The natural histories of species and their genomes: Asymbiotic and ectomycorrhizal amanita fungi

Advances in Botanical Research

Volumn 70, Issue , 2014, Pages 235-257

  Hess, Jaqueline ^a   Pringle, Anne ^b  

^a UNIVERSITY OF OSLO   (Norway)

^b HARVARD UNIVERSITY   (United States)

Author keywords

Adaptive radiation; Ecological genomics; Invasion biology; Mutualism; Transposable elements

Indexed keywords

EID: 84900872907     PISSN: 00652296     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-397940-7.00008-2     Document Type: Chapter

References (87)

1. Alkan C., Sajjadian S., Eichler E.E. Limitations of next-generation genome sequence assembly. Nature Methods 2011, 8:61-65.
2. Bao D., Gong M., Zheng H., Chen M., Zhang L., Wang H., et al. Sequencing and comparative analysis of the straw mushroom (Volvariella volvacea) genome. PLoS One 2013, 8:e58294.
3. Bas K. The unexpected one jumped the North Sea. Field Mycology 2001, 2:40-41.
4. Böhne A., Brunet F., Galiana-Arnoux D., Schultheis C., Volff J.N. Transposable elements as drivers of genomic and biological diversity in vertebrates. Chromosome Research 2008, 16:203-215.
5. Bruns T.D., Szaro T.M., Gardes M., Cullings K.W. A sequence database for the identification of ectomycorrhizal basidiomycetes by phylogenetic analysis. Molecular Ecology 1998, 7:257-272.
6. Chaib de Mares, M. (2013). A genomic perspective on a transition to symbiosis in ectomycorrhizal Amanita. Masters thesis. Retrieved from. http://irs.ub.rug.nl/dbi/521b6392a3b10.
7. Chang S.-T. The origin and early development of straw mushroom cultivation. Economic Botany 1977, 31:374-376.
8. Crombach A., Hogeweg P. Chromosome rearrangements and the evolution of genome structuring and adaptability. Molecular Biology and Evolution 2007, 24:1130-1139.
9. Date K., Mizuno T. VII. Cultivation of fukurotake (Volvariella sp.) mushrooms. Food Reviews International 1997, 13:397-400.
10. Dickie I.A., Bolstridge N., Cooper J.A., Peltzer D.A. Co-invasion by Pinus and its mycorrhizal fungi. New Phytologist 2010, 187:475-484.
11. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 2007, 7:214.
12. Fiston-Lavier A.S., Anxolabéhère D., Quesneville H. A model of segmental duplication formation in Drosophila melanogaster. Genome Research 2007, 17:1458-1470.
13. FRDBI Fungal records database of Britain and Ireland 2013, September, Web site. http://www.fieldmycology.net/FRDBI/FRDBI.asp.
14. Geml J., Laursen G.A., O'Neill K., Nusbaum H.C., Taylor D.L. Beringian origins and cryptic speciation events in the fly agaric (Amanita muscaria). Molecular Ecology 2006, 15:225-239.
15. Geml J., Tulloss R.E., Laursen G.A., Sazanova N.A., Taylor D.L. Evidence for strong inter- and intracontinental phylogeographic structure in Amanita muscaria, a wind-dispersed ectomycorrhizal basidiomycete. Molecular Phylogenetics and Evolution 2008, 48:694-701.
16. Grandaubert J., Balesdent M.H., Rouxel T. Evolutionary and adaptive role of transposable elements in fungal genomes. Advances in Botanical Research 2014, 70:79-107.
17. Halling R.E. Ectomycorrhizae: Co-evolution, significance, and biogeography. Annals of the Missouri Botanical Garden 2001, 88:5-13.
18. Harmon L.J., Weir J.T., Brock C.D., Glor R.E., Challenger W. GEIGER: Investigating evolutionary radiations. Bioinformatics 2008, 24:129-131.
19. Heath T.A., Hedtke S.M., Hillis D.M. Taxon sampling and the accuracy of phylogenetic analyses. Journal of Systematics and Evolution 2008, 46:239-257.
20. Heliconius Genome Consortium Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 2012, 487:94-98.
21. Hess, J., Skrede, I., Wolfe, B.E., LaButti, K., Ohm, R.A., Grigoriev, I.V., et al., (in review). Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi.
22. James T.Y., Kauff F., Schoch C.L., Matheny P.B., Hofstetter V., Cox C.J., et al. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 2006, 443:818-822.
23. Janson E.M., Stireman J.O., Singer M.S., Abbot P. Phytophagous insect-microbe mutualisms and adaptive evolutionary diversification. Evolution 2008, 62:997-1012.
24. Johnson S.D. The pollination niche and its role in the diversification and maintenance of the southern African flora. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 2010, 365:499-516.
25. Jones T., Federspiel N.A., Chibana H., Dungan J., Kalman S., Magee B.B., et al. The diploid genome sequence of Candida albicans. Proceedings of the National Academy of Sciences of the United States of America 2004, 101:7329-7334.
26. Jurka J., Bao W., Kojima K.K. Families of transposable elements, population structure and the origin of species. Biology Direct 2011, 6:44.
27. Kibby G. The invasion of Amanita inopinata continues!. Field Mycology 2005, 6:31.
28. Kidwell M.G., Lisch D.R. Perspective: Transposable elements, parasitic DNA, and genome evolution. Evolution 2001, 55:1-24.
29. Kiester A.R., Lande R., Schemske D.W. Models of coevolution and speciation in plants and their pollinators. The American Naturalist 1984, 124:220-243.
30. Kondrashov F.A. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society B 2012, 279:5048-5057.
31. Kuo M. Volvariella volvacea 2011, Retrieved from the MushroomExpert.Com Web site:. http://www.mushroomexpert.com/volvariella_volvacea.html.
32. Kuo M. Amanita thiersii 2013, Retrieved from the MushroomExpert.Com Web site:. http://www.mushroomexpert.com/amanita_thiersii.html.
33. Kuo M. Amanita polypyramis 2013, Retrieved from the MushroomExpert.Com Web site:. http://www.mushroomexpert.com/amanita_polypyramis.html.
34. Kurtz S., Phillippy A., Delcher A.L., Smoot M., Shumway M., Antonescu C., et al. Versatile and open software for comparing large genomes. Genome Biology 2004, 5:R12.
35. Law R., Lewis D.H. Biotic environments and the maintenance of sex-Some evidence from mutualistic symbioses. Biological Journal of the Linnean Society 1983, 20:249-276.
36. Levin H.L., Moran J.V. Dynamic interactions between transposable elements and their hosts. Nature Reviews. Genetics 2011, 12:615-627.
37. Litsios G., Sims C.A., Wüest R.O., Pearman P.B., Zimmermann N.E., Salamin N. Mutualism with sea anemones triggered the adaptive radiation of clownfishes. BMC Evolutionary Biology 2012, 12:212.
38. Löytynoja A., Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 2008, 320:1632-1635.
39. Lynch M. The origins of genome architecture 2007, Sinauer Associates Inc., Sunderland, MA.
40. Martin F., Aerts A., Ahrén D., Brun A., Danchin E.G.J., Duchaussoy F., et al. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 2008, 452:88-92.
41. Martin F., Kohler A., Murat C., Balestrini R., Coutinho P.M., Jaillon O., et al. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 2010, 464:1033-1038.
42. Martin W., Schnarrenberger C. The evolution of the Calvin cycle from prokaryotic to eukaryotic chromosomes: A case study of functional redundancy in ancient pathways through endosymbiosis. Current Genetics 1997, 32:1-18.
43. Martin F., Selosse M.A. The Laccaria genome: A symbiont blueprint decoded. New Phytologist 2008, 180:296-310.
44. Matheny P.B., Curtis J.M., Hofstetter V., Aime M.C., Moncalvo J.M., Ge Z.W., et al. Major clades of Agaricales: A multilocus phylogenetic overview. Mycologia 2006, 98:982-995.
45. McCutcheon J.P., Moran N.A. Extreme genome reduction in symbiotic bacteria. Nature Reviews. Microbiology 2012, 10:13-26.
46. Mira A., Ochman H., Moran N.A. Deletional bias and the evolution of bacterial genomes. Trends in Genetics 2001, 17:589-596.
47. Moran N.A. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proceedings of the National Academy of Sciences of the United States of America 1996, 93:2873-2878.
48. Moran N.A., McLaughlin H.J., Sorek R. The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 2009, 323:379-382.
49. Moran N.A., Wernegreen J.J. Lifestyle evolution in symbiotic bacteria: Insights from genomics. Trends in Ecology & Evolution 2000, 15:321-326.
50. Nagendran S., Hallen-Adams H.E., Paper J.M., Aslam N., Walton J.D. Reduced genomic potential for secreted plant cell-wall-degrading enzymes in the ectomycorrhizal fungus Amanita bisporigera, based on the secretome of Trichoderma reesei. Fungal Genetics and Biology 2009, 46:427-435.
51. Ohm R.A., Feau N., Henrissat B., Schoch C.L., Horwitz B.A., Barry K.W., et al. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathogens 2012, 8:e1003037.
52. Oliver K.R., Greene W.K. Transposable elements: Powerful facilitators of evolution. BioEssays 2009, 31:703-714.
53. Oliver K.R., Greene W.K. Mobile DNA and the TE-thrust hypothesis: Supporting evidence from the primates. Mobile DNA 2011, 2:8.
54. Oliver K.R., Greene W.K. Transposable elements and viruses as factors in adaptation and evolution: An expansion and strengthening of the TE-Thrust hypothesis. Ecology and Evolution 2012, 2:2912-2933.
55. Oliver K.R., McComb J.A., Greene W.K. Transposable elements: Powerful contributors to angiosperm evolution and diversity. Genome Biology and Evolution 2013, 5:1886-1901.
56. Parra G., Bradnam K., Korf I. CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 2007, 23:1061-1067.
57. Plett J.M., Martin F. Blurred boundaries: Lifestyle lessons from ectomycorrhizal fungal genomes. Trends in Genetics 2011, 27:14-22.
58. Ponce R., Martinsen L., Vicente L.M., Hartl D.L. Novel genes from formation to function. International Journal of Evolutionary Biology 2012, 2012:821645.
59. Pringle A., Adams R.I., Cross H.B., Bruns T.D. The ectomycorrhizal fungus Amanita phalloides was introduced and is expanding its range on the west coast of North America. Molecular Ecology 2009, 18:817-833.
60. Pringle A., Bever J.D., Gardes M., Parrent J.L., Rillig M.C., Klironomos J.N. Mycorrhizal symbioses and plant invasions. Annual Review of Ecology, Evolution, and Systematics 2009, 40:699-715.
61. Pybus O.G., Harvey P.H. Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society B 2000, 267:2267-2272.
62. Raffaele S., Kamoun S. Genome evolution in filamentous plant pathogens: Why bigger can be better. Nature Reviews. Microbiology 2012, 10:417-430.
63. Ramos O.M., Ferrier D.E.K. Mechanisms of gene duplication and translocation and progress towards understanding their relative contributions to animal genome evolution. International Journal of Evolutionary Biology 2012, 2012:846421.
64. Reid D.A. New or interesting records of British hymenomycetes, VII. Notes from the Royal Botanic Garden Edinburgh 1987, 44:503-540.
65. Ridley G. The New Zealand connection-Amanita inopinata-The mystery deepens. Field Mycology 2000, 1:117-118.
66. Rieseberg L.H. Chromosomal rearrangements and speciation. Trends in Ecology & Evolution 2001, 16:351-358.
67. Rouxel T., Grandaubert J., Hane J.K., Hoede C., van de Wouw A.P., Couloux A., et al. Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat-induced point mutations. Nature Communications 2011, 2:202.
68. Ryberg M., Matheny P.B. Asynchronous origins of ectomycorrhizal clades of Agaricales. Proceedings of the Royal Society B 2012, 279:2003-2011.
69. Sacristán S., Vigouroux M., Pedersen C., Skamnioti P., Thordal-Christensen H., Micali C., et al. Coevolution between a family of parasite virulence effectors and a class of LINE-1 retrotransposons. PLoS One 2009, 4:e7463.
70. Schwartz R.S., Mueller R.L. Branch length estimation and divergence dating: Estimates of error in Bayesian and maximum likelihood frameworks. BMC Evolutionary Biology 2010, 10:5.
71. Smith S.E., Read D.J. Mycorrhizal symbiosis 2010, Academic Press, New York. 3rd ed.
72. Suarez A.V., Tsutsui N.D. The evolutionary consequences of biological invasions. Molecular Ecology 2008, 17:351-360.
73. Tamas I., Klasson L., Canbäck B., Näslund A.K., Eriksson A.S., Wernegreen J.J., et al. 50 million years of genomic stasis in endosymbiotic bacteria. Science 2002, 296:2376-2379.
74. Thompson J.N. Specific hypotheses on the geographic mosaic of coevolution. The American Naturalist 1999, 153(S5).
75. Tulloss R.E. Amanita polypyramis. Amanitaceae studies 2013, http://www.amanitaceae.org?Amanita+polypyramis, R.E. Tulloss, Z.L. Yang (Eds.).
76. van Ham R.C.H.J., Kamerbeek J., Palacios C., Rausell C., Abascal F., Bastolla U., et al. Reductive genome evolution in Buchnera aphidicola. Proceedings of the National Academy of Sciences of the United States of America 2003, 100:581-586.
77. Vellinga E.C., Wolfe B.E., Pringle A. Global patterns of ectomycorrhizal introductions. New Phytologist 2009, 181:960-973.
78. Venail J., Dell'Olivo A., Kuhlemeier C. Speciation genes in the genus Petunia. Philosophical Transactions of the Royal Society of London B 2010, 365:461-468.
79. Veneault-Fourrey C., Martin F. Mutualistic interactions on a knife-edge between saprotrophy and pathogenesis. Current Opinion in Plant Biology 2011, 14(444):450.
80. Wang E., Schornack S., Marsh J.F., Gobbato E., Schwessinger B., Eastmond P., et al. A common signaling process that promotes mycorrhizal and oomycete colonization of plants. Current Biology 2012, 22:2242-2246.
81. Werren J.H. Colloquium paper: Selfish genetic elements, genetic conflict, and evolutionary innovation. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:10863-10870.
82. Wolfe B.E., Kuo M., Pringle A. Amanita thiersii is a saprotrophic fungus expanding its range in the United States. Mycologia 2012, 104:22-33.
83. Wolfe B.E., Tulloss R.E., Pringle A. The irreversible loss of a decomposition pathway marks the single origin of an ectomycorrhizal symbiosis. PLoS One 2012, 7:e39597.
84. Yoder J.B., Nuismer S.L. When does coevolution promote diversification?. The American Naturalist 2010, 176:802-817.
85. Zeh D.W., Zeh J.A., Ishida Y. Transposable elements and an epigenetic basis for punctuated equilibria. BioEssays 2009, 31:715-726.
86. Zhang J. Evolution by gene duplication: An update. Trends in Ecology & Evolution 2003, 18:292-298.
87. Zoller S., Lutzoni F. Slow algae, fast fungi: Exceptionally high nucleotide substitution rate differences between lichenized fungi Omphalina and their symbiotic green algae Coccomyxa. Molecular Phylogenetics and Evolution 2003, 29:629-640.