SEARCH

SEARCH BY CITATION

References

  • Adams, K. and Palmer, J. (2003) Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol. Phylogenet. Evol. 29, 380395.
  • Basnitzki, J. and Zohary, D. (1994) Breeding of seed planted artichoke. Plant Breed. Rev. 12, 253269.
  • Bennetzen, J. (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42(1), 251269.
  • Brautigam, A. and Gowik, U. (2010) What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biol. 12(6), 831841.
  • Bundock, P.C., Eliott, F.G., Ablett, G., Benson, A.D., Casu, R.E., Aitken, K.S. and Henry, R.J. (2009) Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnol. J. 7, 347354.
  • Chevreux, B., Pfisterer, T., Drescher, B., Driesel, A., Muller, W., Wetter, T. and Suhai, S. (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14, 11471159.
  • Conesa, A., Gotz, S., Garcia-Gomez, J., Terol, J., Talon, M. and Robles, M. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 36743676.
  • Delseny, M., Han, B. and Hsing, Y. (2010) High throughput DNA sequencing: the new sequencing revolution. Plant Sci. 179, 407422.
  • Der, J., Barker, M., Wickett, N., dePamphilis, C. and Wolf, P. (2011) De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics, 12, 99.
  • Encinar, J., Gonzalez, J., Rodriguez, J. and Tejedor, A. (2002) Biodiesel fuels from vegetable oils: transesterification of Cynara cardunculus L. oils with ethanol. Energy Fuels, 16(2), 443450.
  • Fedorov, A., Merican, A. and Gilbert, W. (2002) Large-scale comparison of intron positions among animal, plant, and fungal genes. Proc. Nat Acad. Sci. USA, 99(25), 1612816133.
  • Finn, R., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J., Gavin, O., Gunasekaran, P., Ceric, G., Forslund, K., Holm, L., Sonnhammer, E., Eddy, S. and Bateman, A. (2010) The Pfam protein families database. Nucleic Acids Res. 38, D211D222.
  • Foti, S., Mauromicale, G., Raccuia, S., Fallico, B., Fanella, F. and Maccarone, E. (1999) Possible alternative utilization of Cynara spp. I. Biomass, grain yield and chemical composition of grain. Ind. Crops Prod. 10(3), 219228.
  • Ganal, M., Altmann, T. and Roder, M. (2009) SNP identification in crop plants. Curr. Opin. Plant Biol. 12(2), 211217.
  • Gebhardt, R. (1997) Antioxidative and protective properties of extracts from leaves of the artichoke (Cynara scolymus L) against hydroperoxide-induced oxidative stress in cultured rat hepatocytes. Toxicol. Appl. Pharmacol. 144, 279286.
  • Gebhardt, R. (1998) Inhibition of cholesterol biosynthesis in primary cultured rat hepatocytes by artichoke (Cynara scolymus L.) extracts. J. Pharmacol. Exp. Ther. 286, 11221128.
  • Gonzalez, J., Gonzalez-Garcia, C., Ramiro, A., Gonzalez, J., Sabio, E., Ganan, J. and Rodriguez, M. (2004) Combustion optimisation of biomass residue pellets for domestic heating with a mural boiler. Biomass Bioenergy, 27, 145154.
  • Goremykin, V., Salamini, F., Velasco, R. and Viola, R. (2009) Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer. Mol. Biol. Evol. 26, 99110.
  • Griffiths-Jones, S., Saini, H., van Dongen, S. and Enright, A. (2008) MiRBase: tools for microRNA genomics. Nucleic Acids Res. D154D158.
  • Hirochika, H., Otsuki, H., Yoshikawa, M., Otsuki, Y., Sugimoto, K. and Takeda, S. (1996) Autonomous transposition of the tobacco retrotransposon Tto1 in rice. Plant Cell, 8(4), 725734.
  • Huang, X. and Madan, A. (1999) CAP3 a DNA sequence assembly program. Genome Res. 9, 868877.
  • Huang, Y., Niu, B., Gao, Y., Fu, L. and Li, W. (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics, 26, 680682.
  • Ierna, A. and Mauromicale, G. (2010) Cynara cardunculus L. genotypes as a crop for energy purposes in a Mediterranean environment. Biomass Bioenergy, 34(5), 754760.
  • Imelfort, M., Duran, C., Batley, J. and Edwards, D. (2009) Discovering genetic polymorphisms in next-generation sequencing data. Plant Biotechnol. J. 7, 312317.
  • Iseli, C., Jongeneel, C.V. and Bucher, P. (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 138148.
  • Jiang, D., Ye, Q., Wang, F. and Cao, L. (2010) The mining of Citrus EST-SNP and its application in cultivar discrimination. Agric. Sci. China, 9(2), 179190.
  • Jimenez-Gomez, J. and Maloof, J. (2009) Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol. 9, 85.
  • Kaur, S., Cogan, N., Pembleton, L., Shinozuka, M., Savin, K., Materne, M. and Forster, J. (2011) Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics, 12, 265.
  • Kim, M., Lee, S., Van, K., Kim, T., Jeong, S., Choi, I., Kim, D., Lee, Y., Park, D., Ma, J., Kim, W., Kim, B., Park, S., Lee, K., Kim, D., Kim, K., Shin, J., Jang, Y., Do Kim, K., Liu, W., Chaisan, T., Kang, Y., Lee, Y., Moon, J., Schmutz, J., Jackson, S., Bhak, J. and Lee, S. (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc. Nat Acad. Sci. USA, 107(51), 2203222037.
  • Lai, Z., Kane, N.C., Kozik, A., Hodgins, K.A., Dlugosch, K.M., Barker, M.S., Matvienko, M., Yu, Q., Turner, K.G., Pearl, S.A., Bell, G.D.M., Zou, Y., Grassa, C., Guggisberg, A., Adams, K.L., Anderson, J.V., Horvath, D.P., Kesseli, R.V., Burke, J.M., Michelmore, R.W. and Rieseberg, L.H. (2012) Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression. Am. J. Bot. 99, 110.
  • Lanteri, S., Saba, E., Cadinu, M., Mallica, G.M., Baghino, L. and Portis, E. (2004) Amplified fragment length polymorphism for genetic diversity assessment in globe artichoke. Theor. Appl. Genet. 108, 15341544.
  • Lanteri, S., Acquadro, A., Comino, C., Mauro, R., Mauromicale, G. and Portis, E. (2006) A first linkage map of globe artichoke (Cynara cardunculus var. scolymus L.) based on AFLP, S-SAP, M-AFLP and microsatellite markers. Theor. Appl. Genet. 112, 15321542.
  • Lanteri, S., Portis, E., Acquadro, A., Mauro, R.P. and Mauromicale, G. (2012) Morphology and SSR fingerprinting of newly developed Cynara cardunculus genotypes exploitable as ornamentals. Euphytica 184(3), 311321.
  • Lapuerta, M., Armas, O., Ballesteros, R. and Fernandez, J. (2005) Diesel emissions from biofuels derived from Spanish potential vegetable oils. Fuel, 84, 773780.
  • Lattanzio, V., Kroon, P.A., Linsalata, V. and Cardinali, A. (2009) Globe artichoke: a functional food and source of nutraceutical ingredients. J. Funct. Foods, 1, 131144.
  • Maccarone, E., Fallico, B., Fanella, F., Mauromicale, G., Raccuia, S. and Foti, S. (1999) Possible alternative utilization of Cynara spp. II. Chemical characterization of their grain oil. Ind. Crops Prod. 10, 229237.
  • Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., Dewell, S.B., Du, L., Fierro, J.M., Gomes, X.V., Godwin, B.C., He, W., Helgesen, S., Ho, C.H., Irzyk, G.P., Jando, S.C., Alenquer, M.L., Jarvie, T.P., Jirage, K.B., Kim, J.B., Knight, J.R., Lanza, J.R., Leamon, J.H., Lefkowitz, S.M., Lei, M., Li, J., Lohman, K.L., Lu, H., Makhijani, V.B., McDade, K.E., McKenna, M.P., Myers, E.W., Nickerson, E., Nobile, J.R., Plant, R., Puc, B.P., Ronan, M.T., Roth, G.T., Sarkis, G.J., Simons, J.F., Simpson, J.W., Srinivasan, M., Tartaro, K.R., Tomasz, A., Vogt, K.A., Volkmer, G.A., Wang, S.H., Wang, Y., Weiner, M.P., Yu, P., Begley, R.F. and Rothberg, J.M. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437(7057), 376380.
  • Marillonnet, S. and Wessler, S. (1997) Retrotransposon insertion into the maize waxy gene results in tissue-specific RNA processing. Plant Cell, 9(6), 967978.
  • Mauro, R., Portis, E., Acquadro, A., Lombardo, S., Mauromicale, G. and Lanteri, S. (2009) Genetic diversity of globe artichoke landraces from Sicilian small-holdings: implications for evolution and domestication of the species. Conserv. Genet. 10, 431440.
  • Metzker, M.L. (2010) Sequencing technologies – the next generation. Nature Rev. Genetics, 11, 3146.
  • Meyer, E., Aglyamova, G., Wang, S., Buchanan-Carter, J., Abrego, D., Colbourne, J., Willis, B. and Matz, M. (2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics, 10, 219.
  • Novaes, E., Drost, D., Farmerie, W., Pappas, G., Grattapaglia, D., Sederoff, R. and Kirst, M. (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics, 9, 312.
  • Palmer, J., Adams, K., Cho, Y., Parkinson, C., Qiu, Y. and Song, K. (2000) Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proc. Nat Acad. Sci. USA, 97, 69606966.
  • Pandino, G., Lombardo, S. and Mauromicale, G. (2011) Chemical and morphological characteristics of new clones and commercial varieties of globe artichoke (Cynara cardunculus var. scolymus). Plant Foods Hum. Nutr. 66, 291297.
  • Parchman, T., Geist, K., Grahnen, J., Benkman, C. and Buerkle, C. (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics, 11, 180.
  • Pavy, N., Parsons, L., Paule, C., MacKay, J. and Bousquet, J. (2006) Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs. BMC Genomics, 7, 174.
  • Perez-Rodriguez, P., Riano-Pachon, D., Correa, L., Rensing, S., Kersten, B. and Mueller-Roeber, B. (2010) PInTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res. 38, D822D827.
  • Portis, E., Barchi, L., Acquadro, A., Macua, J. and Lanteri, S. (2005a) Genetic diversity assessment in cultivated cardoon by AFLP (amplified fragment length polymorphism) and microsatellite markers. Plant Breeding, 124, 299304.
  • Portis, E., Acquadro, A., Comino, C., Mauromicale, G., Saba, E. and Lanteri, S. (2005b) Genetic structure of island populations of wild cardoon [Cynara cardunculus L. var. sylvestris (Lamk) Fiori] detected by AFLPs and SSRs. Plant Sci. 169, 199210.
  • Portis, E., Mauromicale, G., Mauro, R., Acquadro, A., Scaglione, D. and Lanteri, S. (2009) Construction of a reference molecular linkage map of globe artichoke (Cynara cardunculus var. scolymus). Theor. Appl. Genet. 120, 5970.
  • Portis, E., Acquadro, A., Longo, A., Mauro, R., Mauromicale, G. and Lanteri, S. (2010) Potentiality of Cynara cardunculus L. as energy crop. J. Biotechnol. S165S166.
  • Portis, E., Scaglione, D., Acquadro, A., Mauromicale, G., Mauro, R., Knapp, S. and Lanteri, S. (2012) Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex. BMC Res. Notes 5, 252.
  • Ragoussis, J. (2009) Genotyping technologies for genetic research. Annu. Rev. Genomics Hum. Genet. 52, 117133.
  • Rogozin, I., Wolf, Y., Sorokin, A., Mirkin, B. and Koonin, E. (2003) Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr. Biol. 13, 15121517.
  • Sanseverino, W., Roma, G., De Simone, M., Faino, L., Melito, S., Stupka, E., Frusciante, L. and Ercolano, M. (2010) PRGdb: a bioinformatics platform for plant resistance gene analysis. Nucleic Acids Res. 38, D814D821.
  • Scaglione, D., Acquadro, A., Portis, E., Taylor, C., Lanteri, S. and Knapp, S. (2009) Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database. BMC Genomics, 10, 454.
  • Scaglione, D., Acquadro, A., Portis, E., Tirone, M., Knapp, S.J. and Lanteri, S. (2012) RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. BMC Genomics, 13, 3.
  • Schutz, K., Kammerer, D., Carle, R. and Schieber, A. (2004) Identification and quantification of caffeoylquinic acids and flavonolds from artichoke (Cynara scolymus L.) heads, juice, and pomace by HPLC-DAD-ESI/MSn. J. Agric. Food Chem. 52, 40904096.
  • Scott, L., LaFoe, D. and Weil, C. (1996) Adjacent sequences influence DNA repair accompanying transposon excision in maize. Genetics, 142(1), 237246.
  • Shimoda, H., Ninomiya, K., Nishida, N., Yoshino, T., Morikawa, T., Matsuda, H. and Yoshikawa, M. (2003) Anti-hyperlipidemic Sesquiterpenes and new sesquiterpene glycosides from the leaves of artichoke (Cynara scolymus L.): structure requirement and mode of action. Bioorg. Med. Chem. Lett. 13(2), 223228.
  • Sonnante, G., Gatto, A., Morgese, A., Montemurro, F., Sarli, G., Blanco, E. and Pignone, D. (2011) Genetic map of artichoke x wild cardoon: toward a consensus map for Cynara cardunculus. Theor. Appl. Genet. 123, 12151229.
  • Timme, R., Kuehl, J., Boore, J. and Jansen, R. (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, 302312.
  • Trick, M., Long, Y., Meng, J. and Bancroft, I. (2009) Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol. J. 7, 334346.
  • Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D., Cestaro, A., Pruss, D., Pindo, M., FitzGerald, L., Vezzulli, S., Reid, J., Malacarne, G., Iliev, D., Coppola, G., Wardell, B., Micheletti, D., Macalma, T., Facci, M., Mitchell, J., Perazzolli, M., Eldredge, G., Gatto, P., Oyzerski, R., Moretto, M., Gutin, N., Stefanini, M., Chen, Y., Segala, C., Davenport, C., Dematte, L., Mraz, A., Battilana, J., Stormo, K., Costa, F., Tao, Q., Si-Ammour, A., Harkins, T., Lackey, A., Perbost, C., Taillon, B., Stella, A., Solovyev, V., Fawcett, J., Sterck, L., Vandepoele, K., Grando, S., Toppo, S., Moser, C., Lanchbury, J., Bogden, R., Skolnick, M., Sgaramella, V., Bhatnagar, S., Fontana, P., Gutin, A., Van de Peer, Y., Salamini, F. and Viola, R. (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE, 12, e1326.
  • Wang, Y., Li, P., Cao, X., Wang, X., Zhang, A. and Li, X. (2009) Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules. Biochem. Biophys. Res. Commun. 378, 799803.
  • Wang, W., Barnaby, J., Tada, Y., Li, H., Tor, M., Caldelari, D., Lee, D., Fu, X. and Dong, X. (2011) Timing of plant immune responses by a central circadian regulator. Nature, 470, 110126.
  • Wasmuth, J.D. and Blaxter, M.L. (2004) Prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinformatics, 5, 187.
  • Wessler, S., Bureau, T. and White, S. (1995) LTR-retrotransposons and MITES - important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 81, 4821.