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, 12 (2), e0168008
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Complete Chloroplast Genomes From Apomictic Taraxacum (Asteraceae): Identity and Variation Between Three Microspecies

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Complete Chloroplast Genomes From Apomictic Taraxacum (Asteraceae): Identity and Variation Between Three Microspecies

Rubar Hussein M Salih et al. PLoS One.

Abstract

Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnF-GGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in plastomes is important to characterize the nature of evolutionary processes in nuclear and cytoplasmic genomes with the different selection pressures, population structures and breeding systems.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Map of the plastome of Taraxacum amplum (A978).
Genes are shown inside or outside the circle to indicate clockwise or counterclockwise transcription direction respectively. The Inverted Repeat (IR, 24,431bp) is indicated by a thicker line for IR1 and IR2. GC content is show in the inner blue graph. Small Single Copy (SSC) and long single copy (LSC) regions are indicated, and the inverted regions (Inv1 and Inv2) within LSC relative to other species are shown as orange arcs. Short tandem repeats (microsatellites and minisatellites) are indicated by blue dots, palindromes by red dots, forward repeats by green dots and reverse repeats by black dots.
Fig 2
Fig 2. Dot-plot sequence comparison of Taraxacum and Nicotiana chloroplast sequences, showing the Inverted Repeats (IR1 and IR2), hemi-nested inversions between the two plastomes (Inv1 and Inv2) and inversion of the SSC.
Fig 3
Fig 3. Repetitive motif abundance in Taraxacum (only A978 shown since the three accessions were similar) and Lactuca plastomes.
C = Complement repeats, P = Palindromic repeats, F = Forward repeats, R = Reverse repeats.
Fig 4
Fig 4. A radar-plot comparing features of the plastomes of 21 accessions of Asteraceae, showing, from inside to out, sizes of major plastome regions, GC content, genome size and number of different types of genes.
Fig 5
Fig 5. Comparative plastome maps.
Endpoints of the large 22 kb inversion present in most Asteraceae and of a small inversion (3.3 kb in other Asteraceae).
Fig 6
Fig 6. Comparative plastome maps.
Gene order and inversion of the SSC region. Gene sequences were annotated and indicated along the black lines. Genes above the black lines indicate their transcription in reverse direction and genes below the black lines represent their transcription in forward direction.
Fig 7
Fig 7. Comparative plastome maps.
Border position of LSC, IR and SSC region among the 20 Asteraceae plastomes. Genes are indicated by coloured boxes.

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Grant support

This work is supported by a dedicated grant from the Higher Committee for Education Development in Iraq, special to Rubar M.Salih (No. D-10-2398, http://hcediraq.org/HCED_english_website/homeen.html). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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