9 research outputs found

    NeighborNet analysis of cloned ITS1+ITS2 variants.

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    <p>Particular clones belong to: <i>Ranunculus cassubicifolius</i> (“S”-clones), <i>R. notabilis</i> (“N”-clones), their synthetic hybrid (“X”-clones) and the putative hybrid, <i>R. variabilis</i> (“V”-clones). The spring leaf silhouettes illustrate the main phenotypic difference between the <i>auricomus</i> and the <i>cassubicus</i> morphotypes. Italic letters mark clones which exhibit non-compensatory base changes in the ITS1 or ITS2 secondary structures. Bootstrap values are given for the main clusters.</p

    NeighborNet analysis of interspecific ITS1+ITS2 variability within the <i>Ranunculus auricomus</i> complex.

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    <p>NeighborNet analysis of all ITS1+ITS2 sequences obtained by direct sequencing of the studied individuals. The spring leaf silhouettes illustrate the main phenotypic differences between the two morphotypes: the <i>auricomus</i>-morphotype (characteristic for <i>R. notabilis</i>, <i>R. variabilis</i> and the synthetic hybrid <i>R. cassubicifolius</i> × <i>notabilis</i>) and the <i>cassubicus</i>–morphotype (i.e., <i>R. carpaticola</i> and <i>R. cassubicifolius</i>). Individuals belonging to <i>R. carpaticola</i> are marked as “P”, <i>R. cassubicifolius</i> as “S”, <i>R. notabilis</i> as “N” and <i>R. variabilis</i> as “V”, respectively. Identical sequences representing the same ribotype are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103003#pone-0103003-g003" target="_blank">Figure 3</a>. Bootstrap values are given for the main clusters.</p

    ITS Polymorphisms Shed Light on Hybrid Evolution in Apomictic Plants: A Case Study on the <i>Ranunculus auricomus</i> Complex

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    <div><p>The reconstruction of reticulate evolutionary histories in plants is still a major methodological challenge. Sequences of the ITS nrDNA are a popular marker to analyze hybrid relationships, but variation of this multicopy spacer region is affected by concerted evolution, high intraindividual polymorphism, and shifts in mode of reproduction. The relevance of changes in secondary structure is still under dispute. We aim to shed light on the extent of polymorphism within and between sexual species and their putative natural as well as synthetic hybrid derivatives in the <i>Ranunculus auricomus</i> complex to test morphology-based hypotheses of hybrid origin and parentage of taxa. We employed direct sequencing of ITS nrDNA from 68 individuals representing three sexuals, their synthetic hybrids and one sympatric natural apomict, as well as cloning of ITS copies in four representative individuals, RNA secondary structure analysis, and landmark geometric morphometric analysis on leaves. Phylogenetic network analyses indicate additivity of parental ITS variants in both synthetic and natural hybrids. The triploid synthetic hybrids are genetically much closer to their maternal progenitors, probably due to ploidy dosage effects, although exhibiting a paternal-like leaf morphology. The natural hybrids are genetically and morphologically closer to the putative paternal progenitor species. Secondary structures of ITS1-5.8S-ITS2 were rather conserved in all taxa. The observed similarities in ITS polymorphisms suggest that the natural apomict <i>R. variabilis</i> is an ancient hybrid of the diploid sexual species <i>R. notabilis</i> and the sexual species <i>R. cassubicifolius</i>. The additivity pattern shared by <i>R. variabilis</i> and the synthetic hybrids supports an evolutionary and biogeographical scenario that <i>R. variabilis</i> originated from ancient hybridization. Concerted evolution of ITS copies in <i>R. variabilis</i> is incomplete, probably due to a shift to asexual reproduction. Under the condition of comprehensive inter- and intraspecific sampling, ITS polymorphisms are powerful for elucidating reticulate evolutionary histories.</p></div

    5.8S secondary structure model for <i>Ranunculus notabilis</i> 5613-1.

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    <p>(A) The partial 5.8S secondary structure model comprising conserved sequence regions (M1-M3), conserved helices (B5-B8) and highlighted sites affected by nucleotide substitutions (for the whole 5.8S secondary structure see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103003#pone.0103003.s001" target="_blank">Figure S1</a>). (B) A summary Table of 5.8S nucleotide polymorphisms detected in clones.</p

    ITS1 secondary structure model for <i>Ranunculus notabilis</i> 5613-1.

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    <p>Polymorphic sites detected in all studied taxa were highlighted in the secondary structure model for <i>R. notabilis</i> 5613-1. The DNA weblogo summarizes all ITS1 nucleotide polymorphisms detected by direct sequencing (red letters) and both direct sequencing and cloning (green letters). Bonds within the ITS1 secondary structure are shown for all positions which can be affected by either non-compensatory or compensatory ( =  hemi-CBCs) single-stranded nucleotide polymorphisms within helices. Italic letters mark non-compensatory base changes which are present only in a single clone.</p

    List of directly sequenced individuals.

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    a)<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103003#pone.0103003-Hrandl14" target="_blank">[96]</a>.</p>b)<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103003#pone.0103003-Hrandl2" target="_blank">[46]</a>.</p>c)<p>functional sexual seed, but with aposporous initials (for details see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103003#pone.0103003-Hojsgaard1" target="_blank">[58]</a>).</p>d)<p>functional sexual seed, but with low rates of aposporous seeds (for details see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103003#pone.0103003-Hojsgaard1" target="_blank">[58]</a>).</p

    Polymorphisms of ITS1+ITS2 within the <i>Ranunculus auricomus</i> complex as detected by direct sequencing.

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    <p>A summary of all ITS1+ITS2 polymorphic sites (red and white letters) detected through direct sequencing. The three polymorphic sites which are shared by <i>R. notabilis</i>, its synthetic hybrid and the putative natural descendent (i.e., <i>R. variabilis</i>) are highlighted by white letters on black background and underlaid by green stripes. Those shared just by <i>R. notabilis</i> and <i>R. variabilis</i> are underlaid by grey stripes.</p
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