title: 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.
authors.affiliation: Bioinformatics, Orion Genomics Saint Louis, Missouri United States of America. jbedell@oriongenomics.com
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Bedell
authors.forename: Muhammad A
authors.initials: MA
authors.lastname: Budiman
authors.forename: Andrew
authors.initials: A
authors.lastname: Nunberg
authors.forename: Robert W
authors.initials: RW
authors.lastname: Citek
authors.forename: Dan
authors.initials: D
authors.lastname: Robbins
authors.forename: Joshua
authors.initials: J
authors.lastname: Jones
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Flick
authors.forename: Theresa
authors.initials: T
authors.lastname: Rholfing
authors.forename: Jason
authors.initials: J
authors.lastname: Fries
authors.forename: Kourtney
authors.initials: K
authors.lastname: Bradford
authors.forename: Jennifer
authors.initials: J
authors.lastname: McMenamy
authors.forename: Michael
authors.initials: M
authors.lastname: Smith
authors.forename: Heather
authors.initials: H
authors.lastname: Holeman
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Roe
authors.forename: Graham
authors.initials: G
authors.lastname: Wiley
authors.forename: Ian F
authors.initials: IF
authors.lastname: Korf
authors.forename: Pablo D
authors.initials: PD
authors.lastname: Rabinowicz
authors.forename: Nathan
authors.initials: N
authors.lastname: Lakey
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Jeddeloh
authors.forename: Robert A
authors.initials: RA
authors.lastname: Martienssen
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D017124:Conserved Sequence; D018556:Crops, Agricultural / Q000235:genetics; D019175:DNA Methylation; D018744:DNA, Plant / Q000235:genetics*; D019143:Evolution, Molecular; D005374:Filtration / Q000379:methods; D017343:Genes, Plant; D018745:Genome, Plant; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics; D045868:Sorghum / Q000235:genetics*
chemical_list: D018744:DNA, Plant