Comparative Sequencing of Two Species in Allium

Plant genomics and proteomics, our field of interest, has been rapidly developing part of fundamental research with a clearly stated goals in applied science like breeding of economically important crops and identifying beneficial introducible genes in wildlife species (genes of plant virus and fungi resistance and genes of  medical and agricultural important traits). To make our knowledge more useful and safe we have to know broader context of mechanisms in plant genome organization and evolution. These basic principles discovered in plants use to be very often valid in eukaryotes generally. It is obvious that secrets of plant genomes were kept by their enormous size and dynamics in the pre-NGS era. Next generation sequencing is the first straightforward method which can cost-effectively characterize plant genome in few steps and start so let us slowly understand it. Despite of this opportunity genus Allium with many ornamental and food important species stands aside interest of genome sequencing projects. We actually know hardly a few percents of onion or garlic genome, with partial knowledge of genome characteristics (gene density, GC content etc.),(Jakse et al., 2008). Apparently, whole genome sequence assembly of Allium is really challenging and in  relatively big genome (A. cepa 1C=16,5pg) almost impossible from average NGS run, on the other hand repetitive DNA swelling plant genomes make such genome actually well available to be characterized even by just one proper NGS run and the vast majority of repetitive elements can be identified and assembled (Macas et al., 2011). We performed comparative sequencing of two species in Allium and characterized majority of their repetitive elements. Transcriptomic data together with our results the slowly unscramble puzzle of the Allium genome.

Jakse, J., Meyer, J.D., Suzuki, G., McCallum, J., Cheung, F., Town, C.D. and 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. Mol Genet Genomics, 280, 287-292.

Macas, J., Kejnovsky, E., Neumann, P., Novak, P., Koblizkova, A. and Vyskot, B. (2011) Next generation sequencing-based analysis of repetitive DNA in the model dioecious [corrected] plant Silene latifolia. PLoS One, 6, e27335.