Abstract
Sorghum bicolor is a close relative of maize and is a staple crop in Africa and much of the developing world because of its superior tolerance of arid growth conditions. We have generated sequence from the hypomethylated portion of the sorghum genome by applying methylation filtration (MF) technology. The evidence suggests that 96% of the genes have been sequence tagged, with an average coverage of 65% across their length. Remarkably, this level of gene discovery was accomplished after generating a raw coverage of less than 300 megabases of the 735-megabase genome. MF preferentially captures exons and introns, promoters, microRNAs, and simple sequence repeats, and minimizes interspersed repeats, thus providing a robust view of the functional parts of the genome. The sorghum MF sequence set is beneficial to research on sorghum and is also a powerful resource for comparative genomics among the grasses and across the entire plant kingdom. Thousands of hypothetical gene predictions in rice and Arabidopsis are supported by the sorghum dataset, and genomic similarities highlight evolutionarily conserved regions that will lead to a better understanding of rice and Arabidopsis.
Highlights
Sorghum bicolor is a vitally important crop in Africa and much of the developing world
Expected Gene Tagging: An Arabidopsis Simulation If methylation filtration (MF) faithfully represents the genic region of sorghum and contains the vast majority of the genes, the rate of gene tagging should produce results that are similar to wholegenome shotgun coverage [21] at the same level of raw coverage
The eight that are missing may be present in the data but not identified because of sequencing errors; not yet sampled, as we expect only approximately 66% of the nucleotides to be present at this level of coverage; or some of these eight may represent miRNAs conserved in rice but lost in sorghum
Summary
We have generated sequence from the hypomethylated portion of the sorghum genome by applying methylation filtration (MF) technology. The evidence suggests that 96% of the genes have been sequence tagged, with an average coverage of 65% across their length. This level of gene discovery was accomplished after generating a raw coverage of less than 300 megabases of the 735-megabase genome.
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