ARS | Publication request: Pilot Sequencing of Onion Genomic DNA Reveals Fragments of Transposable Elements, Low Gene Densities, and Significant Gene Enrichment After Methyl Filtration

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 22, 2008
Publication Date: July 10, 2008
Citation: Jakse, J., Meyer, J., Suzuki, G., Mccallum, J., Cheung, F., Town, C.D., Havey, M.J. 2008. Pilot Sequencing of Onion Genomic DNA Reveals Fragments of Transposable Elements, Low Gene Densities, and Significant Gene Enrichment After Methyl Filtration. Molecular Genetics and Genomics. 280(4):287-292.

Interpretive Summary: Onion is one of the most economically important vegetables. Genetic analysis of onion is hindered by its extremely large amount of DNA, over 6 and 16 times that of maize and rice, respectively. In this study, we sequenced onion large regions of the onion DNA to estimate gene densities and investigate the nature and distribution of repetitive DNAs. Complete sequences from two large onion regions were AT rich (64.8%) and had long tracts of degenerated retroviral elements and transposons, similar to other larger plant genomes. Random DNA clones from onion were end sequenced and only two of 486 ends showed significant (e<-25) non-organellar hits to the protein databases. These end sequences were AT rich (63.4%), similar to the other sequenced regions. A total of 499,997 bp of onion DNA yielded an estimated mean density of one gene per 168 kb, among the lowest reported to date. Methyl filtration is a technique to reduce the frequencies of repetitive DNAs before sequencing and was highly effective relative to random sequencing 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 DNAs should be an efficient approach to reveal genic sequences in onion. These results are important for geneticists and breeders as an aid in the cloning of genes from onion.

Technical Abstract: Onion (Allium cepa) is a diploid (2n=2x=16) monocot with one of the largest nuclear genomes among cultivated plants, over 6 and 16 times that of maize and rice, respectively. In this study, we sequenced onion BACs 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 two of 486 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.