Nuclear and chloroplast microsatellite genotypes for Pinus pinaster at Fuencaliente (Ciudad Real, Spain)

One line per combined nuclear-chloroplast individual genotype, comprising 12 nSSR diploid loci and 6 cpSSR haploid regions. For nSSR, the two alleles at each locus are listed in consecutive columns. Missing data coded with zeros. Needle samples collected in the field. DNA extracted with Invisorb DNA Plant HTS 96 Kit. Electrophoresis of amplified products with LI-COR 4300 DNA Analyzer for cpSSRs, and 3130xL and 3500 Genetic Analyzers (Applied Biosystems) for nSSRs. Fragment size determination through visual inspection using external size markers and reference samples with known allele size for cpSSR, and internal size standard and GeneMapper software (Applied Biosystems) for nSSR

Total repeat and SSR distribution in <i>C</i>. <i>cardunculus</i> var. <i>scolymus</i> chloroplast genome.

<p>(a) Repeat distribution among four different regions: coding sequence, intronic sequence, intergenic space region and overlapping region. (b) SSR distribution according to type: mononucleotide, dinucleotide, trinucleotide, and tetranucleotide repeats. SSR number and percentages (in brackets) are provided. (c) SSR type distribution between coding and non-coding regions.</p

Phylogenetic tree based on maximum parsimony of 69 accessions belonging to the Asteraceae family.

<p>Seven coding regions were used: <i>matk</i>, <i>ndhD</i>, <i>ndhF</i>, <i>ndhI</i>, <i>rbcL</i>, <i>rpoB</i> and the first exon of <i>rpoC1</i>, for a total of 1,811 parsimony-informative characters. Sequences from <i>C</i>. <i>cardunculus</i> were obtained from this work. Bootstrap values for each node were set greater than 50%. Species for which the complete cp genome is available are shaded.</p

Complete Chloroplast Genome of the Multifunctional Crop Globe Artichoke and Comparison with Other Asteraceae

<div><p>With over 20,000 species, Asteraceae is the second largest plant family. High-throughput sequencing of nuclear and chloroplast genomes has allowed for a better understanding of the evolutionary relationships within large plant families. Here, the globe artichoke chloroplast (cp) genome was obtained by a combination of whole-genome and BAC clone high-throughput sequencing. The artichoke cp genome is 152,529 bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 25,155 bp, representing the longest IRs found in the Asteraceae family so far. The large (LSC) and the small (SSC) single-copy regions span 83,578 bp and 18,641 bp, respectively. The artichoke cp sequence was compared to the other eight Asteraceae complete cp genomes available, revealing an IR expansion at the SSC/IR boundary. This expansion consists of 17 bp of the <i>ndhF</i> gene generating an overlap between the <i>ndhF</i> and <i>ycf1</i> genes. A total of 127 cp simple sequence repeats (cpSSRs) were identified in the artichoke cp genome, potentially suitable for future population studies in the <i>Cynara</i> genus. Parsimony-informative regions were evaluated and allowed to place a <i>Cynara</i> species within the Asteraceae family tree. The eight most informative coding regions were also considered and tested for “specific barcode” purpose in the Asteraceae family. Our results highlight the usefulness of cp genome sequencing in exploring plant genome diversity and retrieving reliable molecular resources for phylogenetic and evolutionary studies, as well as for specific barcodes in plants.</p></div

Comparison of the border positions of LSC, SSC, and IR regions among nine sequenced Asteraceae chloroplast genomes.

<p>Genes are indicated in boxes and their extensions in the corresponding regions are displayed above boxes.</p

Genes present in the globe artichoke cp genome.

<p>^aGene containing two introns</p><p>^bGene containing a single intron</p><p>^cTwo gene copies in the IRs</p><p>^dGene divided into two independent transcription units</p><p>^ePseudogenes</p><p>Genes present in the globe artichoke cp genome.</p

Visualization of alignment of nine Asteraceae cp genome sequences.

<p>VISTA-based identity plot showing sequence identity among eight cp genomes already published (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120589#sec002" target="_blank">Materials and Methods</a> for accession numbers) and the artichoke cp genome, set as a reference. Sequence identity is shown as a percentage between 50–100% on y-axis. On x-axis, artichoke genes are indicated on top lines, and arrows represent their orientation. Genome regions are distinguished by colors. CNS: conserved non-coding sequences.</p

Artichoke cp genome map.

<p>Genes shown on the outside of the large circle are transcribed clockwise; genes on the inside are transcribed counterclockwise. Thick lines of the small circle indicate IRs. Pseudogenes are marked with '*'.</p

Csillery_Lalague_etal_phasedSNPdata

This file includes the phased SNP data (with a rate of 12.4% missing data instead of 24.6% after using PHASE software

Coding regions and their parsimony-informative rate.

<p>Length: refers to sequence length in <i>Cynara cardunculus</i> var. <i>scolymus</i></p><p>Aligned length: refers to the alignment of nine Asteraceae considered in the comparative analysis (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120589#sec002" target="_blank">Materials and Methods</a>)</p><p>Pars.: parsimony</p><p>Uninf. uninformative</p><p>Inf.: informative</p><p>C.I.: consistency index</p><p>R.I.: retention index</p><p>Coding regions and their parsimony-informative rate.</p