Hierarchical clustering of 21 flavonoid biosynthesis genes.

<p>Red, green and black colors in the heat-map represent relative gene expression levels. The scale bar denotes the log (FPKM+1)/(mean expression levels across the three treatment groups). The green color indicates down-regulated expression compared with the mean expression levels, and the red color indicates up-regulated expression compared to the mean. Three clusters (I, II and III) were indicated with brackets.</p

<b>List of ncRNAs from </b><b><i>S. miltiorrhiza</i></b><b> and </b><b><i>A. thaliana</i></b><b> sharing sequence similarity.</b>

<p><b>List of ncRNAs from </b><b><i>S. miltiorrhiza</i></b><b> and </b><b><i>A. thaliana</i></b><b> sharing sequence similarity.</b></p

Complex Interplay among DNA Modification, Noncoding RNA Expression and Protein-Coding RNA Expression in <i>Salvia miltiorrhiza</i> Chloroplast Genome

<div><p><i>Salvia miltiorrhiza</i> is one of the most widely used medicinal plants. As a first step to develop a chloroplast-based genetic engineering method for the over-production of active components from <i>S. miltiorrhiza</i>, we have analyzed the genome, transcriptome, and base modifications of the <i>S. miltiorrhiza</i> chloroplast. Total genomic DNA and RNA were extracted from fresh leaves and then subjected to strand-specific RNA-Seq and Single-Molecule Real-Time (SMRT) sequencing analyses. Mapping the RNA-Seq reads to the genome assembly allowed us to determine the relative expression levels of 80 protein-coding genes. In addition, we identified 19 polycistronic transcription units and 136 putative antisense and intergenic noncoding RNA (ncRNA) genes. Comparison of the abundance of protein-coding transcripts (cRNA) with and without overlapping antisense ncRNAs (asRNA) suggest that the presence of asRNA is associated with increased cRNA abundance (<i>p</i><0.05). Using the SMRT Portal software (v1.3.2), 2687 potential DNA modification sites and two potential DNA modification motifs were predicted. The two motifs include a TATA box–like motif (CPGDMM1, “TATANNNATNA”), and an unknown motif (CPGDMM2 “WNYANTGAW”). Specifically, 35 of the 97 CPGDMM1 motifs (36.1%) and 91 of the 369 CPGDMM2 motifs (24.7%) were found to be significantly modified (<i>p</i><0.01). Analysis of genes downstream of the CPGDMM1 motif revealed the significantly increased abundance of ncRNA genes that are less than 400 bp away from the significantly modified CPGDMM1motif (<i>p</i><0.01). Taking together, the present study revealed a complex interplay among DNA modifications, ncRNA and cRNA expression in chloroplast genome.</p></div

Characterizing the chloroplast genome of <i>Mammillaria elongata</i> DC. 1828 in the Cactaceae family and unveiling its phylogenetic affinities within the genus <i>Mammillaria</i>

With its nearly 200 species, the Mammillaria genus is the most species-rich within the Cactaceae family, yet surprisingly, few of its chloroplast genomes have been studied. We focused on the species Mammillaria elongata DC. 1828, a petite cactus native to Mexico and favored by horticulturists, yet whose phylogenetic relationships remain uncertain due to a lack of genomic data. We extracted the DNA from a sample obtained in China, sequenced it using the NovaSeq 6000 platform, and assembled the chloroplast genome using GetOrganelle software. Our assembly resulted in a chloroplast genome of 110,981 base pairs with an overall GC content of 36.28%, which included 100 genes (95 unique). Notably, several protein-coding genes were absent. Phylogenetic analysis using 59 shared genes across nine Mammillaria species and one Obregonia species revealed that M. elongata and M. gracilis are closely related, suggesting a recent common ancestor and possible shared evolutionary pressures or ecological niches. This study provides crucial genomic data for M. elongata and hints at intriguing phylogenetic relationships within the Mammillaria genus.</p

Putative enzymes involved in the production of the active compounds in the leaf samples of <i>E</i>. <i>pseudowushanense</i>.

<p>Putative enzymes involved in the production of the active compounds in the leaf samples of <i>E</i>. <i>pseudowushanense</i>.</p

Identification of putative DNA modification sites and motifs in the <i>S. miltiorrhiza</i> chloroplast genome using SMRT technology.

<p>(A) Distribution of interpulse duration (IPD) Ratio across the genome. “▴” indicate that the corresponding IPD ratio (“▴”) has a <i>p</i><0.05, which suggests that the base at this position is modified. (B) Sequence LOGO for putative DNA modification motif 1 (DMM1). (C) Sequence LOGO for putative DNA modification motif 2 (DMM2).</p

A putative model for the light-induced flavonoids biosynthesis in <i>E</i>. <i>pseudowushanense</i>.

<p>A putative model for the light-induced flavonoids biosynthesis in <i>E</i>. <i>pseudowushanense</i>.</p

Volcano plot showing the distribution of log10(p value) vs. log2(Fold Change).

<p>The horizontal axis represents the log2(Fold Change) between the two samples indicated on the top or on the right of the figure, while the vertical axis represents the log10(p value) for the differential expressions between the two samples. Each point represent a gene, red points indicate p value ≤ 0.05, while blue points indicate that p value > 0.05.</p

Sequence length distribution of the unigene sequences.

<p>The X-axis shows the range of lengths of the transcript sequences. The Y-axis shows the number of unigenes.</p

Correlation analysis between flavonol contents and expression profiles of the related genes.

<p>Correlation analysis between flavonol contents and expression profiles of the related genes.</p