Additional file 1: of Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring

Table S1. The ratio of split-reads mapped to each cpDNA of six Populus species using Bowtie and BWA. Table S2. The genome size of P. trichocarpa cpDNA was estimated using each of twelve sets of simulated reads (60 bp–10 k, 60 bp–100 k, 60 bp–1 M, 60 bp–10 M, 80 bp–10 k, 80 bp–100 k, 80 bp–1 M, 80 bp–10 M, 100 bp–10 k, 100 bp–100 k, 100 bp–1 M and 100 bp–10 M). Table S3. Basic statistics of 13 assemblies used for further analyses. Table S4. The cpDNA and gDNA ratios of read datasets for the three poplar clones I45, I69 and NL895. Table S5. The positions, reference and alternative base, types (Replace|Insert|Delete) and the genotypes of all 401 variants identified in the three poplar clones. (XLSX 31 kb

Distribution of <i>Lycoris longituba</i> variants ants by flower colors based on a bivariate (<i>a*</i> and <i>b*</i>) (A) and trivariate (<i>a*</i>, <i>b*</i>, and <i>L*</i>) CIELAB data (B), respectively.

<p>The flower colors were identified by the RHSCC value.</p

The HPLC–ESI/MS/MS of anthocyanins in <i>Lycoris longituba</i>.

<p>Mass spectra of anthocyanin components. (A) cyanidin 3-sophoroside, (B) cyanidin 3-xylosylglucoside, (C) cyanidin 3-sambubioside, and (D) pelargonidin 3-xylosylglucoside.</p

Flowers of four representative colors, purple (A), red (B), orange (C), and yellow (D), for <i>Lycoris longituba</i> variants sampled from a natural population.

<p>Flowers of four representative colors, purple (A), red (B), orange (C), and yellow (D), for <i>Lycoris longituba</i> variants sampled from a natural population.</p

The multivariate relationships between <i>C^*</i> and <i>L^*</i> values, showing different patterns depending on petal colors, purple, red, orange, and yellow (see Fig. 1), in <i>Lycoris longituba</i> flowers.

<p>The multivariate relationships between <i>C^*</i> and <i>L^*</i> values, showing different patterns depending on petal colors, purple, red, orange, and yellow (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022098#pone-0022098-g001" target="_blank">Fig. 1</a>), in <i>Lycoris longituba</i> flowers.</p

Petal anthocyanin mean values (in peak areas %) of 44 <i>Lycoris longituba</i> varieties.

a<p>Cy: cyanidin; Pg: pelargonidin; 3So: 3-sophoroside; 3GXyGlc: 3-xylosylglucoside; 3Sa: 3-sambubioside; U: the unidentified fifth anthocyanin(sample limitations did not allow complete confirmation of the identity). Data are expressed as percentage.</p>b<p>TA: total anthocyanin; TF: total flavones and flavonols in mg per 100 mg dry petals; CI: copigment index = TF/TA.</p><p>-: not detected.</p

Petal colors and color parameters of 44 <i>Lycoris longituba</i> variants.

<p><i>a^*</i>, <i>b^*</i>, chromatic components; <i>C^*</i>, chroma; <i>h</i>, hue angle (°); <i>L^*</i>, lightness; RHSCC, Royal Horticultural Society Colour Chart.</p

Chromatographic and spectral data of anthocyanins detected in 44 <i>Lycoris longituba</i> varieties.

a<p>Cy, cyanidin; Pg, pelargonidin; So, sophorose; XyGlc, xylosylglucoside ; Sa, sambubioside.</p>b<p>t_R, retention time.</p>c<p>λ, absorption wavelength.</p

The HPLC chromatogram of <i>Lycoris longituba</i> petal extracts detected by light wavelength = 516 nm.

<p>Peak labels: (1) cyanidin 3-sophoroside (Cy3So); (2) cyanidin 3-xylosylglucoside) (Cy3XyGlc); (3) cyanidin 3-sambubioside (Cy3Sa); (4) pelargonidin 3- xylosylglucoside (Pg3XyGlc); (5) Unidentified. Two colors, red and blue, denote the HPLC chromatograms of two different <i>L. longituba</i> varieties, LL52 and LL27, respectively.</p

A Comprehensive Analysis of the Transcriptomes of <i>Marssonina brunnea</i> and Infected Poplar Leaves to Capture Vital Events in Host-Pathogen Interactions

<div><p>Background</p><p>Understanding host-pathogen interaction mechanisms helps to elucidate the entire infection process and focus on important events, and it is a promising approach for improvement of disease control and selection of treatment strategy. Time-course host-pathogen transcriptome analyses and network inference have been applied to unravel the direct or indirect relationships of gene expression alterations. However, time series analyses can suffer from absent time points due to technical problems such as RNA degradation, which limits the application of algorithms that require strict sequential sampling. Here, we introduce an efficient method using independence test to infer an independent network that is exclusively concerned with the frequency of gene expression changes.</p><p>Results</p><p>Highly resistant NL895 poplar leaves and weakly resistant NL214 leaves were infected with highly active and weakly active <i>Marssonina brunnea</i>, respectively, and were harvested at different time points. The independent network inference illustrated the top 1,000 vital fungus-poplar relationships, which contained 768 fungal genes and 54 poplar genes. These genes could be classified into three categories: a fungal gene surrounded by many poplar genes; a poplar gene connected to many fungal genes; and other genes (possessing low degrees of connectivity). Notably, the fungal gene M6_08342 (a metalloprotease) was connected to 10 poplar genes, particularly including two disease-resistance genes. These core genes, which are surrounded by other genes, may be of particular importance in complicated infection processes and worthy of further investigation.</p><p>Conclusions</p><p>We provide a clear framework of the interaction network and identify a number of candidate key effectors in this process, which might assist in functional tests, resistant clone selection, and disease control in the future.</p></div