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Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene enrichment after methyl filtration

  • Jernej Jakše
  • Jenelle D. F. Meyer
  • Go Suzuki
  • John McCallum
  • Foo Cheung
  • Christopher D. Town
  • Michael J. HaveyEmail author
Original Paper

Abstract

Sequencing of the onion (Allium cepa) genome is challenging because it has one of the largest nuclear genomes among cultivated plants. We undertook pilot sequencing of onion genomic DNA to estimate gene densities and investigate the nature and distribution of repetitive DNAs. Complete sequences from two onion BACs were AT rich (64.8%) and revealed long tracts of degenerated retroviral elements and transposons, similar to other larger plant genomes. Random BACs were end sequenced and only 3 of 460 ends showed significant (e < −25) non-organellar hits to the protein databases. The BAC-end sequences were AT rich (63.4%), similar to the completely sequenced BACs. A total of 499,997 bp of onion genomic DNA yielded an estimated mean density of one gene per 168 kb, among the lowest reported to date. Methyl filtration was highly effective relative to random shotgun reads in reducing frequencies of anonymous sequences from 82 to 55% and increasing non-organellar protein hits from 4 to 42%. Our results revealed no evidence for gene-dense regions and indicated that sequencing of methyl-filtered genomic fragments should be an efficient approach to reveal genic sequences in the onion genome.

Keywords

Bacterial artificial chromosome Reduced representation Retrovirus Transposon 

Notes

Acknowledgments

This work was completed in compliance with the current laws governing genetic experimentation in Japan, New Zealand, and USA and was supported by the Initiative for Future Agriculture and Food Systems Grant no. 2001-52100-11344 from the USDA Cooperative State Research, Education, and Extension Service and a Fulbright-Hayes Post-doctoral Fellowship to JJ.

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Jernej Jakše
    • 1
    • 2
  • Jenelle D. F. Meyer
    • 1
  • Go Suzuki
    • 3
  • John McCallum
    • 4
  • Foo Cheung
    • 5
  • Christopher D. Town
    • 5
  • Michael J. Havey
    • 6
    Email author
  1. 1.Department of HorticultureUniversity of WisconsinMadisonUSA
  2. 2.Agronomy Department, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
  3. 3.Laboratory of Plant Molecular Genetics, Division of Natural ScienceOsaka Kyoiku UniversityKashiwaraJapan
  4. 4.Crop and Food ResearchChristchurchNew Zealand
  5. 5.The Institute for Genomic ResearchRockvilleUSA
  6. 6.Agricultural Research Service, USDA, Department of HorticultureUniversity of WisconsinMadisonUSA

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