Between Two Fern Genomes

GigaScience

Volumn 3, Issue 1, 2014, Pages

  Sessa, Emily B ^a   Banks, Jo A ^b   Barker, Michael S ^c   Der, Joshua P ^d,m   Duffy, Aaron M ^e   Graham, Sean W ^f   Hasebe, Mitsuyasu ^g   Langdale, Jane ^h   Li, Fay Wei ⁱ   Marchant, D B ^a,j   Pryer, Kathleen M ⁱ   Rothfels, Carl J ^f,n   Roux, Stanley J ^k   Salmi, Mari L ^k   Sigel, Erin M ⁱ   Soltis, Douglas E ^a,j   Soltis, Pamela S ^a,j   Stevenson, Dennis W ^l   Wolf, Paul G ^e  

^a UNIVERSITY OF FLORIDA   (United States)

^b PURDUE UNIVERSITY   (United States)

^c University of Arizona   (United States)

^d PENNSYLVANIA STATE UNIVERSITY   (United States)

^e UTAH STATE UNIVERSITY   (United States)

^f UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^g NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

^h UNIVERSITY OF OXFORD   (United Kingdom)

ⁱ DUKE UNIVERSITY   (United States)

^j UNIVERSITY OF FLORIDA   (United States)

^k UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^l NEW YORK BOTANICAL GARDEN   (United States)

^m CALIFORNIA STATE UNIVERSITY   (United States)

ⁿ UNIVERSITY OF CALIFORNIA   (United States)

more..

Author keywords

Azolla; Ceratopteris; Comparative analyses; Ferns; Genomics; Land plants; Monilophytes

Indexed keywords

ARABIDOPSIS; AZOLLA; CERATOPTERIS; CLADISTICS; FERN; GENE FUNCTION; GENE IDENTIFICATION; GENOME ANALYSIS; GENOMICS; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; PLANT GENE; PLANT GENOME; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; SPECIES DIVERSITY; TAXONOMIC IDENTIFICATION;

EID: 84925036498     PISSN: None     EISSN: 2047217X     Source Type: Journal    
DOI: 10.1186/2047-217X-3-15     Document Type: Review

References (95)

1. Smith AR, Pryer K, Schuettpelz E, Korall P, Schneider H, Wolf P. A classification for extant ferns. Taxon 2006, 55:705-731.
2. George LO, Bazzaz FA. The fern understory as an ecological filter: Emergence and establishment of canopy-tree seedlings. Ecology 1999, 80:833-845.
3. George LO, Bazzaz FA. The fern understory as an ecological filter: Growth and survival of canopy-tree seedlings. Ecology 1999, 80:846-856.
4. Siccama TG, Bormann FH, Likens GE. The Hubbard Brook ecosystem study: Productivity, nutrients, and phytosociology of the herbaceous layer. Ecol Monogr 1970, 40:389-402.
5. Ellwood MDF, Foster WA. Doubling the estimate of invertebrate biomass in a rainforest canopy. Nature 2004, 429:549-551. 10.1038/nature02560, 15175749.
6. Watkins JE, Cardelús CL. Ferns in an angiosperm world: Cretaceous radiation into the epiphytic niche and diversification on the forest floor. Int J Plant Sci 2012, 173:695-710.
7. Marrs RH, Le Duc MG, Mitchell RJ, Goddard D, Paterson S, Pakeman RJ. The ecology of Bracken: Its role in succession and implications for control. Ann Bot 2000, 85:3-15.
8. Walker LR. Effects of fern thickets on woodland development on landslides in Puerto Rico. J Veg Sci 1994, 5:525-532.
9. Tryon RM. Development and evolution of fern floras of oceanic islands. Biotropica 1970, 2:76-84.
10. Allison SD, Vitousek PM. Rapid nutrient cycling in leaf litter from invasive plants in Hawai'i. Oecologia 2004, 141:612-619. 10.1007/s00442-004-1679-z, 15549401.
11. Pemberton RW, Ferriter AP. Old World climbing fern (Lygodium microphyllum), a dangerous invasive weed in Florida. American Fern Journal 1998, 88:165-175.
12. de AL LC, Kelty MJ. Establishment and control of hay-scented fern: a native invasive species. Biol Invasions 1999, 1:223-236.
13. Pryer KM, Schneider H, Smith AR, Cranfill R, Wolf PG, Hunt JS, Sipes SD. Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 2001, 409:618-622. 10.1038/35054555, 11214320.
14. Pryer KM, Schneider H, Zimmer EA, Banks JA. Deciding among green plants for whole genome studies. Trends Plant Sci 2002, 7:550-554. 10.1016/S1360-1385(02)02375-0, 12475497.
15. Pryer KM, Schuettpelz E, Wolf PG, Schneider H, Smith AR, Cranfill R. Phylogeny and evolution of ferns (Monilophytes) with a focus on the early leptosporangiate divergences. Am J Bot 2004, 91:1582-1598. 10.3732/ajb.91.10.1582, 21652310.
16. Schuettpelz E, Pryer KM. Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy. Proc Natl Acad Sci 2009, 106:11200-11205. 10.1073/pnas.0811136106, 2708725, 19567832.
17. Schneider H, Schuettpelz E, Pryer K, Cranfill R, Magallón SA, Lupia R. Ferns diversified in the shadow of angiosperms. Nature 2004, 428:554-557.
18. Smith SA, Beaulieu JM, Donoghue MJ. An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants. Proc Natl Acad Sci 2010, 107:5897-5902. 10.1073/pnas.1001225107, 2851901, 20304790.
19. Grewe F, Guo W, Gubbels EA, Hansen AK, Mower JP. Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes. BMC Evol Biol 2013, 13:8. 10.1186/1471-2148-13-8, 3553075, 23311954.
20. Rai HS, Graham SW. Utility of a large, multigene plastid data set in inferring higher-order relationships in ferns and relatives (monilophytes). Am J Bot 2010, 97:1444-1456. 10.3732/ajb.0900305, 21616899.
21. TimeTree. [http://timetree.org].
22. Hedges SB, Dudley J, Kumar. TimeTree: A public knowledge-base of divergence times among organisms. Bioinformatics 2006, 22:2971-2972. 10.1093/bioinformatics/btl505, 17021158.
23. The 1000 Plants Project. [http://www.onekp.com].
24. Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter EJ, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel B, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw J, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, et al. A phylotranscriptomics analysis of the origin and early diversification of land plants. Proc Natl Acad Sci 2014, (In Press).
25. Amborella Genome Project The Amborella genome and the evolution of flowering plants. Science 2013, 342:1241089-1-10. Amborella Genome Project.
26. Bateman RM, DiMichele WA. Heterospory: the most iterative key innovation in the evolutionary history of the plant kingdom. Biol Rev 1994, 69:345-417.
27. Britton DM. Chromosome studies on ferns. Am J Bot 1953, 40:575-583.
28. Britton DM. The significance of chromosome numbers in ferns. Ann Mo Bot Gard 1974, 61:310-317.
29. Love A, Love D, Pichi-Sermolli REG. Cytotaxonomical Atlas of the Pteridophyta 1977, J. Cramer: Vaduz, Liechtenstein.
30. Manton I. Problems of Cytology and Evolution in the Pteridophyta 1950, Cambridge: Cambridge University Press.
31. Klekowski EJ, Baker HG. Evolutionary significance of polyploidy in the Pteridophyta. Science 1966, 153:305-307. 10.1126/science.153.3733.305, 17780002.
32. Ghatak J. Biosystematic survey of the pteridophytes from Shevaroy Hills, South India. Nucleus 1977, 20:105-108.
33. Barker MS, Wolf PG. Unfurling fern biology in the genomics age. Bioscience 2010, 60:177-185.
34. Bainard JD, Henry TA, Bainard LD, Newmaster SG. DNA content variation in monilophytes and lycophytes: large genomes that are not endopolyploid. Chromosome Res 2011, 19:763-775. 10.1007/s10577-011-9228-1, 21847691.
35. Bennett MD, Leitch IJ. Nuclear DNA amounts in pteridophytes. Ann Bot 2001, 87:335-345.
36. Garcia S, Leitch IJ, Anadon-Rosell A, Canela MA, Galvez F, Garnatje T, Gras A, Hidalgo O, Johnston E, Mas de Xaxars G, Pellicer J, Siljak-Yakovlev S, Vallés J, Vitales D, Bennett MD. Recent updates and developments to plant genome size databases. Nucleic Acids Res 2013, 42:D1159-D1166. 3965065, 24288377.
37. Hanson L, Leitch IJ. DNA amounts for five pteridophyte species fill phylogenetic gaps in C-value data. Bot J Linn Soc 2002, 140:169-173.
38. Obermayer R, Leitch IJ, Hanson L, Bennett MD. Nuclear DNA C-values in 30 species double the familial representation in pteridophytes. Ann Bot 2002, 90:209-217. 10.1093/aob/mcf167, 12197518.
39. Leitch IJ, Soltis DE, Soltis PS, Bennett MD. Evolution of DNA amounts across land plants (Embryophyta). Ann Bot 2005, 95:207-217. 10.1093/aob/mci014, 15596468.
40. Nakazato T, Barker MS, Rieseberg LH, Gastony GJ. Evolution of the nuclear genome of ferns and lycophytes. Biology and Evolution of Ferns and Lycophytes 2008, Cambridge, UK: Cambridge University Press, Ranker TA, Haufler CH.
41. Chiarugi A. Tavole chromosomiche delle Pteridophyta. Caryologia 1960, 13:27-150.
42. Fabbri F. Primo supplemento alle tavole chromosomiche delle Pteridophyta di Alberto Chiarugi. Caryologia 1963, 16:237-335.
43. Gastony GJ, Gottlieb LD. Genetic variation in the homosporous fern Pellaea andromedifolia. Am J Bot 1985, 72:257-267.
44. Haufler CH, Soltis DE. Genetic evidence suggests that homosporous ferns with high chromosome numbers are diploid. Proc Natl Acad Sci 1986, 83:4389-4393. 10.1073/pnas.83.12.4389, 323738, 16593713.
45. Haufler CH. Electrophoresis is modifying our concepts of evolution in homosporous pteridophytes. Am J Bot 1987, 74:953-966.
46. Wolf PG, Haufler CH, Sheffield E. Electrophoretic evidence for genetic diploidy in the bracken fern (Pteridium aquilinum). Science 1987, 236:947-949. 10.1126/science.236.4804.947, 17812749.
47. Soltis DE. Genetic evidence for diploidy in Equisetum. Am J Bot 1986, 73:908-913.
48. Soltis PS, Soltis DE. Estimated rates of intragametophytic selfing in lycopods. Am J Bot 1988, 75:248-256.
49. McGrath JM, Hickok LG, Pichersky E. Assessment of gene copy number in the homosporous ferns Ceratopteris thalictroides and C. richardii (Parkeriaceae) by restriction fragment length polymorphims. Plant Syst Evol 1994, 189:203-210.
50. DeYoung B, Weber T, Hass B, Banks JA. Generating autotetraploid sporophytes and their use in analyzing mutations affecting gametophyte development in the fern Ceratopteris. Genetics 1997, 147:809-814. 1208200, 9335615.
51. Banks JA. The TRANSFORMER genes of the fern Ceratopteris simultaneously promote meristem and archegonia development and repress antheridia development in the developing gametophyte. Genetics 1997, 147:1885-1897. 1208354, 9409844.
52. Strain E, Hass B, Banks JA. Characterization of mutations that feminize gametophytes of the fern Ceratopteris. Genetics 2001, 159:1271-1281. 1461853, 11729168.
53. Nakazato T, Jung MK, Housworth EA, Rieseberg LH, Gastony GJ. Genetic map-based analysis of genome structure in the homosporous fern Ceratopteris richardii. Genetics 2006, 173:1585-1597. 10.1534/genetics.106.055624, 1526675, 16648591.
54. Barker MS. Evolutionary genomic analyses of ferns reveal that high chromosome numbers are a product of high retention and fewer rounds of polyploidy relative to angiosperms. American Fern Journal 2009, 99:136-141.
55. Soltis PS, Soltis DE. The role of genetic and genomic attributes in the success of polyploids. Proc Natl Acad Sci 2000, 97:7051-7057. 10.1073/pnas.97.13.7051, 34383, 10860970.
56. Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, dePamphilis CW, Wall PK, Soltis PS. Polyploidy and angiosperm diversification. Am J Bot 2009, 96:336-348. 10.3732/ajb.0800079, 21628192.
57. Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, dePamphilis CW. Ancestral polyploidy in seed plants and angiosperms. Nature 2011, 473:97-100. 10.1038/nature09916, 21478875.
58. Initiative TAG. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815. 10.1038/35048692, 11130711.
59. Barker MS, Vogel H, Schranz ME. Paleopolyploidy in the Brassicales: Analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales. Genome Biology and Evolution 2009, 1:391-399. 2817432, 20333207.
60. Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis CW, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LGG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 2011, 332:960-963. 10.1126/science.1203810, 3166216, 21551031.
61. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, HH S, Nishiyama T, Perroud P-F, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto SI, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 2008, 319:64-69. 10.1126/science.1150646, 18079367.
62. Qiu Y-L, Yu J. Azolla - a model organism for plant genomic studies. Genomics Proteomics Bioinformatics 2003, 1:15-25.
63. Brouwer P, Bräutigam A, Külahoglu C, Tazelaar AOE, Kurz S, Nierop KGJ, van der Werf A, Weber APM, Schluepmann H. Azolla domestication towards a biobased economy?. New Phytol 2014, 202:1069-1082. 10.1111/nph.12708, 24494738.
64. Stergianou KK, Fowler K. Chromosome numbers and taxonomic implications in the fern genus Azolla (Azollaceae). Plant Syst Evol 1990, 173:223-239.
65. Perkins SK, Peters GA. The Azolla-Anabaena symbiosis: endophyte continuity in the Azolla life- cycle is facilitated by epidermal trichomes. New Phytol 1993, 123:53-64.
66. Ran L, Larsson J, Vigil-Stenman T, Nylander JAA, Ininbergs K, Zheng W-W, Lapidus A, Lowry S, Haselkorn R, Bergman B. Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium. PLoS One 2010, 5:e11486. 10.1371/journal.pone.0011486, 2900214, 20628610.
67. Brinkhuis H, Schouten S, Collinson ME, Sluijs A, Damsté JSS, Dickens GR, Huber M, Cronin TM, Onodera J, Takahashi K, Bujak JP, Stein R, van der Burgh J, Eldrett JS, Harding IC, Lotter AF, Sangiorgi F, Cittert HVK-V, de Leeuw JW, Matthiessen J, Backman J, Moran K, . the Expedition 302 Scientists Episodic fresh surface waters in the Eocene Arctic Ocean. Nature 2006, 441:606-609. 10.1038/nature04692, 16752440, the Expedition 302 Scientists.
68. Bujak JP. The Azolla Story: climate change and Arctic hydrocarbons. GEO ExPro 2007, 4:66-72.
69. Speelman EN, Van Kempen MML, Barke J, Brinkhuis H, Reichart GJ, Smolders AJP, Roelofs JGM, Sangiorgi F, De Leeuw JW, Lotter AF, Sinninghe Damsté JS. The Eocene Arctic Azolla bloom: environmental conditions, productivity and carbon drawdown. Geobiology 2009, 7:155-170. 10.1111/j.1472-4669.2009.00195.x, 19323694.
70. Bujak JP, Bujak AA. How a unique plant called Azolla changed our climate. Geoscientist magazine 2014, 24:10-15.
71. This lowly fern has massive green potential. [http://www.theglobeandmail.com/globe-debate/this-lowly-fern-has-massive-green-potential/article18907003/].
72. The Azolla Genome Project. [http://www.azollagenome.net/].
73. Scientific American: Can the Fern That Cooled the Planet Do It Again?. [http://www.scientificamerican.com/article/can-the-fern-that-cooled-the-planet-do-it-again/].
74. Experiment.com: Azolla, a Little Fern with Massive Green Potential. [https://experiment.com/projects/azolla-a-little-fern-with-massive-green-potential].
75. Li F-W, Pryer KM. Crowdfunding the Azolla fern genome project: a grassroots approach. GigaScience 2014, 3:16. 10.1186/2047-217X-3-16, 4178311, 25276348.
76. Plackett ARG, Huang L, Sanders HL, Langdale JA. High-efficiency stable transformation of the model fern species Ceratopteris richardii via microparticle bombardment. Plant Physiol 2014, 165:3-14. 10.1104/pp.113.231357, 4012588, 24623851.
77. Muthukumar B, Joyce BL, Elless MP, Stewart CN. Stable transformation of ferns using spores as targets: Pteris vittata (Chinese brake fern) and Ceratopteris thalictroides (C-fern 'Express'). Plant Physiol 2013, 163:648-658. 10.1104/pp.113.224675, 3793046, 23933990.
78. Eberle J, Nemacheck J, Wen C-K, Hasebe M, Banks JA. Ceratopteris: A model system for studying sex-determining mechanisms in plants. Int J Plant Sci 1995, 156:359-366.
79. Banks JA, Hickok LG, Webb MA. The programming of sexual phenotype in the homosporous fern Ceratopteris richardii. Int J Plant Sci 1993, 154:522-534.
80. Nakazato T, Jung MK, Housworth EA, Rieseberg LH, Gastony GJ. A genomewide study of reproductive barriers between allopatric populations of a homosporous fern, Ceratopteris richardii. Genetics 2007, 177:1141-1150. 10.1534/genetics.107.076851, 2034619, 17720917.
81. Janoušek B, Hobza R, Vyskot B. Chromosomes and Sex Differentiation. Plant Genome Diversity. Volume 2 2012, 167-186. Vienna: Springer Vienna, Leitch IJ.
82. Banks JA. Gametophyte development in ferns. Annu Rev Plant Physiol Plant Mol Biol 1999, 50:163-186. 10.1146/annurev.arplant.50.1.163, 15012207.
83. Salmi ML, Bushart TJ, Stout SC, Roux SJ. Profile and analysis of gene expression changes during early development in germinating spores of Ceratopteris richardii. Plant Physiol 2005, 138:1734-1745. 10.1104/pp.105.062851, 1176442, 15965014.
84. Hickok LG, Warne TR, Slocum MK. Ceratopteris richardii: Applications for experimental plant biology. Am J Bot 1987, 74:1304-1316.
85. Hickok LG, Warne TR, Fribourg RS. The biology of the fern Ceratopteris and its use as a model system. Int J Plant Sci 1995, 156:332-345.
86. Cooke TJ, Hickey LJ, Sugai M. The fern Ceratopteris richardii as a lower plant model system for studying the genetic regulation of plant photomorphogenesis. Int J Plant Sci 1995, 156:367-373.
87. Chasan R. Ceratopteris: A model plant for the 90s. Plant Science News 1992, 4:113-115.
88. Salmi ML, Roux SJ. Gene expression changes induced by space flight in single-cells of the fern Ceratopteris richardii. Planta 2008, 229:151-159. 10.1007/s00425-008-0817-y, 18807069.
89. Warne TR, Renzaglia KS, Hickok LG. Ceratopteris richardii - a simple model system for teaching and research. Plant Physiol 1993, 102:87.
90. C-fern.org. [http://www.c-fern.org].
91. Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marcais G, Puiu D, Roberts M, Wegrzyn JL, de Jong PJ, Neale DB, Salzberg SL, Yorke JA, Langley CH. Sequencing and assembly of the 22-Gb loblolly pine genome. Genetics 2014, 196:875-890. 10.1534/genetics.113.159715, 24653210.
92. Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu L-S, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JF, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, et al. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol 2014, 15:R59. 10.1186/gb-2014-15-3-r59, 4053751, 24647006.
93. Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin Y-C, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hallman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Kaller M, Luthman J, Lysholm F, Niittyla T, Olson A, Rilakovic N, Ritland C, Rossello JA, Sena J, et al. The Norway spruce genome sequence and conifer genome evolution. Nature 2013, 497:579-584. 10.1038/nature12211, 23698360.
94. Soltis PS, Soltis DE. A conifer genome spruces up plant phylogenomics. Genome Biol 2013, 14:122. 10.1186/gb-2013-14-6-122, 3706884, 23805854.
95. Hahn MW, Zhang SV, Moyle LC. Sequencing, assembling, and correcting draft genomes using recombinant populations. G3 Genes, Genomes, Genetics 2014, 4:669-679.