman J. Sex in the mucoralean fungi. Mycoses. 2014;57:18–24.
Wetzel J, Burmester A, Kolbe M, Wöstemeyer J. The mating-related loci sexM and sexP of the zygomycetous fungus Mucor mucedo and their transcriptional regulation by trisporoid pheromones. Microbiology. 2012;158:1016–23.
Halary S, Daubois L, Terrat Y, Ellenberger S, Wöstemeyer J, Hijri M. Mating type gene homologues and putative sex pheromone-sensing pathway in arbuscular mycorrhizal fungi, a presumably asexual plant root symbiont. PLoS ONE. 2013;8:1–12.
Riley R, Charron P, Idnurm A, Farinelli L, Dalpé Y, Martin F, et al. Extreme diversification of the mating type-high-mobility group (MATA-HMG) gene family in a plant-associated arbuscular mycorrhizal fungus. N Phytol. 2014;201:254–68.
Mateus ID, Masclaux FG, Aletti C, Rojas EC, Savary R, Dupuis C, et al. Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis. ISME J. 2019;13:1226–38.
Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, et al. Mash screen: high-throughput sequence containment estimation for genome discovery. Genome Biol. 2019;20:1–13.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:1–21.
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv Prepr. 2012;arXiv:1207–9.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Marchler-Bauer A, Bryant SH. CD-search: protein domain annotations on the fly. Nucleic Acids Res. 2004;32:327–31.
Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2019;20:1160–6.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35:1547–9.
Paradis E, Claude J, Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics. 2004;20:289–90.
Yu G, Smith DK, Zhu H, Guan Y, Lam TTY. Ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8:28–36.
Coordinators NR. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2016;44:7–19.
Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011;27:1009–10.
Fraser JA, Heitman J. Evolution of fungal sex chromosomes. Mol Microbiol. 2004;51:299–306.
Hartmann HA, Kahmann R, Bolker M. The pheromone response factor coordinates filamentous growth and pathogenicity in Ustilago maydis. EMBO J. 1996;15:1632–41.
Lin X, Jackson JC, Feretzaki M, Xue C, Heitman J. Transcription factors Mat2 and Znf2 operate cellular circuits orchestrating opposite- and same-sex mating in Cryptococcus neoformans. PLoS Genet. 2010;6:30.
Sugimoto A, Lino Y, Maeda T, Watanabe Y, Yamamoto M. Schizosaccharomyces pombe ste11+encodes a transcription factor with an HMG motif that is a critical regulator of sexual development. Genes Dev. 1991;5:1990–9.
Västermark Å, Almén MS, Simmen MW, Fredriksson R, Schiöth HB. Functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster EamA (DUF6) before the radiation of Viridiplantae. BMC Evol Biol. 2011;11:123.
Mondo SJ, Lastovetsky OA, Gaspar ML, Schwardt NH, Barber CC, Riley R, et al. Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi. Nat Commun. 2017;8:1843.
Helber N, Wippel K, Sauer N, Schaarschmidt S, Hause B, Requena N. A versatile monosaccharide transporter that operates in the arbuscular mycorrhizal fungus Glomus sp is crucial for the symbiotic relationship with plants. Plant Cell. 2011;23:3812–23.
Lee SC, Idnurm A. Fungal sex: the mucoromycota. Microbiol Spectrum. 2017;5. https://doi.org/10.1128/microbiolspec.FUNK-0041-2017.
Croll D, Wille L, Gamper H, Mathimaran N, Lammers PJ, Corradi N, et al. Genetic diversity and host plant preferences revealed by simple sequence repeat and mitochondrial markers in a population of the arbuscular mycorrhizal fungus Glomus intraradices. N Phytol. 2008;178:672–87.
Liu X, Feng Z, Zhu H, Yao Q. Exogenous abscisic acid and root volatiles increase sporulation of Rhizophagus irregularis DAOM 197198 in asymbiotic and pre-symbiotic status. Mycorrhiza. 2019;29:581–9.
Ceballos I, Ruiz M, Fernández C, Peña R, Rodríguez A, Sanders IR. The in vitro mass-produced model Mycorrhizal fungus, Rhizophagus irregularis, significantly increases yields of the globally important food security crop cassava. PLoS ONE. 2013;8:e70633.
Kim HS, Han KY, Kim KJ, Han DM, Jahng KY, Chae KS. The veA gene activates sexual development in Aspergillus nidulans. Fungal Genet Biol. 2002;37:72–80.
Trilla JA, Cos T, Duran A, Roncero C. Characterization of CHS4 (CAL2), a gene of Saccharomyces cerevisiae involved in chitin biosynthesis and allelic to SKT5 and CSD4. Yeast. 1997;13:795–807.
Chew E, Aweiss Y, Lu C, Banuett F. Fuz1, a MYND domain protein, is required for cell morphogenesis in Ustilago maydis. Mycologia. 2008;100:31–46.
Moser MJ, Geiser JR, Davis TN. Ca2+-calmodulin promotes survival of pheromone-induced growth arrest by activation of calcineurin and Ca2+-calmodulin-dependent protein kinase. Mol Cell Biol. 1996;16:4824–31.
Friesen H, Lunz R, Doyle S, Segall J. Mutation of the SPS1-encoded protein kinase of Saccharomyces cerevisiae leads to defects in transcription and morphology during spore formation. Genes Dev. 1994;8:2162–75.
Fischer JA, McCann MP, Snetselaar KM. Methylation is involved in the Ustilago maydis mating response. Fungal Genet Biol. 2001;34:21–35.
Briza P, Breitenbach M, Ellinger A, Segall J. Isolation of two developmentally regulated genes involved in spore wall maturation in Saccharomyces cerevisiae. Genes Dev. 1990;4:1775–89.
Shirk K, Jin H, Giddings TH, Winey M, Yu HG. The Aurora kinase Ipl1 is necessary for spindle pole body cohesion during budding yeast meiosis. J Cell Sci. 2011;124:2891–6.
Zhou J, Arora M, Stone DE. The yeast pheromone-responsive Gα protein stimulates recovery from chronic pheromone treatment by two mechanisms that are activated at distinct levels of stimulus. Cell Biochem Biophys. 1999;30:193–212.
Berndt P, Lanver D, Kahmann R. The AGC Ser/Thr kinase Aga1 is essential for appressorium formation and maintenance of the actin cytoskeleton in the smut fungus Ustilago maydis. Mol Microbiol. 2010;78:1484–99.
Longhese MP, Foiani M, Muzi-Falconi M, Lucchini G, Plevani P. DNA damage checkpoint in budding yeast. EMBO J. 1998;17:5525–8.
Cartagena-Lirola H, Guerini I, Manfrini N, Lucchini G, Longhese MP. Role of the Saccharomyces cerevisiae Rad53 checkpoint kinase in signaling double-strand breaks during the meiotic cell cycle. Mol Cell Biol. 2008;28:4480–93.
Source: Ecology - nature.com