SEARCH

SEARCH BY CITATION

References

  • Abrouk, M., Murat, F., Pont, C. et al. (2010) Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends Plant Sci., 15, 479487.
  • Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403410.
  • Bhaduri, P.N. and Bose, P.C. (1947) Cytogenetical investigations in some common cucurbits, with special reference to fragmentation of chromosomes as physical basis of speciation. J. Genet. 48, 237256.
  • Cavagnaro, P.F., Senalik, D.A., Yang, L., Simon, P.W., Harkins, T.T., Kodira, C.D., Huang, S. and Weng, Y. (2010) Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics, 11, 569.
  • Chen, J.F., Staub, J.E., Tashiro, Y., Isshiki, S. and Miyazaki, S. (1997) Successful interspecific hybridization between Cucumis sativus L. and C. hystrix Chakr. Euphytica, 96, 413419.
  • Cheng, Z.K., Presting, G.G., Buell, C.R., Wing, R.A. and Jiang, J.M. (2001) High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics, 157, 17491757.
  • Cheng, F., Mandakova, T., Wu, J., Xie, Q., Lysak, M.A. and Wang, X. (2013) Deciphering the diploid ancestral genome of the mesohexaploid Brassica rapa. Plant Cell, 25, 15411554.
  • Danin-Poleg, Y., Reis, N., Baudracco-Arnas, S., Pitrat, M., Staub, J.E., Oliver, M., Arus, P., deVicente, C.M. and Katzir, N. (2000) Simple sequence repeats in Cucumis mapping and map merging. Genome, 43, 963974.
  • Darling, A.E., Mau, B., Blattner, F.R. and Perna, N.T. (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 13941403.
  • Darling, A.E., Mau, B. and Perna, N.T. (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE, 5, e11147.
  • Diaz, A., Fergany, M., Formisano, G. et al. (2011) A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.). BMC Plant Biol. 11, 111.
  • Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 17921797.
  • Foissac, S., Gouzy, J., Rombauts, S., Mathe, C., Amselem, J., Sterck, L., van de Peer, Y., Rouze, P. and Schiex, T. (2008) Genome annotation in plants and fungi, EuGene as a model platform. Curr. Bioinform. 3, 8797.
  • Garcia-Mas, J., Benjak, A., Sanseverino, W. et al. (2012) The genome of melon (Cucumis melo L.). Proc. Natl Acad. Sci. USA, 109, 1187211877.
  • Ghebretinsae, A.G., Thulin, M. and Barber, J.C. (2007) Relationships of cucumbers and melons unraveled: molecular phylogenetics of Cucumis and related genera (Benincaseae, Cucurbitaceae). Am. J. Bot. 94, 12561266.
  • Gonzalez, V.M., Benjak, A., Henaff, E.M., Mir, G., Casacuberta, J.M., Garcia-Mas, J. and Puigdomenech, P. (2010) Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy. BMC Plant Biol. 10, 246.
  • Guo, S., Zhang, J., Sun, H. et al. (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat. Genet. 45, 5158.
  • Han, Y.J. and Wessler, S.R. (2010) MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res. 38, e199.
  • Han, Y., Zhang, Z., Liu, C., Liu, J., Huang, S.W., Jiang, J. and Jin, W.W. (2009) Centromere repositioning in cucurbit species: implication of the genomic impact from centromere activation and inactivation. Proc. Natl Acad. Sci. USA, 106, 1493714941.
  • Hoffmann, A.A. and Rieseberg, L.H. (2008) Revisiting the impact of inversions in evolution: from population genetic markers to drivers of adaptive shifts and speciation? Annu. Rev. Ecol. Evol. Syst. 39, 2142.
  • Huang, S., Li, R., Zhang, Z. et al. (2009) The genome of the cucumber, Cucumis sativus L. Nat. Genet. 41, 12751281.
  • Illa, E., Sargent, D.J., Girona, E.L. et al. (2011) Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family. BMC Evol. Biol. 11, 9.
  • Jung, S., Cestaro, A., Troggio, M. et al. (2012) Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. BMC Genomics, 13, 129.
  • Karpen, G.H. and Allshire, R.C. (1997) The case for epigenetic effects on centromere identity and function. Trends Genet. 13, 489496.
  • Katzir, N., Danin-Poleg, Y., Tzori, G., Karchi, Z., Lavi, U. and Cregan, P.B. (1996) Length polymorphism and homologies of microsatellites in several Cucurbitaceae species. Theor. Appl. Genet. 93, 12821290.
  • Kirkbride, J.H. (1993) Biosystematic Monograph of the Genus Cucumis (Cucurbitaceae): Botanical Identification of Cucumbers and Melons. Boone, NC: Parkway Publishers.
  • Kirkpatrick, M. (2010) How and why chromosome inversions evolve. PLoS Biol. 8, e1000501.
  • Koch, M.A. and Kiefer, M. (2005) Genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species – Capsella rubella, Arabidopsis lyrata subsp petraea, and A. thaliana. Am. J. Bot. 92, 761767.
  • Koo, D.-H., Nam, Y.-W., Choi, D., Bang, J.-W., de Jong, H. and Hur, Y. (2010) Molecular cytogenetic mapping of Cucumis sativus and C. melo using highly repetitive DNA sequences. Chromosome Res. 18, 325336.
  • Kosambi, D.D. (1944) The estimation of map distance from recombination values. Ann. Eugen. 12, 172175.
  • Kozhukhow, S.A. (1930) Karyological investigations of the genus Cucumis. Bull. Appl. Bot. Plant Breed. 23, 357366.
  • Krzywinski, M., Schein, J., Birol, İ., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J. and Marra, M.A. (2009) Circos: an information aesthetic for comparative genomics. Genome Res. 19, 16391645.
  • Lagercrantz, U. (1998) Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics, 150, 12171228.
  • Li, D., Cuevas, H.E., Yang, L. et al. (2011a) Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping. BMC Genomics, 12, 396.
  • Li, Z., Zhang, Z.H., Yan, P.C., Huang, S.W., Fei, Z.J. and Lin, K. (2011b) RNASeq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics, 12, 540.
  • Livingstone, K.D., Lackney, V.K., Blauth, J.R., van Wijk, R. and Jahn, M.K. (1999) Genome mapping in Capsicum and the evolution of genome structure in the Solanaceae. Genetics, 152, 11831202.
  • Lowry, D.B. and Willis, J.H. (2010) A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation. PLoS Biol. 8, e1000500.
  • Luo, M.C., Deal, K.R., Akhunov, E.D. et al. (2009) Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proc. Natl Acad. Sci. USA, 106, 1578015785.
  • Lysak, M.A., Berr, A., Pecinka, A., Schmidt, R., McBreen, K. and Schubert, I. (2006) Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc. Natl Acad. Sci. USA, 103, 52245229.
  • Mandakova, T. and Lysak, M.A. (2008) Chromosomal phylogeny and karyotype evolution in = 7 crucifer species (Brassicaceae). Plant Cell, 20, 25592570.
  • Margulies, M., Egholm, M., Altman, W.E. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376380.
  • Murat, F., Xu, J.H., Tannier, E., Abrouk, M., Guilhot, N., Pont, C., Messing, J. and Salse, J. (2010) Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res. 20, 15451557.
  • Murray, M.G. and Thompson, W.F. (1980) Rapid isolation of high molecular weight DNA. Nucleic Acids Res. 8, 43214325.
  • Neuhausen, S.L. (1992) Evaluation of restriction fragment length polymorphism in Cucumis melo. Theor. Appl. Genet. 83, 379384.
  • van Ooijen, J.W. and Voorrips, R.E. (2001) JoinMap Version 3.0 Software for the calculation of genetic linkage maps. Plant Research International, Wageningen.
  • Park, Y., Katzir, N., Brotman, Y., King, J., Bertrand, F. and Havey, M. (2004) Comparative mapping of ZYMV resistances in cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). Theor. Appl. Genet. 109, 707712.
  • Renner, S.S., Schaefer, H. and Kocyan, A. (2007) Phylogenetics of Cucumis (Cucurbitaceae): cucumber (C. sativus) belongs in an Asian/Australian clade far from melon (C. melo). BMC Evol. Biol. 7, 58.
  • Rocchi, M., Archidiacono, N. and Stanyon, R. (2006) Ancestral genomes reconstruction: an integrated, multi-disciplinary approach is needed. Genome Res. 16, 14411444.
  • Ruiz-Herrera, A., Farre, M. and Robinson, T.J. (2012) Molecular cytogenetic and genomic insights into chromosomal evolution. Heredity, 108, 2836.
  • Salse, J. (2012) In silico archeogenomics unveils modern plant genome organisation, regulation and evolution. Curr. Opin. Plant Biol. 15, 122130.
  • Schaefer, H. (2007) Cucumis (Cucurbitaceae) must include Cucumella, Dicoelospernium, Mukia, Myrmecosicyos, and Oreosyce: a recircumscription based on nuclear and plastid DNA data. BLUMEA, 52, 165177.
  • Schubert, I. and Lysak, M.A. (2011) Interpretation of karyotype evolution should consider chromosome structural constraints. Trends Genet. 27, 207216.
  • Sebastian, P., Schaefer, H., Telford, I.R.H. and Renner, S.S. (2010) Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia. Proc. Natl Acad. Sci. USA, 107, 1426914273.
  • Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J.M. and Birol, İ. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 11171123.
  • Soderlund, C., Bomhoff, M. and Nelson, W.M. (2011) SyMAP v3.4: a turnkey synteny system with application to plant genomes. Nucleic Acids Res. 39, e68.
  • Thiel, T., Michalek, W., Varshney, R.K. and Graner, A. (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106, 411422.
  • Trivedi, R.N. and Roy, R.P. (1970) Cytological studies in Cucumis and Citrullus. Cytologia, 35, 561671.
  • Vilanova, S., Sargent, D.J., Arus, P. and Monfort, A. (2008) Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria (the strawberry). BMC Plant Biol. 8, 67.
  • Whitaker, T.W. (1933) Cytological and phylogenetic studies in the Cucurbitaceae. Bot. Gaz. 94, 780790.
  • Wu, F.N. and Tanksley, S.D. (2010) Chromosomal evolution in the plant family Solanaceae. BMC Genomics, 11, 182.
  • Xu, Z. and Wang, H. (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265W268.
  • Yang, L., Koo, D.-H., Li, Y., Zhang, X., Luan, F., Havey, M.J., Jiang, J. and Weng, Y. (2012) Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly. Plant J. 71, 895906.
  • Yogeeswaran, K., Frary, A., York, T.L., Amenta, A., Lesser, A.H., Nasrallah, J.B., Tanksley, S.D. and Nasrallah, M.E. (2005) Comparative genome analyses of Arabidopsis spp.: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. Genome Res. 15, 505515.