Sorghum Genome Sequencing by Methylation Filtration

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.

Stress‐induced changes in the Arabidopsis thaliana transcriptome analyzed using whole‐genome tiling arrays

“…available, Poplar trichocarpa, Oryza sativa and Sorghum bicolor (Goff et al, 2002;Yu et al, 2002;Bedell et al, 2005;Tuskan et al, 2006). Compared with annotated exons, novel stress-specific TARs are in general much less conserved (Figure 6a).…”

Roles of microRNA in plant defense and virus offense interaction

“…miRNAs have also been identified in other plant species, such as Nicotiana tabacum (Billoud et al 2005), Zea mays (Dezulian et al 2005), Sorghum bicolor (Bedell et al 2005), Populus Tuskan et al 2006), Gossypium hirsutum (Qiu et al 2007), Brassica napus ) and Vitis vinifera (Velasco et al 2007). Furthermore, miRNAs were predicted to play important roles in mosses Physcomitrella (Arazi et al 2005), and unicellular green alga C. reinhardtii (Zhao et al 2007).…”

Tobacco Transcription Factors: Novel Insights into Transcriptional Regulation in the Solanaceae

“…MF has already been applied successfully in maize (Zea mays), sorghum (Sorghum bicolor), and cowpea (Vigna unguiculata; Rabinowicz et al, 1999;Palmer et al, 2003;Whitelaw et al, 2003;Chen et al, 2007). The development of MF followed studies of genome architecture that revealed that repetitive elements tend to form clusters within plant genomes that become heavily methylated (hypermethylated), leaving stretches of less-methylated (hypomethylated), low-copy gene-rich space scattered in islands throughout the genome (Bennetzen et al, 1994;Bedell et al, 2005).…”