Chloroplast Genome Variation in Upland and Lowland Switchgrass

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 individua...

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Bibliographic Details
Published in:PloS one 2011-08, Vol.6 (8), p.e23980-e23980
Main Authors: Young, Hugh A, Lanzatella, Christina L, Sarath, Gautam, Tobias, Christian M, Newbigin, Edward
Format: Article
Language:English
Subjects:
Agriculture
Analysis
Annotations
Barley
Base pairs
Base Sequence
Bioinformatics
Biology
Breeding
chloroplast genome
Chloroplasts
Conservation
Conserved sequence
data collection
Deoxyribonucleic acid
DNA
Ecosystem
Ecosystems
Ecotype
Ecotypes
Evolution
Genes
Genes, Plant
Genome, Chloroplast - genetics
Genomes
Genomics
highlands
Hordeum vulgare
intergenic DNA
Introns
Kinetics
lowland
microsatellite repeats
Molecular Sequence Data
Nucleotide sequence
Panicum virgatum
Phylogenetics
ploidy
Poaceae - genetics
Polymorphism
Polymorphism, Genetic
rice
Sequence Alignment
Simple sequence repeats
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Summer
Switchgrass
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Description
Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0023980