title: Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene enrichment after methyl filtration.
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.
authors.affiliation: Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA.
authors.forename: Jernej
authors.initials: J
authors.lastname: Jakse
authors.forename: Jenelle D F
authors.initials: JD
authors.lastname: Meyer
authors.forename: Go
authors.initials: G
authors.lastname: Suzuki
authors.forename: John
authors.initials: J
authors.lastname: McCallum
authors.forename: Foo
authors.initials: F
authors.lastname: Cheung
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Town
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Havey
mesh_terms: D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D008969:Molecular Sequence Data; D019697:Onions / Q000235:genetics*; D018626:Retroelements / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D018626:Retroelements