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Analyses of complete genomes and large collections of gene transcripts have shown …


Biology Articles » Mycology » An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens » References

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- An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens

1.   Kenrick P, Crane PR: The origin and early evolution of plants on land.Nature 1997, 389:33-39.       2.   Graham LE, Cook ME, Busse JS: The origin of plants: body plan changes contributing to a major evolutionary radiation.Proc Natl Acad Sci U S A 2000, 97(9):4535-4540.       3.   Taylor TN, Kerp H, Hass H: Life history biology of early land plants: deciphering the gametophyte phase.Proc Natl Acad Sci U S A 2005, 102(16):5892-5897.       4.   Anderson LE: Bryology 1947-1972.Ann Miss Bot Gard 1974, 61(3):56-85.       5.   Crum HA: Structural Diversity of Bryophytes.Michigan , The University of Michigan Herbarium; 2001.       6.   Schuster RM: Phytogeography of the Bryophyta.In New Manual of Bryology. Edited by: Schuster RM. Nichinan ; 1983:463-626.       7.   Dickson JH: Bryophytes of the Pleistocene.In The British record and its chorological and ecological implication. London and New York , Cambridge University Press; 1973:256 pp.       8.   Frahm JP: Moose - lebende Fossilien.BuZ 1994, 24(3):120-124.       9.   Newton AE, Wikström N, Bell N, Forrest LL, Ignatov MS: Dating the diversification of the pleurocarpous mosses.In Pleurocarpous mosses: Systematics and Evolution. Volume Special Volume 71. Edited by: Tangney N. CRC Press, Boca Raton , Systematics Association; 2006.       10.   Heinrichs J, Hentschel J, Wilson R, Feldberg K, Schneider H: Evolution of leafy liverworts (Jungermanniidae, Marchantiophyta): estimating divergence times from chloroplast DNA sequences using penalized likelihood with integrated fossil evidence.Taxon 2007., 56:       11.   Ohno S: Evolution by gene duplication.New York , Springer; 1970.       12.   Taylor JS, Raes J: Duplication and divergence: the evolution of new genes and old ideas.Annu Rev Genet 2004, 38:615-643.       13.   De Bodt S, Maere S, Van de Peer Y: Genome duplication and the origin of angiosperms.Trends Ecol Evol 2005, 20(11):591-597.       14.   Bowers JE, Chapman BA, Rong J, Paterson AH: Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events.Nature 2003, 422(6930):433-438.       15.   Crane PR, Lidgard S: Angiosperm diversification and paleolatitudinal gradients in Cretaceous floristic diversity.Science 1989, 246:675-678.       16.   Blanc G, Wolfe KH: Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution.Plant Cell 2004, 16:1679-1691.       17.   Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).Science 2006, 313(5793):1596-1604.       18.   Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA, Ma H, Depamphilis CW: Widespread genome duplications throughout the history of flowering plants.Genome Res 2006, 15:15.       19.   Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y: Modeling gene and genome duplications in eukaryotes.Proc Natl Acad Sci U S A 2005, 102:5454-5459.       20.   Seoighe C, Gehring C: Genome duplication led to highly selective expansion of the Arabidopsis thaliana genome.Trends Genet 2004, 20:461-464.       21.   Freeling M, Thomas BC: Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity.Genome Res 2006, 16(7):805-814.       22.   Lang D, Eisinger J, Reski R, Rensing SA: Representation and high-quality annotation of the Physcomitrella patens transcriptome demonstrates a high proportion of proteins involved in metabolism among mosses.Plant Biol 2005, 7:228-237.       23.   Rensing SA, Fritzowsky D, Lang D, Reski R: Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens.BMC Genomics 2005, 6(1):43.       24.   Rensing SA, Rombauts S, Van de Peer Y, Reski R: Moss transcriptome and beyond.Trends Plant Sci 2002, 7(12):535-538.       25.   Li WH, Gu Z, Wang H, Nekrutenko A: Evolutionary analyses of the human genome.Nature 2001, 409(6822):847-849.       26.   Li WH: Molecular evolution.Sunderland , Sinauer; 1997.       27.   Lynch M, Conery JS: The evolutionary fate and consequences of duplicate genes.Science 2000, 290:1151-1155.       28.   Stenoien HK: Adaptive basis of codon usage in the haploid moss Physcomitrella patens.Heredity 2005, 94:87-93.       29.   Takezaki N, Rzhetsky A, Nei M: Phylogenetic test of the molecular clock and linearized trees.Mol Biol Evol 1995, 12(5):823-833.       30.   Vandepoele K, De Vos W, Taylor JS, Meyer A, Van de Peer Y: Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates.Proc Natl Acad Sci U S A 2004, 101(6):1638-1643.       31.   Wikstrom N, Savolainen V, Chase MW: Evolution of the angiosperms: calibrating the family tree.Proc Biol Sci 2001, 268(1482):2211-2220.       32.   Chaw SM, Chang CC, Chen HL, Li WH: Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes.J Mol Evol 2004, 58(4):424-441.       33.   Linder HP, Hardy CR, Rutschmann F: Taxon sampling effects in molecular clock dating: an example from the African Restionaceae.Mol Phylogenet Evol 2005, 35(3):569-582.       34.   Koch MA, Haubold B, Mitchell-Olds T: Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis and related genera (Brassicaceae).Mol Biol Evol 2000, 17:1483-1498.       35.   Van de Peer Y: Computational approaches to unveiling ancient genome duplications.Nat Rev Genet 2004, 5(10):752-763.       36.   Schween G, Hohe A, Schulte J, Reski R: Effect of ploidy level on growth, differentiation and phenotype in Physcomitrella patens.The Bryologist 2005, 108:27-35.       37.   Schween G, Egener T, Fritzkowsky D, Granado J, Guitton MC, Hartmann N, Hohe A, Holtorf H, Lang D, Lucht JM, Reinhard C, Rensing SA, Schlink K, Schulte J, Reski R: Large-scale analysis of 73,329 gene-disrupted Physcomitrella mutants: production parameters and mutant phenotypes.Plant Biology 2005, 7:238-250.       38.   Cove DJ: Genetics of Bryophyta.In New manual of Bryology. Edited by: Schuster RM. Tokyo , Hatt Botanical Laboratory; 1983:222-231.       39.   Feldman M, Levy AA: Allopolyploidy--a shaping force in the evolution of wheat genomes.Cytogenet Genome Res 2005, 109(1-3):250-258.       40.   Ma XF, Gustafson JP: Genome evolution of allopolyploids: a process of cytological and genetic diploidization.Cytogenet Genome Res 2005, 109(1-3):236-249.       41.   Fritsch R: Index to bryophyte chromosome counts.In Bryophytorum Bibliotheca. Volume 40. Edited by: Frahm JP, Gradstein SR. Berlin, Stuttgart , J. Cramer / Gebrueder Borntraeger; 1991.       42.   Engel PP: The induction of biochemical and morphological mutants in the moss Physcomitrella patens.American Journal of Botany 1968, 55(4):438-446.       43.   Reski R, Faust M, Wang XH, Wehe M, Abel WO: Genome analysis of the moss Physcomitrella patens (Hedw.) B.S.G.Mol Gen Genet 1994, 244(4):352-359.       44.   Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.Bioinformatics 2005, 21(18):3674-3676.       45.   Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R: The Gene Ontology (GO) database and informatics resource.Nucleic Acids Research 2004, 32 Database issue:D258-61.       46.   Blanc G, Hokamp K, Wolfe KH: A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome.Genome Res 2003, 13(2):137-144.       47.   Paterson AH, Chapman BA, Kissinger JC, Bowers JE, Feltus FA, Estill JC: Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon.Trends Genet 2006, 22(11):597-602.       48.   Glime JM: Bryophyte Ecology.In Volume 1 Physiological Ecology. Volume 1. Edited by: Glime JM. Ebook sponsored by Michigan Technological University and the International Association of Bryologists.; 2007.       49.   Koprivova A, Meyer AJ, Schween G, Herschbach C, Reski R, Kopriva S: Functional knockout of the adenosine 5'-phosphosulfate reductase gene in Physcomitrella patens revives an old route of sulfate assimilation.Journal of Biological Chemistry 2002, 277(35):32195-32201.       50.   Sperling P, Lee M, Girke T, Zahringer U, Stymne S, Heinz E: A bifunctional delta-fatty acyl acetylenase/desaturase from the moss Ceratodon purpureus. A new member of the cytochrome b5 superfamily.Eur J Biochem 2000, 267(12):3801-3811.       51.   Zank TK, Zahringer U, Beckmann C, Pohnert G, Boland W, Holtorf H, Reski R, Lerchl J, Heinz E: Cloning and functional characterisation of an enzyme involved in the elongation of Delta6-polyunsaturated fatty acids from the moss Physcomitrella patens.The Plant Journal 2002, 31(3):255-268.       52.   Von Schwartzenberg K, Schultze W, Kassner H: The moss Physcomitrella patens releases a tetracyclic diterpene.Plant Cell Reports 2004, 22(10):780-786.       53.   Kaewsuwan S, Cahoon EB, Perroud PF, Wiwat C, Panvisavas N, Quatrano RS, Cove DJ, Bunyapraphatsara N: Identification and functional characterization of the moss Physcomitrella patens delta5-desaturase gene involved in arachidonic and eicosapentaenoic acid biosynthesis.J Biol Chem 2006, 281(31):21988-21997.       54.   Girke T, Schmidt H, Zahringer U, Reski R, Heinz E: Identification of a novel delta 6-acyl-group desaturase by targeted gene disruption in Physcomitrella patens.The Plant Journal 1998, 15(1):39-48.       55.   Senger T, Wichard T, Kunze S, Gobel C, Lerchl J, Pohnert G, Feussner I: A multifunctional lipoxygenase with fatty acid hydroperoxide cleaving activity from the moss Physcomitrella patens.J Biol Chem 2005, 280(9):7588-7596.       56.   Stumpe M, Bode J, Gobel C, Wichard T, Schaaf A, Frank W, Frank M, Reski R, Pohnert G, Feussner I: Biosynthesis of C9-aldehydes in the moss Physcomitrella patens.Biochim Biophys Acta 2006, 1761(3):301-312.       57.   Otsuka M, Kenmoku H, Ogawa M, Okada K, Mitsuhashi W, Sassa T, Kamiya Y, Toyomasu T, Yamaguchi S: Emission of ent-kaurene, a diterpenoid hydrocarbon precursor for gibberellins, into the headspace from plants.Plant Cell Physiol 2004, 45(9):1129-1138.       58.   Hayashi K, Kawaide H, Notomi M, Sakigi Y, Matsuo A, Nozaki H: Identification and functional analysis of bifunctional ent-kaurene synthase from the moss Physcomitrella patens.FEBS Lett 2006, 580(26):6175-6181.       59.   Frank W, Ratnadewi D, Reski R: Physcomitrella patens is highly tolerant against drought, salt and osmotic stress.Planta 2005, 220(3):384-394.       60.   Oliver MJ, Dowd SE, Zaragoza J, Mauget SA, Payton PR: The rehydration transcriptome of the desiccation-tolerant bryophyte Tortula ruralis: transcript classification and analysis.BMC Genomics 2004, 5(1):89.       61.   Takezawa D, Minami A: Calmodulin-binding proteins in bryophytes: identification of abscisic acid-, cold-, and osmotic stress-induced genes encoding novel membrane-bound transporter-like proteins.Biochemical and Biophysical Research Communications 2004, 317(2):428-436.       62.   Bharali B, Bates JW: Detoxification of dissolved SO2 (bisulfite) by terricolous mosses.Ann Bot (Lond) 2006, 97(2):257-263.       63.   Heber U, Bilger W, Bligny R, Lange OL: Phototolerance of lichens, mosses and higher plants in an alpine environment: analysis of photoreactions.Planta 2000, 211(6):770-780.       64.   Heber U, Bukhov NG, Shuvalov VA, Kobayashi Y, Lange OL: Protection of the photosynthetic apparatus against damage by excessive illumination in homoiohydric leaves and poikilohydric mosses and lichens.J Exp Bot 2001, 52(363):1999-2006.       65.   Heber U, Bilger W, Shuvalov VA: Thermal energy dissipation in reaction centres and in the antenna of photosystem II protects desiccated poikilohydric mosses against photo-oxidation.J Exp Bot 2006, 57(12):2993-3006.       66.   Iseli C, Jongeneel CV, Bucher P: ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.1999, 138-148.       67.   Schiex T, Gouzy J, Moisan A, de Oliveira Y: FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences.Nucleic Acids Res 2003, 31(13):3738-3741.       68.   Birney E, Clamp M, Durbin R: GeneWise and Genomewise.Genome Res 2004, 14(5):988-995.       69.   Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite.Trends Genet 2000, 16(6):276-277.       70.   Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood.Comput Appl Biosci 1997, 13(5):555-556.       71.   Zharkikh A, Li WH: Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock.Mol Biol Evol 1992, 9(6):1119-1147.       72.   GO slim[http://www.geneontology.org/GO.slims.shtml]       73.   Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing.J Royal Stat Soc B 1995, 57:289-300.       74.   R project[http://www.r-project.org/]       75.   KEGG / KAAS[http://www.genome.jp/kegg/kaas/]    


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