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Title: Chloroplast genome variation in upland and lowland switchgrass

item Young, Hugh
item Lanzatella-Craig, Christina
item Sarath, Gautam
item Tobias, Christian

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/1/2011
Publication Date: 8/24/2011
Citation: Young, H.A., Lanzatella-Craig, C., Sarath, G., Tobias, C.M. 2011. Chloroplast genome variation in upland and lowland switchgrass. PLoS One. 6(8): e23980. Available:

Interpretive Summary: Switchgrass grows in diverse locations and specific individuals have adapted to either upland or lowland locations over time. These differences are reflected in genetic diversity that is contained in the chloroplast genome. We sequenced two individuals chloroplast genomes and analyzed differences corresponding to upland and lowland ecotypes. These variations are useful for the purposes of classification. The sequences are useful for the purpose of designing and optimizing plastid transformation vectors.

Technical Abstract: Switchgrass (Panicum virgatum L.) exists at multiple ploidies and two phenotypically distinct ecotypes. To facilitate interploidal comparisons and to understand the extent of sequence variation within existing breeding pools, two complete switchgrass chloroplast genomes were sequenced from individuals representative of the upland and lowland ecotypes. The results demonstrated a very high degree of conservation in gene content and order with other sequenced plastid genomes. The lowland ecotype reference sequence (Kanlow Lin1) was 139,677 base pairs while the upland sequence (Summer Lin2) was 139,619 base pairs. Alignments between the lowland reference sequence and short-read sequence data from existing sequence datasets identified as either upland or lowland confirmed known polymorphisms and indicated the presence of other differences. Insertions and deletions principally occurred near stretches of homopolymer simple sequence repeats in intergenic regions while most SNPs occurred in intergenic regions and introns within the single copy portions of the genome. The polymorphism rate between upland and lowland switchgrass ecotypes was found to be similar to rates reported between chloroplast genomes of indica and japonica subspecies of rice which were believed to have diverged 0.2-0.4 million years ago.