title: Chloroplast genome variation in upland and lowland switchgrass.
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 Single Nucleotide Polymorphisms (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.
authors: Genomics and Gene Discovery Research Unit, United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, United States of America.
authors: Hugh A
authors: HA
authors: Young
authors: Christina L
authors: CL
authors: Lanzatella
authors: Gautam
authors: G
authors: Sarath
authors: Christian M
authors: CM
authors: Tobias
mesh_terms: D001483:Base Sequence; D017753:Ecosystem; D060146:Ecotype; D017343:Genes, Plant; D054628:Genome, Chloroplast / Q000235:genetics*; D007700:Kinetics; D008969:Molecular Sequence Data; D006109:Poaceae / Q000235:genetics*; D011110:Polymorphism, Genetic; D016415:Sequence Alignment