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Volumn 20, Issue 1, 2013, Pages 93-108

De novo assembly and functional annotation of the olive (Olea europaea) transcriptome

(18)  Muñoz Mérida, Antonio a   González Plaza, Juan José b   Cañada, Andrés c   Blanco, Ana María d   Del Carmen García López, Maria e   Rodríguez, José Manuel c   Pedrola, Laia f   Sicardo, M Dolores g   Hernández, M Luisa g   De La Rosa, Raúl h   Belaj, Angjelina h   Gil Borja, Mayte d   Luque, Francisco e   Martínez Rivas, José Manuel g   Pisano, David G c   Trelles, Oswaldo a   Valpuesta, Victoriano b   Beuzón, Carmen R b  


Author keywords

454 pyrosequencing; genomics; Olea europaea; Sanger sequencing; transcriptome

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTOME;

EID: 84874483118     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dss036     Document Type: Article
Times cited : (75)

References (48)
  • 1
    • 4344582315 scopus 로고    scopus 로고
    • Olive groves: 'The life and identity of the Mediterranean'
    • Loumou, A. and Giourga, C. 2003, Olive groves: 'The life and identity of the Mediterranean', Agric. Hum. Values, 20, 87-95.
    • (2003) Agric. Hum. Values , vol.20 , pp. 87-95
    • Loumou, A.1    Giourga, C.2
  • 2
    • 84874498081 scopus 로고    scopus 로고
    • FAOSTAT home page Columbia URL
    • FAOSTAT home page Columbia URL: http://www.columbia.edu/cgi-bin/cul/ resolve?ASL9609, 2008.
    • (2008)
  • 3
    • 77956555618 scopus 로고    scopus 로고
    • A consensus list of microsatellite markers for olive genotyp-ing
    • Baldoni, L., Cultrera, N., Mariotti, R., et al. 2009, A consensus list of microsatellite markers for olive genotyp-ing, Mol. Breed., 24, 213-31.
    • (2009) Mol. Breed. , vol.24 , pp. 213-231
    • Baldoni, L.1    Cultrera, N.2    Mariotti, R.3
  • 4
    • 49749112354 scopus 로고    scopus 로고
    • Physiological, biochemical and molecular changes occurring during olive development and ripening
    • Conde, C., Delrot, S. and Geros, H. 2008, Physiological, biochemical and molecular changes occurring during olive development and ripening, J. Plant Physiol., 165, 1545-62.
    • (2008) J. Plant Physiol. , vol.165 , pp. 1545-1562
    • Conde, C.1    Delrot, S.2    Geros, H.3
  • 5
    • 0030451625 scopus 로고    scopus 로고
    • Isolation of triploid and tetraploid olive (Olea europaea L.) plants from mixoploid cv. 'Frantoio' and 'Leccino' mutants by in vivo and in vitro selection
    • Rugini, E., Pannelli, G., Ceccarelli, M. and Muganu, M. 1996, Isolation of triploid and tetraploid olive (Olea europaea L.) plants from mixoploid cv. 'Frantoio' and 'Leccino' mutants by in vivo and in vitro selection, Plant Breed., 115, 23-7.
    • (1996) Plant Breed. , vol.115 , pp. 23-27
    • Rugini, E.1    Pannelli, G.2    Ceccarelli, M.3    Muganu, M.4
  • 6
    • 0037777875 scopus 로고    scopus 로고
    • A first linkage map of olive (Olea europaea L.) cultivars using RAPD, AFLP, RFLP and SSR markers
    • De la Rosa, R., Angiolillo, A., Guerrero, C., et al. 2003, A first linkage map of olive (Olea europaea L.) cultivars using RAPD, AFLP, RFLP and SSR markers, Theor. Appl. Genet., 106, 1273-82.
    • (2003) Theor. Appl. Genet. , vol.106 , pp. 1273-1282
    • De La Rosa, R.1    Angiolillo, A.2    Guerrero, C.3
  • 8
    • 0000981673 scopus 로고    scopus 로고
    • Salinity Tolerance in Olive
    • Janick, J., (ed.), John Wiley & Sons, Inc.: Oxford, UK
    • Gucci, R. and Tattini, M. 2010, Salinity Tolerance in Olive, in Horticultural Reviews, Janick, J., (ed.), John Wiley & Sons, Inc.: Oxford, UK, 21, 177-214.
    • (2010) Horticultural Reviews , vol.21 , pp. 177-214
    • Gucci, R.1    Tattini, M.2
  • 9
    • 0141442239 scopus 로고
    • Genetic variability and heritability of some characters in cross-bred olive seedlings
    • Bellini, E. 1993, Genetic variability and heritability of some characters in cross-bred olive seedlings, Olivae, 49, 21-34.
    • (1993) Olivae , vol.49 , pp. 21-34
    • Bellini, E.1
  • 10
    • 77952020969 scopus 로고    scopus 로고
    • Optimizing early flowering and pre-selection for short juvenile period in olive seedlings
    • Moreno-Alias, I., Rapoport, H.F., Lopez, R., Leon, L. and De la Rosa, R. 2010, Optimizing early flowering and pre-selection for short juvenile period in olive seedlings, HortScience, 45, 519-22.
    • (2010) HortScience , vol.45 , pp. 519-522
    • Moreno-Alias, I.1    Rapoport, H.F.2    Lopez, R.3    Leon, L.4    De La Rosa, R.5
  • 12
    • 49649093546 scopus 로고    scopus 로고
    • Fatty acid composition of advanced olive selections obtained by crossbreeding
    • León, L., De la Rosa, R., Gracia, A., Barranco, D. and Rallo, L. 2008, Fatty acid composition of advanced olive selections obtained by crossbreeding, J. Sci. Food Agric., 88, 1921-6.
    • (2008) J. Sci. Food Agric. , vol.88 , pp. 1921-1926
    • León, L.1    De La Rosa, R.2    Gracia, A.3    Barranco, D.4    Rallo, L.5
  • 13
    • 70349662156 scopus 로고    scopus 로고
    • Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development
    • Alagna, F., D'Agostino, N., Torchia, L., et al. 2009, Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development, BMC Genomics, 10, 399.
    • (2009) BMC Genomics , vol.10 , pp. 399
    • Alagna, F.1    D'Agostino, N.2    Torchia, L.3
  • 14
    • 72449160784 scopus 로고    scopus 로고
    • Computational annotation of genes differentially expressed along olive fruit development
    • Galla, G., Barcaccia, G., Ramina, A., et al. 2009, Computational annotation of genes differentially expressed along olive fruit development, BMC Plant Biol., 9, 128.
    • (2009) BMC Plant Biol. , vol.9 , pp. 128
    • Galla, G.1    Barcaccia, G.2    Ramina, A.3
  • 15
    • 79251537445 scopus 로고    scopus 로고
    • Generation and analysis of expressed sequence tags from Olea europaea L. Comp
    • Ozgenturk, N.O., Oruc, F., Sezerman, U., et al. 2010, Generation and analysis of expressed sequence tags from Olea europaea L. Comp, Funct. Genomics, 2010, 757512.
    • (2010) Funct. Genomics , vol.2010 , pp. 757512
    • Ozgenturk, N.O.1    Oruc, F.2    Sezerman, U.3
  • 16
    • 82155164153 scopus 로고    scopus 로고
    • High-throughput sequencing of RNA silencing-asso-ciated small RNAs in olive (Olea europaea L.)
    • Donaire, L., Pedrola, L., De la Rosa, R. and Llave, C. 2011, High-throughput sequencing of RNA silencing-asso-ciated small RNAs in olive (Olea europaea L.), PLoS ONE, 6, e27916.
    • (2011) PLoS ONE , vol.6
    • Donaire, L.1    Pedrola, L.2    De La Rosa, R.3    Llave, C.4
  • 17
    • 41249098849 scopus 로고    scopus 로고
    • A high quality draft consensus sequence of the genome of a heterozygous grapevine variety
    • Velasco, R., Zharkikh, A., Troggio, M., et al. 2007, A high quality draft consensus sequence of the genome of a heterozygous grapevine variety, PLoS ONE, 2, e1326.
    • (2007) PLoS ONE , vol.2
    • Velasco, R.1    Zharkikh, A.2    Troggio, M.3
  • 18
    • 34848886909 scopus 로고    scopus 로고
    • The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    • Jaillon, O., Aury, J.M., Noel, B., et al. 2007, The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla, Nature, 449, 463-7.
    • (2007) Nature , vol.449 , pp. 463-467
    • Jaillon, O.1    Aury, J.M.2    Noel, B.3
  • 19
    • 33748760611 scopus 로고    scopus 로고
    • The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    • Tuskan, G.A., DiFazio, S., Jansson, S., et al. 2006, The genome of black cottonwood, Populus trichocarpa (Torr. & Gray), Science, 313, 1596-604.
    • (2006) Science , vol.313 , pp. 1596-1604
    • Tuskan, G.A.1    Difazio, S.2    Jansson, S.3
  • 20
    • 79952708903 scopus 로고    scopus 로고
    • Molecular studies in olive (Olea europaea L.): Overview on DNA markers applications and recent advances in genome analysis
    • Bracci, T., Busconi, M., Fogher, C. and Sebastiani, L. 2011, Molecular studies in olive (Olea europaea L.): overview on DNA markers applications and recent advances in genome analysis, Plant Cell Rep., 30, 449-62.
    • (2011) Plant Cell Rep. , vol.30 , pp. 449-462
    • Bracci, T.1    Busconi, M.2    Fogher, C.3    Sebastiani, L.4
  • 21
    • 1942510634 scopus 로고    scopus 로고
    • Pectin esterase gene family in strawberry fruit: Study of FaPE1, a ripening-specific isoform
    • Castillejo, C., De La Fuente, J.I., Iannetta, P., Botella, M.A. and Valpuesta, V. 2004, Pectin esterase gene family in strawberry fruit: study of FaPE1, a ripening-specific isoform, J. Exp. Bot., 55, 909.
    • (2004) J. Exp. Bot. , vol.55 , pp. 909
    • Castillejo, C.1    De La Fuente, J.I.2    Iannetta, P.3    Botella, M.A.4    Valpuesta, V.5
  • 22
    • 20444369212 scopus 로고    scopus 로고
    • Molecular cloning and characterization of genes encoding two microsomal oleate desaturases (FAD2) from olive
    • Hernández, M.L., Mancha, M. and Mart́inez-Rivas, J.M. 2005, Molecular cloning and characterization of genes encoding two microsomal oleate desaturases (FAD2) from olive, Phytochemistry, 66, 1417-26.
    • (2005) Phytochemistry , vol.66 , pp. 1417-1426
    • Hernández, M.L.1    Mancha, M.2    Mart́inez-Rivas, J.M.3
  • 23
    • 0002535878 scopus 로고
    • TRIzol: A new reagent for optimal single-step isolation of RNA
    • Simms, D., Cizdziel, P.E. and Chomczynski, P. 1993, TRIzol: A new reagent for optimal single-step isolation of RNA, Focus, 15, 99-102.
    • (1993) Focus , vol.15 , pp. 99-102
    • Simms, D.1    Cizdziel, P.E.2    Chomczynski, P.3
  • 25
    • 0035046755 scopus 로고    scopus 로고
    • Reverse transcriptase template switching: A SMART approach for full-length cDNA library construction
    • Zhu, Y.Y., Machleder, E.M., Chenchik, A., Li, R. and Siebert, P.D. 2001, Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction, Biotechniques, 30, 892-7.
    • (2001) Biotechniques , vol.30 , pp. 892-897
    • Zhu, Y.Y.1    MacHleder, E.M.2    Chenchik, A.3    Li, R.4    Siebert, P.D.5
  • 26
    • 2342483696 scopus 로고    scopus 로고
    • Simple cDNA normalization using kamchatka crab duplex specific nuclease
    • Zhulidov, P.A., Bogdanova, E.A., Shcheglov, A.S., et al. 2004, Simple cDNA normalization using kamchatka crab duplex specific nuclease, Nucleic Acids Res., 32, e37.
    • (2004) Nucleic Acids Res. , vol.32
    • Zhulidov, P.A.1    Bogdanova, E.A.2    Shcheglov, A.S.3
  • 27
    • 0036912415 scopus 로고    scopus 로고
    • A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas
    • Shagin, D.A., Rebrikov, D.V., Kozhemyako, V.B., et al. 2002, A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas, Genome Res., 12, 1935-42.
    • (2002) Genome Res. , vol.12 , pp. 1935-1942
    • Shagin, D.A.1    Rebrikov, D.V.2    Kozhemyako, V.B.3
  • 28
    • 35648998424 scopus 로고    scopus 로고
    • Construction of cDNA library of cotton mutant (Xiangmian-18) library during gland forming stage
    • Xie, Y.F., Wang, B.C., Li, B., et al. 2007, Construction of cDNA library of cotton mutant (Xiangmian-18) library during gland forming stage, Colloids Surf. B Biointerfaces, 60, 258-63.
    • (2007) Colloids Surf. B Biointerfaces , vol.60 , pp. 258-263
    • Xie, Y.F.1    Wang, B.C.2    Li, B.3
  • 29
    • 60549093037 scopus 로고    scopus 로고
    • Ice-binding proteins from enoki and shiitake mushrooms
    • Raymond, J.A. and Janech, M.G. 2009, Ice-binding proteins from enoki and shiitake mushrooms, Cryobiology, 58, 151-6.
    • (2009) Cryobiology , vol.58 , pp. 151-156
    • Raymond, J.A.1    Janech, M.G.2
  • 30
    • 41149167170 scopus 로고    scopus 로고
    • Rapid tran-scriptome characterization for a nonmodel organism using 454 pyrosequencing
    • Vera, J., Wheat, C., Fescemyer, H., et al. 2008, Rapid tran-scriptome characterization for a nonmodel organism using 454 pyrosequencing, Mol. Ecol., 17, 1636-47.
    • (2008) Mol. Ecol. , vol.17 , pp. 1636-1647
    • Vera, J.1    Wheat, C.2    Fescemyer, H.3
  • 31
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies, M., Egholm, M., Altman, W.E., et al. 2005, Genome sequencing in microfabricated high-density picolitre reactors, Nature, 437, 376-80.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3
  • 32
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang, X. and Madan, A. 1999, CAP3: a DNA sequence assembly program, Genome Res., 9, 868-77.
    • (1999) Genome Res. , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 34
    • 79955769112 scopus 로고    scopus 로고
    • Comprehensive transcrip-tome analysis of the highly complex Pisum sativum genome using next generation sequencing
    • Franssen, S., Shrestha, R., Brautigam, A., Bornberg-Bauer, E. and Weber, A. 2011, Comprehensive transcrip-tome analysis of the highly complex Pisum sativum genome using next generation sequencing, BMC Genomics, 12, 227.
    • (2011) BMC Genomics , vol.12 , pp. 227
    • Franssen, S.1    Shrestha, R.2    Brautigam, A.3    Bornberg-Bauer, E.4    Weber, A.5
  • 36
    • 0026030641 scopus 로고
    • Database of hom-ology-derived protein structures and the structural meaning of sequence alignment
    • Sander, C. and Schneider, R. 1991, Database of hom-ology-derived protein structures and the structural meaning of sequence alignment, Proteins, 9, 56-68.
    • (1991) Proteins , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 37
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost, B. 1999, Twilight zone of protein sequence alignments, Protein Eng., 12, 85-94.
    • (1999) Protein Eng. , vol.12 , pp. 85-94
    • Rost, B.1
  • 38
    • 24644503098 scopus 로고    scopus 로고
    • Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
    • Conesa, A., Gotz, S., Garcia-Gomez, J.M., Terol, J., Talon, M. and Robles, M. 2005, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 21, 3674-6.
    • (2005) Bioinformatics , vol.21 , pp. 3674-3676
    • Conesa, A.1    Gotz, S.2    Garcia-Gomez, J.M.3    Terol, J.4    Talon, M.5    Robles, M.6
  • 40
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. Roy. Stat. Soc. B Met., 57, 289-300.
    • (1995) J. Roy. Stat. Soc. B Met. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 41
    • 84874467945 scopus 로고    scopus 로고
    • Libro II. Variabilidad y Selección
    • Rallo, L., Barranco, D., Caballero, J.M., et al. (eds.) MAPA y Ediciones Mundi-Prensa: Madrid
    • Tous, J., Del Ŕio, C., Caballero, J.M. and Rallo, L. 2005, Libro II. Variabilidad y Selección. In: Rallo, L., Barranco, D., Caballero, J.M., et al. (eds.), Variedades de olivo en España, Junta de Andalućia. MAPA y Ediciones Mundi-Prensa: Madrid.
    • (2005) Variedades de Olivo en España, Junta de Andalućia
    • Tous, J.1    Del Ŕio, C.2    Caballero, J.M.3    Rallo, L.4
  • 42
    • 0001987589 scopus 로고
    • Juvenility and maturity of plants as influenced by their ontogenetical and physiological ageing
    • Fortanier, E.J. and Jonkers, H. 1976, Juvenility and maturity of plants as influenced by their ontogenetical and physiological ageing, Acta Hort. (ISHS), 56, 37-44.
    • (1976) Acta Hort. (ISHS) , vol.56 , pp. 37-44
    • Fortanier, E.J.1    Jonkers, H.2
  • 43
    • 0000111557 scopus 로고
    • Juvenility and maturation in conifers: Current concepts
    • Greenwood, M.S. 1995, Juvenility and maturation in conifers: current concepts, Tree Physiol., 15, 433-8.
    • (1995) Tree Physiol. , vol.15 , pp. 433-438
    • Greenwood, M.S.1
  • 44
    • 0025602622 scopus 로고
    • Phase change and the regulation of shoot morphogenesis in plants
    • Poethig, R. 1990, Phase change and the regulation of shoot morphogenesis in plants, Science, 250, 923-30.
    • (1990) Science , vol.250 , pp. 923-930
    • Poethig, R.1
  • 45
    • 0035984046 scopus 로고    scopus 로고
    • Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing
    • Van der Hoeven, R., Ronning, C., Giovannoni, J., Martin, G. and Tanksley, S. 2002, Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing, Plant Cell, 14, 1441-56.
    • (2002) Plant Cell , vol.14 , pp. 1441-1456
    • Van Der Hoeven, R.1    Ronning, C.2    Giovannoni, J.3    Martin, G.4    Tanksley, S.5
  • 46
    • 84874457604 scopus 로고    scopus 로고
    • in The Tree of Life Web Project, http://tolweb.org/
    • McCourt, R.M., Chapman, R.L., Buchheim, M. and Mishler, B.D. 1996, Green plants. http://tolweb.org/Green-plants/2382/1996.01.01 in The Tree of Life Web Project, http://tolweb.org/.
    • (1996) Green Plants
    • McCourt, R.M.1    Chapman, R.L.2    Buchheim, M.3    Mishler, B.D.4
  • 47
    • 84874476347 scopus 로고    scopus 로고
    • Uniprot taxonomy
    • Uniprot taxonomy. http://www.uniprot.org/taxonomy/.
  • 48
    • 84858591092 scopus 로고    scopus 로고
    • Developing a core collection of olive (Olea europaea L.) based on molecular markers (DArTs, SSRs, SNPs) and agronomic traits
    • Belaj, A., Dominguez-Garćia, M., Atienza, S., et al. 2012, Developing a core collection of olive (Olea europaea L.) based on molecular markers (DArTs, SSRs, SNPs) and agronomic traits, Tree Genet. Genomes, 8, 365-78.
    • (2012) Tree Genet. Genomes , vol.8 , pp. 365-378
    • Belaj, A.1    Dominguez-Garćia, M.2    Atienza, S.3


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