Chloroplast genome variation in upland and lowland switchgrass - PubMed (original) (raw)

Chloroplast genome variation in upland and lowland switchgrass

Hugh A Young et al. PLoS One. 2011.

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Map of the chloroplast genome of P. virgatum cv. Kanlow Lin1.

The thick lines of the inner circle indicate the locations of the inverted repeats (IRb and IRa) which separate the SSC and LSC regions. Genes on the outside of the map are transcribed in a counter-clockwise direction and those on the inside are transcribed clockwise. Genes containing introns are marked with exon numbers (e.g. ycf3.e2). Transfer RNAs are indicated by gray bars.

Figure 2

Figure 2. MultiPip analysis showing sequence similarity of cp genomes.

(A) MultiPipMaker was used to align the two switchgrass cp genomes. There is a 21 bp insertion in rpoC2 of Summer Lin2. (B) MultiPip alignment of cp genomes from members of Poales demonstrates sequence similarity, indicated by red (75–100%), green (50–75%), and white (<50%). The earliest diverging member, Typha latifolia, is used as the reference genome. Arrows indicate gene losses and/or IR expansions occurring in switchgrass Lin1 and Lin2 cp genomes. Regions of the cp genome are indicated across the top (LSC, IRb, SSC, IRa).

Figure 3

Figure 3. Mononucleotide microsatellite length polymorphisms in Kanlow Lin1.

(A) The total incidence of mononucleotide repeats is indicated based on repeat length (bp) and location in the plastid genome. (B) The rates of homopolymer incidence per kb are indicated for each genomic region. IR – inverted repeat; LSC – long single copy; SSC – short single copy.

Figure 4

Figure 4. Overlap and classification of Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletion (InDel) differences.

Illumina RNAseq data from upland and lowland genotypes were aligned to the Lin1 reference sequence. (A) Overlap of SNPs identified within 1.53 million Illumina sequences that aligned from pooled upland genotypes (Up) and 82,656 Illumina sequences from pooled lowland (Low) genotypes with SNPs identified within the Lin2 reference genome. Numbers in red indicate the total of both variable and invariant differences that were detected. (B) The variant positions within the Illumina data were aggregated and summarized by position and by type of variation. TN, transition; TV, transversion; indel, insertion/deletion.

Figure 5

Figure 5. Phylogenetic Analyses.

An aligned data set of 61 protein-coding genes from 15 taxa of the order Poales was used for phylogenetic analyses. The evolutionary history was inferred using the Maximum Parsimony (A) and Maximum Likelihood (B) methods. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap tests (500 replicates) are shown next to the branches. There were a total of 41,397 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 . All positions containing gaps and missing data were eliminated. Subfamily groupings are indicated by solid lines on the right margin.

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