Sorghum genome sequencing by methylation filtration

Joseph A. Bedell, Muhammad A. Budiman, Andrew Nunberg, Robert W. Citek, Dan Robbins, Joshua Jones, Elizabeth Flick, Theresa Rohlfing, Jason Fries, Kourtney Bradford, Jennifer McMenamy, Michael Smith, Heather Holeman, Bruce A. Roe, Graham Wiley, Ian F Korf, Pablo D. Rabinowicz, Nathan Lakey, W. Richard McCombie, Jeffrey A. JeddelohRobert A. Martienssen

Research output: Contribution to journalArticle

129 Scopus citations

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. Copyright:

Original languageEnglish (US)
JournalPLoS Biology
Volume3
Issue number1
DOIs
StatePublished - Jan 2005

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Fingerprint Dive into the research topics of 'Sorghum genome sequencing by methylation filtration'. Together they form a unique fingerprint.

  • Cite this

    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., Richard McCombie, W., ... Martienssen, R. A. (2005). Sorghum genome sequencing by methylation filtration. PLoS Biology, 3(1). https://doi.org/10.1371/journal.pbio.0030013