title: A genome-wide survey of switchgrass genome structure and organization.
abstract: The perennial grass, switchgrass (Panicum virgatum L.), is a promising bioenergy crop and the target of whole genome sequencing. We constructed two bacterial artificial chromosome (BAC) libraries from the AP13 clone of switchgrass to gain insight into the genome structure and organization, initiate functional and comparative genomic studies, and assist with genome assembly. Together representing 16 haploid genome equivalents of switchgrass, each library comprises 101,376 clones with average insert sizes of 144 (HindIII-generated) and 110 kb (BstYI-generated). A total of 330,297 high quality BAC-end sequences (BES) were generated, accounting for 263.2 Mbp (16.4%) of the switchgrass genome. Analysis of the BES identified 279,099 known repetitive elements, >50,000 SSRs, and 2,528 novel repeat elements, named switchgrass repetitive elements (SREs). Comparative mapping of 47 full-length BAC sequences and 330K BES revealed high levels of synteny with the grass genomes sorghum, rice, maize, and Brachypodium. Our data indicate that the sorghum genome has retained larger microsyntenous regions with switchgrass besides high gene order conservation with rice. The resources generated in this effort will be useful for a broad range of applications.
authors.affiliation: Department of Plant Pathology, University of California Davis, Davis, California, United States of America.
authors.forename: Manoj K
authors.initials: MK
authors.lastname: Sharma
authors.forename: Rita
authors.initials: R
authors.lastname: Sharma
authors.forename: Peijian
authors.initials: P
authors.lastname: Cao
authors.forename: Jerry
authors.initials: J
authors.lastname: Jenkins
authors.forename: Laura E
authors.initials: LE
authors.lastname: Bartley
authors.forename: Morgan
authors.initials: M
authors.lastname: Qualls
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.forename: Daniel
authors.initials: D
authors.lastname: Rokhsar
authors.forename: Pamela C
authors.initials: PC
authors.lastname: Ronald
mesh_terms: D001482:Base Composition; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D018628:Gene Dosage; D018745:Genome, Plant; D015698:Genomic Library; D018895:Microsatellite Repeats; D008897:Panicum / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D026801:Synteny