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References

  • Aggarwal RK, Brar DS, Khush GS. 1997. Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization. Molecular & General Genetics 254: 112.
  • Akaike H. 1974. A new look at the statistical model identification. IEEE Transactions on Automatic Control 19: 716723.
  • Alvarez I, Costa A, Feliner GN. 2008. Selecting single-copy nuclear genes for plant phylogenetics: a preliminary analysis for the Senecioneae (Asteraceae). Journal of Molecular Evolution 66: 276291.
  • Alvarez I, Wendel JF. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417434.
  • Bailey CD, Doyle JJ. 1999. Potential phylogenetic utility of the low-copy nuclear gene pistillata in dicotyledonous plants: comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae. Molecular Phylogenetics and Evolution 13: 2030.
  • Barker NP, Clark LG, Davis JI, Duvall MR, Guala GF, Hsiao C, Kellogg EA, Linder HP, Mason-Gamer RJ, Mathews SY et al . 2001. Phylogeny and subfamilial classification of the grasses (Poaceae). Annals of the Missouri Botanical Garden 88: 373457.
  • Chapman MA, Chang J, Weisman D, Kesseli RV, Burke JM. 2007. Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae). Theoretical and Applied Genetics 115: 747755.
  • Childs KL, Hamilton JP, Zhu W, Ly E, Cheung F, Wu H, Rabinowicz PD, Town CD, Buell CR, Chan AP. 2007. The TIGR plant transcript assemblies database. Nucleic Acids Research 35: D846D851.
  • Crawford DJ, Mort ME. 2004. Single-locus molecular markers for inferring relationships at lower taxonomic levels: observations and comments. Taxon 53: 631635.
  • Delannoy E, Stanley WA, Bond CS, Small ID. 2007. Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles. Biochemical Society Transactions 35: 16431647.
  • Felsenstein J. 1985. Confidence limits on phylogenies – an approach using the bootstrap. Evolution 39: 783791.
  • Fulton TM, van der Hoeven R, Eannetta NT, Tanksley SD. 2002. Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14: 14571467.
  • Ge S, Sang T, Lu BR, Hong DY. 1999. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proceedings of the National Academy of Sciences, USA 96: 1440014405.
  • Howarth DG, Baum DA. 2002. Phylogenetic utility of a nuclear intron from nitrate reductase for the study of closely related plant species. Molecular Phylogenetics and Evolution 23: 525528.
  • Hughes CE, Eastwood RJ, Bailey CD. 2006. From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction. Philosophical Transactions of the Royal Society B – Biological Sciences 361: 211225.
  • Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C et al . 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463U5.
  • Jain M, Khurana P, Tyagi AK, Khurana JP. 2008. Genome-wide analysis of intronless genes in rice and Arabidopsis. Functional & Integrative Genomics 8: 6978.
  • Lurin C, Andres C, Aubourg S, Bellaoui M, Bitton F, Bruyere C, Caboche M, Debast C, Gualberto J, Hoffmann B et al . 2004. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell 16: 20892103.
  • Mort ME, Crawford DJ. 2004. The continuing search: low-copy nuclear sequences for lower-level plant molecular phylogenetic studies. Taxon 53: 257261.
  • Nayar NM. 1973. Origin and cytogenetics of rice. Advances in Genetics Incorporating Molecular Genetic Medicine 17: 153292.
  • O'Toole N, Hattori M, Andres C, Iida K, Lurin C, Schmitz-Linneweber C, Sugita M, Small I. 2008. On the expansion of the pentatricopeptide repeat gene family in plants. Molecular Biology and Evolution 25: 11201128.
  • Olsen KM, Schaal BA. 1999. Evidence on the origin of cassava: phylogeography of manihot esculenta. Proceedings of the National Academy of Sciences, USA 96: 55865591.
  • Padolina JM. 2006. Phylogenetic reconstruction of Phalaenopsis using nuclear and chloroplast DNA sequence data and using Phalaenopsis as a natural system for assessing methods to reconstruct hybrid evolution in phylogenetic analyses. PhD dissertation, The University of Texas at Austin, Austin, TX, USA.
  • Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817818.
  • Pusnik M, Small I, Read LK, Fabbro T, Schneider A. 2007. Pentatricopeptide repeat proteins in trypanosoma brucei function in mitochondrial ribosomes. Molecular and Cellular Biology 27: 68766888.
  • Rambaut A. 1996. Se-al: sequence alignment editor. Oxford, UK: University of Oxford. http://evolve.zoo.ox.ac.uk/ .
  • Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 19: 15721574.
  • Rudinger M, Polsakiewicz M, Knoop V. 2008. Organellar RNA editing and plant-specific extensions of pentatricopeptide repeat proteins in jungermanniid but not in marchantiid liverworts. Molecular Biology and Evolution 25: 14051414.
  • Salone V, Rudinger M, Polsakiewicz M, Hoffmann B, Groth-Malonek M, Szurek B, Small I, Knoop V, Lurin C. 2007. A hypothesis on the identification of the editing enzyme in plant organelles. FEBS Letters 581: 41324138.
  • Sang T. 2002. Utility of low-copy nuclear gene sequences in plant phylogenetics. Critical Reviews in Biochemistry and Molecular Biology 37: 121147.
  • Shaw J, Lickey EB, Beck JT, Farmer SB, Liu WS, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL. 2005. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92: 142166.
  • Small RL, Cronn RC, Wendel JF. 2004. Use of nuclear genes for phylogeny reconstruction in plants. Australian Systematic Botany 17: 145170.
  • Small RL, Wendel JF. 2000. Phylogeny, duplication, and intraspecific variation of Adh sequences in new world diploid cottons (Gossypium L., Malvaceae). Molecular Phylogenetics and Evolution 16: 7384.
  • Steele PR, Guisinger-Bellian M, Linder CR, Jansen RK. 2008. Phylogenetic utility of 141 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related families of rosids. Molecular Phylogenetics and Evolution 48: 10131026.
  • Strand AE, LeebensMack J, Milligan BG. 1997. Nuclear DNA-based markers for plant evolutionary biology. Molecular Ecology 6: 113118.
  • Swofford DL. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4b10. Sunderland, MA, USA: Sinauer Associates, Inc.
  • Tank DC, Sang T. 2001. Phylogenetic utility of the glycerol-3-phosphate acyltransferase gene: evolution and implications in Paeonia (Paeoniaceae). Molecular Phylogenetics and Evolution 19: 421429.
  • Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A et al . 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 15961604.
  • Walker NS, Stiffler N, Barkan A. 2007. POGs/PlantRBP: a resource for comparative genomics in plants. Nucleic Acids Research 35: D852D856.
  • Wing RA, Ammiraju JSS, Luo MZX, Kim H, Yu YS, Kudrna D, Goicoechea JL, Wang WM, Nelson W, Rao K et al . 2005. The Oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species. Plant Molecular Biology 59: 5362.
  • Wu FN, Mueller LA, Crouzillat D, Petiard V, Tanksley SD. 2006. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 174: 14071420.
  • Yuan YW, Olmstead RG. 2008. Evolution and phylogenetic utility of the PHOT gene duplicates in the Verbena complex (Verbenaceae): dramatic intron size variation and footprint of ancestral recombination. American Journal of Botany 95: 11661176.
  • Zou XH, Zhang FM, Zhang JG, Zang LL, Tang L, Wang J, Sang T, Ge S. 2008. Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biology 9: R49.