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2011
D. M. Melotto-Passarin, Tambarussi, E. V., Dressano, K., De Martin, V. F., and Carrer, H., Characterization of chloroplast DNA microsatellites from Saccharum spp and related species, vol. 10, pp. 2024-2033, 2011.
Asano T, Tsudzuki T, Takahashi S, Shimada H, et al. (2004). Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes. DNA Res. 11: 93-99. http://dx.doi.org/10.1093/dnares/11.2.93 PMid:15449542 Bortiri E, Coleman-Derr D, Lazo GR, Anderson OD, et al. (2008). The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes. BMC Res. Notes 1: 61. http://dx.doi.org/10.1186/1756-0500-1-61 PMid:18710514    PMCid:2527572 Bremer K (2002). Gondwanan evolution of the grass alliance of families (Poales). Evolution 56: 1374-1387. PMid:12206239 Calsa JT, Carraro DM, Benatti MR, Barbosa AC, et al. (2004). Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome. Curr. Genet. 46: 366-373. http://dx.doi.org/10.1007/s00294-004-0542-4 PMid:15526204 Cardle L, Ramsay L, Milbourne D, Macaulay M, et al. (2000). Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156: 847-854. PMid:11014830    PMCid:1461288 Ceresini PC, Silva CLSP, Missio RF, Souza EC, et al. (2005). Satellypus: analysis and database of microsatellites from ESTs of Eucalyptus. Genet. Mol. Biol. 28: 589-600. http://dx.doi.org/10.1590/S1415-47572005000400014 Clegg MT (1993). Chloroplast gene sequences and the study of plant evolution. Proc. Natl. Acad. Sci. U. S. A. 90: 363-367. http://dx.doi.org/10.1073/pnas.90.2.363 Daniell H, Lee SB, Grevich J, Saski C, et al. (2006). Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor. Appl. Genet. 112: 1503-1518. http://dx.doi.org/10.1007/s00122-006-0254-x PMid:16575560 Dechering KJ, Cuelenaere K, Konings RN and Leunissen JA (1998). Distinct frequency-distributions of homopolymeric DNA tracts in different genomes. Nucleic Acids Res. 26: 4056-4062. http://dx.doi.org/10.1093/nar/26.17.4056 PMid:9705519    PMCid:147789 Dick CW and Heuertz M (2008). The complex biogeographic history of a widespread tropical tree species. Evolution 62: 2760-2774. http://dx.doi.org/10.1111/j.1558-5646.2008.00506.x PMid:18764917 Ellegren H (2004). Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 5: 435-445. http://dx.doi.org/10.1038/nrg1348 PMid:15153996 Felsenstein J (1985). Confidence limits on phytogenies: an approach using the bootstrap. Evolution 39: 783. http://dx.doi.org/10.2307/2408678 Goulding SE, Olmstead RG, Morden CW and Wolfe KH (1996). Ebb and flow of the chloroplast inverted repeat. Mol. Gen. Genet. 252: 195-206. http://dx.doi.org/10.1007/BF02173220 Grass Phylogeny Working Group (2001). Phylogeny and subfamilial classification of the grasses (Poaceae). Ann. Miss. Bot. Gard. 88: 373-457. http://dx.doi.org/10.2307/3298585 Kalendar R (2008). Software FastPCR: a PCR primer and Probe Design and Repeat Sequence Searching Software with Additional Tools for the Manipulation and Analysis of DNA and Protein. Available at [http://www.biocenter.helsinki.fi/bi/programs/fastpcr.htm.]. Accessed February 2, 2010. Kelchner SA (2000). The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann. Miss. Bot. Gard. 87: 482-498. http://dx.doi.org/10.2307/2666142 Levinson G and Gutman GA (1987). Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4: 203-221. PMid:3328815 Lovett ST (2004). Encoded errors: mutations and rearrangements mediated by misalignment at repetitive DNA sequences. Mol. Microbiol. 52: 1243-1253. http://dx.doi.org/10.1111/j.1365-2958.2004.04076.x PMid:15165229 Marshall HD, Newton C and Ritland K (2001). Sequence-repeat polymorphisms exhibit the signature of recombination in lodgepole pine chloroplast DNA. Mol. Biol. Evol. 18: 2136-2138. http://dx.doi.org/10.1093/oxfordjournals.molbev.a003757 PMid:11606712 Metzgar D, Bytof J and Wills C (2000). Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res. 10: 72-80. PMid:10645952    PMCid:310501 Moxon ER and Wills C (1999). DNA microsatellites: agents of evolution? Sci. Am. 280: 94-99. http://dx.doi.org/10.1038/scientificamerican0199-94 PMid:9891422 Nei M and Kumar Ed S (2000). Molecular Evolution and Phylogenetics. Oxford University Press, New York. Nishikawa T, Vaughan DA and Kadowaki K (2005). Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes. Theor. Appl. Genet. 110: 696-705. http://dx.doi.org/10.1007/s00122-004-1895-2 PMid:15650813 Palmieri DA, Novelli VM, Bastianel M, Cristofani-Yaly M, et al. (2007). Frequency and distribution of microsatellites from ESTs of Citrus. Genet. Mol. Biol. 30: 1009-1018. http://dx.doi.org/10.1590/S1415-47572007000500029 Powell W, Machray GC and Provan J (1996). Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1: 215-222. Rajendrakumar P, Biswal AK, Balachandran SM, Srinivasarao K, et al. (2007). Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions. Bioinformatics 23: 1-4. http://dx.doi.org/10.1093/bioinformatics/btl547 PMid:17077096 Raubeson LA, Peery R, Chumley TW, Dziubek C, et al. (2007). Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8: 174. http://dx.doi.org/10.1186/1471-2164-8-174 PMid:17573971    PMCid:1925096 Rose O and Falush D (1998). A threshold size for microsatellite expansion. Mol. Biol. Evol. 15: 613-615. PMid:9580993 Saski C, Lee SB, Daniell H, Wood TC, et al. (2005). Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Mol. Biol. 59: 309–322. http://dx.doi.org/10.1007/s11103-005-8882-0 PMid:16247559 Silva JAF (2001). Preliminary analysis of microsatellite markers derived from sugarcane expressed sequence tags (ESTs). Genet. Mol. Biol. 24: 155-159. http://dx.doi.org/10.1590/S1415-47572001000100021 Subramanian S, Mishra RK and Singh L (2003). Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol. 4: R13. http://dx.doi.org/10.1186/gb-2003-4-2-r13 PMid:12620123    PMCid:151303 Tambarussi EV, Melotto-Passarin DM, Barbosa AL, Brigati JB, et al. (2009). In silico analysis of simple sequence repeats from chloroplast genomes of Solanaceae species. Crop Breed. Appl. Biotech. 9: 344-352. Tamura K, Dudley J, Nei M and Kumar S (2007). MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596-1599. http://dx.doi.org/10.1093/molbev/msm092 PMid:17488738 Thompson JD, Higgins DG and Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680. http://dx.doi.org/10.1093/nar/22.22.4673 PMid:7984417    PMCid:308517 Timme R, Kuehl EJ, Boore JL and Jansen RK (2007). A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Am. J. Bot. 94: 302-312. http://dx.doi.org/10.3732/ajb.94.3.302 PMid:21636403 Tóth G, Gaspari Z and Jurka J (2000). Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 10: 967-981. http://dx.doi.org/10.1101/gr.10.7.967 PMid:10899146    PMCid:310925 Varshney RK, Thiel T, Stein N, Langridge P, et al. (2002). In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol. Biol. Lett. 7: 537-546. PMid:12378259 Wu YQ and Huang Y (2007). An SSR genetic map of Sorghum bicolor (L.) Moench and its comparison to a published genetic map. Genome 50: 84-89. http://dx.doi.org/10.1139/g06-133 PMid:17546074
2010
V. Pandolfi, Jorge, E. C., Melo, C. M. R., Albuquerque, A. C. S., and Carrer, H., Gene expression profile of the plant pathogen Fusarium graminearum under the antagonistic effect of Pantoea agglomerans, vol. 9, pp. 1298-1311, 2010.
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