Sorghum genome sequencing by methylation filtration

Bedell, J. A., Budiman, M. A., Nunberg, A., Citek, R. W., Robbins, D., Jones, J., Flick, E., Rohlfing, T., Fries, J., Bradford, K., McMenamy, J., Smith, M., Holeman, H., Roe, B. A., Wiley, G., Korf, I. F., Rabinowicz, P. D., Lakey, N., McCombie, W. R., Jeddeloh, J. A., Martienssen, R. A. (2005) Sorghum genome sequencing by methylation filtration. PLoS Biology, 3 (1). e13. ISSN 1544-9173

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URL: http://www.ncbi.nlm.nih.gov/pubmed/15660154
DOI: 10.1371/journal.pbio.0030013

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.

Item Type: Paper
Uncontrolled Keywords: ORYZA-SATIVA L. oryza sativa L. MAIZE GENOME maize genome DNA METHYLATION DNA methylation GENE-EXPRESSION gene expression DRAFT draft SEQUENCE sequence PLANT GENOMES plant genomes RICE RETROTRANSPOSONS retrotransposons REGIONS DROUGHT drought
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein methylation
CSHL Authors:
Communities: CSHL labs > Martienssen lab
CSHL labs > McCombie lab
Depositing User: CSHL Librarian
Date Deposited: 17 Jan 2012 16:21
Last Modified: 11 Apr 2013 19:55
PMCID: PMC539327
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22534

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