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


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.


Bacterial artificial chromosome Reduced representation Retrovirus Transposon 



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.


  1. Adams SP, Hartman TPV, Lim YK, Chase MW, Leitch AR (2001) Loss and recovery of Arabidopsis-type telomere repeat sequences 5′-(TTTAGGG)n-3′ in the evolution of a major radiation of flowering plants. Proc R Soc Lond Ser B 268:1541–1546CrossRefGoogle Scholar
  2. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218CrossRefGoogle Scholar
  3. Bark OH, Havey MJ (1995) Similarities and relationships among open-pollinated populations of the bulb onion as estimated by nuclear RFLPs. Theor Appl Genet 90:607–614CrossRefGoogle Scholar
  4. Chou HH, Holmes MH (2001) DNA sequence quality trimming and vector removal. Bioinformatics 17:1093–104PubMedCrossRefGoogle Scholar
  5. Do S, Suzuki G, Mukai Y (2003) Genomic organization of a novel root alliinase gene, ALL1, in onion. Gene 325:17–24CrossRefGoogle Scholar
  6. Fajkus J, Sykorova E, Leitch AR (2005) Telomeres in evolution and evolution of telomeres. Chrom Res 13:469–479PubMedCrossRefGoogle Scholar
  7. Hanelt P (1990) Taxonomy, evolution, and history. In: Brewster J, Rabinowitch H (eds) Onions and allied crops, vol 1. CRC Press, Boca Raton, pp 1–26Google Scholar
  8. Havey M (1992) Restriction enzyme analysis of the chloroplast and nuclear 45s ribosomal DNA of Allium sections Cepa and Phyllodolon. Plant Syst Evol 183:17–31CrossRefGoogle Scholar
  9. Jiang N, Wessler SR (2001) Insertion preference of maize and rice miniature inverted repeat transposable elements as revealed by the analysis of nested elements. Plant Cell 13:2553–2564PubMedCrossRefGoogle Scholar
  10. Kirk JTO, Rees H, Evans G (1970) Base composition of nuclear DNA with the genus Allium. Heredity 25:507–512CrossRefGoogle Scholar
  11. Klaas M (1998) Applications and impact of molecular markers on evolutionary and diversity studies in the genus Allium. Plant Breed 117:297–308CrossRefGoogle Scholar
  12. Kuhl JC, Cheung F, Yuan Q, Martin W, Zewdie Y, McCallum J, Catanach A, Rutherford P, Sink KC, Jenderek M, Prince JP, Town CD, Havey MJ (2004) A unique set of 11,008 onion (Allium cepa) ESTs reveals expressed sequence and genomic differences between monocot orders Asparagales and Poales. Plant Cell 16:114–125PubMedCrossRefGoogle Scholar
  13. Marra MA, Kucaba TA, Dietrich NL, Green ED, Brownstein B, Wilson RK, McDonald KM, Hillier LW, McPherson JD, Waterston RH (1997) High throughput fingerprint analysis of large-insert clones. Genome Res 11:1072–1084Google Scholar
  14. McCallum JA, Pither-Joyce M, Shaw M (2002) Sulfur deprivation and genotype affect gene expression and metabolism of onion roots. J Am Soc Hort Sci 127:583–589Google Scholar
  15. McCullough AJ, Kangasjarvi J, Gengenbach BG, Jones RJ (1992) Plastid DNA in develoing maize endosperm: genome structure, methylation, and transcript accumulation patterns. Plant Physiol 100:958–964PubMedCrossRefGoogle Scholar
  16. Meyers BC, Tingey SV, Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 110:1660–1676CrossRefGoogle Scholar
  17. Palmer LE, Rabinowicz PD, O’Shaughnessy AL, Balija VS, Nascimento LU, Dike S, de la Bastide M, Martienssen RA, McCombie WR (2003) Maize genome sequencing by methylation filtration. Science 302:2115–2117PubMedCrossRefGoogle Scholar
  18. Pop M, Kosack D, Salzberg S (2004) Hierarchical scaffolding with Bambus. Genome Res 14:149–159PubMedCrossRefGoogle Scholar
  19. van Raamsdonk L, Wietsma W, de Vries J (1992) Crossing experiments in Allium L. section Cepa. Bot J Linn Soc 109:293–303CrossRefGoogle Scholar
  20. Rabinowicz P, Schutz K, Dedhia N, Yordan C, Parnell L, Stein L, McCombie W, Martienssen R (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nature Genet 23:305–308PubMedCrossRefGoogle Scholar
  21. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765–768PubMedCrossRefGoogle Scholar
  22. Schwartz S, Zhang Z, Frazer K, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W (2000) PipMakerA web server for aligning two genomic DNA sequences. Genome Res 10:577–586PubMedCrossRefGoogle Scholar
  23. Smit AFA, Hubley R, Green P (1996) RepeatMasker Open-3.0., verified February 2008
  24. Stack SM, Comings DE (1979) The chromosomes and DNA of Allium cepa. Chromosoma 70:161–181CrossRefGoogle Scholar
  25. Suzuki G, Do G, Mukai Y (2002) Efficient storage and screening system for onion BAC clones. Breed Sci (Japan) 52:157–159Google Scholar
  26. Suzuki G, Ura A, Saito N, Do G, So B, Yamamoto M, Mukai Y (2001) BAC FISH analysis in Allium cepa. Genes Genet Syst (Japan) 76:251–255CrossRefGoogle Scholar
  27. Vicient CM, Suoniemi A, Anamthawat-Jonsson K, Tanskanen J, Beharav A, Nevo E, Schulman AH (1999) Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11:1769–1784PubMedCrossRefGoogle Scholar
  28. Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL, SanMiguel P, Lakey N, Bedell J, Yuan Y, Budiman MA, Resnick A, Van Aken S, Utterback T, Riedmuller S, Williams M, Feldblyum T, Schubert K, Beachy R, Fraser CM, Quackenbush J (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302:2118–2120PubMedCrossRefGoogle Scholar

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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