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.
Highlights
The C4 perennial grass, switchgrass (Panicum virgatum L.), a member of Paniceae tribe of the Panicoideae subfamily of the Poaceae is a promising bioenergy crop [1,2]
To estimate insert size, .180 clones were randomly picked from each library
Further repetitive regions longer than the read length and similarity in homoeologous regions may lead to potential misassemblies, which could require a great deal of directed sequencing to accurately resolve [22]
Summary
The C4 perennial grass, switchgrass (Panicum virgatum L.), a member of Paniceae tribe of the Panicoideae subfamily of the Poaceae is a promising bioenergy crop [1,2]. The work reported here is part of an effort directed towards generating the genetic and genomic resources for switchgrass needed for gene discovery and breeding efforts [8,9]. An accurate estimate of genome structure and composition prior to full genome sequencing is needed. Generation and sequencing of BAC libraries is an efficient strategy to obtain this information and support assembly of the large and complex underlying genomes [11,12,13,14,15,16]. An EcoRI-generated BAC library was reported from the SL93 2001-1 genotype of Alamo switchgrass [17]. Based on the analysis of homoeologous genomic regions harboring orthologs of the rice Brassinosteroid insensitive 1 (OsBRI1), those authors made an attempt to provide a glimpse of switchgrass genome structure and complexity. Additional libraries are required to achieve unbiased and near-complete representation for genomewide studies
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