Exploring plant biodiversity: the Physcomitrella genome and beyond
Tài liệu tham khảo
Terasawa, 2007, The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants, Mol. Biol. Evol., 24, 699, 10.1093/molbev/msl198
Sugiura, 2003, Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus, Nucleic Acids Res., 31, 5324, 10.1093/nar/gkg726
Qiu, 2006, The deepest divergences in land plants inferred from phylogenomic evidence, Proc. Natl. Acad. Sci. U. S. A., 103, 15511, 10.1073/pnas.0603335103
Turmel, 2007, An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus, BMC Genomics, 8, 137, 10.1186/1471-2164-8-137
Turmel, 2006, The chloroplast genome sequence of Chara vulgaris sheds new light into the closest green algal relatives of land plants, Mol. Biol. Evol., 23, 1324, 10.1093/molbev/msk018
Rensing, 2008, The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants, Science, 319, 64, 10.1126/science.1150646
Schween, 2003, Unique tissue-specific cell cycle in Physcomitrella, Plant Biol., 5, 50, 10.1055/s-2003-37984
Rensing, 2002, Moss transcriptome and beyond, Trends Plant Sci., 7, 535, 10.1016/S1360-1385(02)02363-4
Sterck, 2007, How many genes are there in plants (… and why are they there)?, Curr. Opin. Plant Biol., 10, 199, 10.1016/j.pbi.2007.01.004
Rensing, 2005, Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens, BMC Genomics, 6, 43, 10.1186/1471-2164-6-43
Stenoien, 2007, Compact genes are highly expressed in the moss Physcomitrella patens, J. Evol. Biol., 20, 1223, 10.1111/j.1420-9101.2007.01301.x
Axtell, 2007, Common functions for diverse small RNAs of land plants, Plant Cell, 19, 1750, 10.1105/tpc.107.051706
Fattash, 2007, Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution, BMC Plant Biol., 7, 13, 10.1186/1471-2229-7-13
Axtell, 2006, A two-hit trigger for siRNA biogenesis in plants, Cell, 127, 565, 10.1016/j.cell.2006.09.032
Lang, 2005, Representation and high-quality annotation of the Physcomitrella patens transcriptome demonstrates a high proportion of proteins involved in metabolism among mosses, Plant Biol., 7, 228, 10.1055/s-2005-837578
Nishiyama, 2003, Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution, Proc. Natl. Acad. Sci. U. S. A., 100, 8007, 10.1073/pnas.0932694100
von Stackelberg, 2006, Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites, BMC Plant Biol., 6, 9, 10.1186/1471-2229-6-9
Yoon, 2004, A molecular timeline for the origin of photosynthetic eukaryotes, Mol. Biol. Evol., 21, 809, 10.1093/molbev/msh075
Zimmer, 2007, Dating the early evolution of plants: detection and molecular clock analyses of orthologs, Mol. Genet. Genomics, 278, 393, 10.1007/s00438-007-0257-6
Renzaglia, 2007, Bryophyte phylogeny: advancing the molecular and morphological frontiers, The Bryologist, 110, 179, 10.1639/0007-2745(2007)110[179:BPATMA]2.0.CO;2
Waters, 2003, Molecular adaptation and the origin of land plants, Mol. Phylogenet. Evol., 29, 456, 10.1016/j.ympev.2003.07.018
Wellman, 2003, Fragments of the earliest land plants, Nature, 425, 282, 10.1038/nature01884
Floyd, 2007, The ancestral developmental tool kit of land plants, Int. J. Plant Sci., 168, 1, 10.1086/509079
Taylor, 2005, Life history biology of early land plants: deciphering the gametophyte phase, Proc. Natl. Acad. Sci. U. S. A., 102, 5892, 10.1073/pnas.0501985102
Hernick, 2008, Earth's oldest liverworts – Metzgeriothallus sharonae sp. nov. from the Middle Devonian (Givetian) of eastern New York, USA, Rev. Palaeobot. Palynol., 148, 154, 10.1016/j.revpalbo.2007.09.002
Hedges, 2004, A molecular timescale of eukaryote evolution and the rise of complex multicellular life, BMC Evol. Biol., 4, 2, 10.1186/1471-2148-4-2
Richardt, 2007, PlanTAPDB: a phylogeny-based resource of plant transcription associated proteins, Plant Physiol., 143, 1452, 10.1104/pp.107.095760
Fujita, 2008, Convergent evolution of shoots in land plants: lack of auxin polar transport in moss shoots, Evol. Dev., 10, 176, 10.1111/j.1525-142X.2008.00225.x
Lienard, 2008, Water transport by aquaporins in the extant plant Physcomitrella patens, Plant Physiol., 146, 1207, 10.1104/pp.107.111351
Machida, 2006, Genes for the peptidoglycan synthesis pathway are essential for chloroplast division in moss, Proc. Natl. Acad. Sci. U. S. A., 103, 6753, 10.1073/pnas.0510693103
Suppanz, 2007, An integrated physiological and genetic approach to the dynamics of FtsZ targeting and organisation in a moss, Physcomitrella patens, Protoplasma, 232, 1, 10.1007/s00709-007-0284-5
Gremillon, 2007, Filamentous temperature-sensitive Z (FtsZ) isoforms specifically interact in the chloroplasts and in the cytosol of Physcomitrella patens, New Phytol., 176, 299, 10.1111/j.1469-8137.2007.02169.x
Kopriva, 2007, The putative moss 3′-phosphoadenosine-5′-phosphosulfate reductase is a novel form of adenosine-5′-phosphosulfate reductase without an iron-sulfur cluster, J. Biol. Chem., 282, 22930, 10.1074/jbc.M702522200
Hirano, 2007, The GID1-mediated gibberellin perception mechanism is conserved in the lycophyte Selaginella moellendorffii but not in the bryophyte Physcomitrella patens, Plant Cell, 19, 3058, 10.1105/tpc.107.051524
Reski, 2006, Small molecules on the move: homeostasis, crosstalk, and molecular action of phytohormones, Plant Biol. (Stuttg.), 8, 277, 10.1055/s-2006-924190
Vandenbussche, 2007, Evolutionary conservation of plant gibberellin signalling pathway components, BMC Plant Biol., 7, 65, 10.1186/1471-2229-7-65
Yasumura, 2007, Step-by-step acquisition of the gibberellin-DELLA growth-regulatory mechanism during land-plant evolution, Curr. Biol., 17, 1225, 10.1016/j.cub.2007.06.037
Maizel, 2005, The floral regulator LEAFY evolves by substitutions in the DNA binding domain, Science, 308, 260, 10.1126/science.1108229
Benlloch, 2007, Floral initiation and inflorescence architecture: a comparative view, Ann. Bot. (Lond.), 100, 659, 10.1093/aob/mcm146
De Bodt, 2003, And then there were many: MADS goes genomic, Trends Plant Sci., 8, 475, 10.1016/j.tplants.2003.09.006
Riese, 2005, Isolation and characterization of new MIKC*-type MADS-box genes from the moss Physcomitrella patens, Plant Biol., 7, 307, 10.1055/s-2005-865640
Singer, 2007, Clues about the ancestral roles of plant MADS-box genes from a functional analysis of moss homologues, Plant Cell Rep., 26, 1155, 10.1007/s00299-007-0312-0
Verelst, 2007, MIKC* MADS-protein complexes bind motifs enriched in the proximal region of late pollen-specific Arabidopsis promoters, Plant Physiol., 143, 447, 10.1104/pp.106.089805
Menand, 2007, An ancient mechanism controls the development of cells with a rooting function in land plants, Science, 316, 1477, 10.1126/science.1142618
Rensing, 2007, An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens, BMC Evol. Biol., 7, 130, 10.1186/1471-2148-7-130
Newton, 2006, Dating the diversification of the pleurocarpous mosses
Rizzon, 2006, Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice, PLOS Comput. Biol., 2, e115, 10.1371/journal.pcbi.0020115
Kamisugi, 2006, The mechanism of gene targeting in Physcomitrella patens: homologous recombination, concatenation and multiple integration, Nucleic Acids Res., 34, 6205, 10.1093/nar/gkl832
Puchta, 2005, The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution, J. Exp. Bot., 56, 1
Nishiyama, 2007, Evolutionary developmental biology of nonflowering land plants, Int. J. Plant Sci., 168, 37, 10.1086/509609
Markmann-Mulisch, 2007, Differential requirements for RAD51 in Physcomitrella patens and Arabidopsis thaliana development and DNA damage repair, Plant Cell, 19, 3080, 10.1105/tpc.107.054049
Hohe, 2003, A tool for understanding homologous recombination in plants, Plant Cell Rep., 21, 1135, 10.1007/s00299-003-0644-3
Cove, 2006, Mosses as model systems for the study of metabolism and development, Annu. Rev. Plant Biol., 57, 497, 10.1146/annurev.arplant.57.032905.105338
Decker, 2006, Moss systems biology en route: phytohormones in Physcomitrella development, Plant Biol., 8, 397, 10.1055/s-2006-923952
Decker, 2008, Current achievements in the production of complex biopharmaceuticals with moss bioreactors, Bioprocess Biosyst. Eng., 31, 3, 10.1007/s00449-007-0151-y
Khandelwal, 2007, Moonlighting activity of presenilin in plants is independent of γ-secretase and evolutionarily conserved, Proc. Natl. Acad. Sci. U. S. A., 104, 13337, 10.1073/pnas.0702038104
Schween, 2005, Large-scale analysis of 73329 Physcomitrella plants transformed with different gene disruption libraries: production parameters and mutant phenotypes, Plant Biol., 7, 228, 10.1055/s-2005-837692
Cuming, 2007, Microarray analysis of transcriptional responses to abscisic acid and osmotic, salt, and drought stress in the moss, Physcomitrella patens, New Phytol., 176, 275, 10.1111/j.1469-8137.2007.02187.x
Heintz, 2006, Rapid alteration of the phosphoproteome in the moss Physcomitrella patens after cytokinin treatment, J. Proteome Res., 5, 2283, 10.1021/pr060152e
Quatrano, 2007, Physcomitrella patens: mosses enter the genomic age, Curr. Opin. Plant Biol., 10, 182, 10.1016/j.pbi.2007.01.005
Kim, 2007, Recombination and linkage disequilibrium in Arabidopsis thaliana, Nat. Genet., 39, 1151, 10.1038/ng2115
Clark, 2007, Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana, Science, 317, 338, 10.1126/science.1138632
Jackson, 2006, Comparative sequencing of plant genomes: choices to make, Plant Cell, 18, 1100, 10.1105/tpc.106.042192
Green, 2007, 2x genomes – does depth matter?, Genome Res., 17, 1547, 10.1101/gr.7050807
Katari, 2005, Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana, Genome Res., 15, 496, 10.1101/gr.3239105
Havecker, 2004, The diversity of LTR retrotransposons, Genome Biol., 5, 225, 10.1186/gb-2004-5-6-225
Adl, 2005, The new higher level classification of eukaryotes with emphasis on the taxonomy of protests, J. Eukaryot. Microbiol., 52, 399, 10.1111/j.1550-7408.2005.00053.x
Kelman, 2004, Charophyte algae from the Rhynie chert, Trans. R. Soc. Edinburgh, Earth Sci., 94, 445, 10.1017/S0263593300000808
Reyes-Prieto, 2007, Phylogeny of nuclear-encoded plastid-targeted proteins supports an early divergence of glaucophytes within Plantae, Mol. Biol. Evol., 24, 2358, 10.1093/molbev/msm186
Lemieux, 2007, A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies, BMC Biol., 5, 2, 10.1186/1741-7007-5-2