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Construction of a fosmid library of cucumber (Cucumis sativus) and comparative analyses of the eIF4E and eIF(iso)4E regions from cucumber and melon (Cucumis melo)

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Abstract

A fosmid library of cucumber was synthesized as an unrestricted resource for researchers and used for comparative sequence analyses to assess synteny between the cucumber and melon genomes, both members of the genus Cucumis and the two most economically important plants in the family Cucurbitaceae. End sequencing of random fosmids produced over 680 kilobases of cucumber genomic sequence, of which 25% was similar to ribosomal DNAs, 25% to satellite sequences, 20% to coding regions in other plants, 4% to transposable elements, 13% to mitochondrial and chloroplast sequences, and 13% showed no hits to the databases. The relatively high frequencies of ribosomal and satellite DNAs are consistent with previous analyses of cucumber DNA. Cucumber fosmids were selected and sequenced that carried eukaryotic initiation factors (eIF) 4E and iso(4E), genes associated with recessively inherited resistances to potyviruses in a number of plants. Indels near eIF4E and eIF(iso)4E mapped independently of the zym, a recessive locus conditioning resistance to Zucchini yellow mosaic virus, establishing that these candidate genes are not zym. Cucumber sequences were compared with melon BACs carrying eIF4E and eIF(iso)4E and revealed extensive sequence conservation and synteny between cucumber and melon across these two independent genomic regions. This high degree of microsynteny will aid in the cloning of orthologous genes from both species, as well as allow for genomic resources developed for one Cucumis species to be used for analyses in other species.

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Acknowledgments

We gratefully acknowledge the support of USDA-CSREES-NRI grant 2003-35300-13204 and technical assistance of Emily Haack, John Piekarski, and Amy Stein.

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Authors and Affiliations

  1. Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA

    J. D. F. Meyer

  2. Vegetable Crops Unit, Agricultural Research Service, US Department of Agriculture, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA

    M. J. Havey

  3. IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348, Cabrils (Barcelona), Spain

    W. Deleu & J. Garcia-Mas

Authors
  1. J. D. F. Meyer
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  2. W. Deleu
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  3. J. Garcia-Mas
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  4. M. J. Havey
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Correspondence to M. J. Havey.

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Communicated by Y. Van den Peer.

Names are necessary to report factually on available data; however, the US Department of Agriculture (USDA) neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable.

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Meyer, J.D.F., Deleu, W., Garcia-Mas, J. et al. Construction of a fosmid library of cucumber (Cucumis sativus) and comparative analyses of the eIF4E and eIF(iso)4E regions from cucumber and melon (Cucumis melo). Mol Genet Genomics 279, 473–480 (2008). https://doi.org/10.1007/s00438-008-0326-5

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  • DOI: https://doi.org/10.1007/s00438-008-0326-5

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