Summary of general features for <i>Spirodela</i> mitochondrial genome.

a<p>coding sequences include identified mitochondrial genes, pseudogenes, ORFs and <i>cis</i>-spliced introns.</p

The fraction of each codon usage among the same amino acid in <i>Spirodela</i> compared to that in <i>Oryza</i>.

<p>Black bar was <i>Spirodela</i> and grey was <i>Oryza</i>. The fraction of each codon usage was shown on Y-axis.</p

<i>de novo</i> assembly statistics for the <i>Spirodela</i> mitochondrial genome.

a<p>Coverage cut-off: minimum coverage required to form a contig.</p>b<p>Average chloroplast coverage was cited from <i>Spirodela</i> chloroplast genome assembly <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046747#pone.0046747-Wang1" target="_blank">[11]</a>.</p

Pipeline of mitochondrial genome assembly.

<p>Details were described in Methods.</p

The gene map of <i>Spirodela polyrhiza</i> mitochondrial genome.

<p>Genes indicated as closed boxes on the outside of the circle are transcribed clockwise, whereas those on the inside were transcribed counter-clockwise. Pseudogenes were indicated with the prefix “Ψ”. The biggest repeat pair was also marked by arrows. The genome coordinate and GC content are shown in the inner circle.</p

The Mitochondrial Genome of an Aquatic Plant, <em>Spirodela polyrhiza</em>

<div><h3>Background</h3><p><em>Spirodela polyrhiza</em> is a species of the order Alismatales, which represent the basal lineage of monocots with more ancestral features than the Poales. Its complete sequence of the mitochondrial (mt) genome could provide clues for the understanding of the evolution of mt genomes in plant.</p> <h3>Methods</h3><p><em>Spirodela polyrhiza</em> mt genome was sequenced from total genomic DNA without physical separation of chloroplast and nuclear DNA using the SOLiD platform. Using a genome copy number sensitive assembly algorithm, the mt genome was successfully assembled. Gap closure and accuracy was determined with PCR products sequenced with the dideoxy method.</p> <h3>Conclusions</h3><p>This is the most compact monocot mitochondrial genome with 228,493 bp. A total of 57 genes encode 35 known proteins, 3 ribosomal RNAs, and 19 tRNAs that recognize 15 amino acids. There are about 600 RNA editing sites predicted and three lineage specific protein-coding-gene losses. The mitochondrial genes, pseudogenes, and other hypothetical genes (ORFs) cover 71,783 bp (31.0%) of the genome. Imported plastid DNA accounts for an additional 9,295 bp (4.1%) of the mitochondrial DNA. Absence of transposable element sequences suggests that very few nuclear sequences have migrated into <em>Spirodela</em> mtDNA. Phylogenetic analysis of conserved protein-coding genes suggests that <em>Spirodela</em> shares the common ancestor with other monocots, but there is no obvious synteny between <em>Spirodela</em> and rice mtDNAs. After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly four-fifths of the <em>Spirodela</em> mitochondrial genome is of unknown origin and function. Although it contains a similar chloroplast DNA content and range of RNA editing as other monocots, it is void of nuclear insertions, active gene loss, and comprises large regions of sequences of unknown origin in non-coding regions. Moreover, the lack of synteny with known mitochondrial genomic sequences shed new light on the early evolution of monocot mitochondrial genomes.</p> </div

Comparison of synteny in conserved gene loci of <i>Spirodela</i> and <i>Oryza</i> mitochondrial genomes.

<p>The annotated protein-coding genes were indicated for <i>Spirodela</i> and <i>Oryza</i>. Major conserved regions were bridged by lines. The visualized genome synteny was performed by GSV: a web-based genome synteny viewer <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046747#pone.0046747-Revanna1" target="_blank">[23]</a>.</p

Simultaneous Synthesis and Assembly of Silver Nanoparticles to Three-Demensional Superstructures for Sensitive Surface-Enhanced Raman Spectroscopy Detection

Construction of superstructures with controllable morphologies from NPs is of great scientific and technological importance. A one-step method for simultaneous synthesis and assembly of Ag NPs to three-dimensional (3D) nanoporous superstructures is demonstrated. By varying the adsorption time of Ag precursors, an array of well-defined Ag superstructures with different morphologies are harvested. A “hot spot”-rich substrate for surface-enhanced Raman spectroscopy is established, which exhibits high sensitivity in trace detection of molecules. It is believed that the presented 3D nanoporous Ag superstructures hold great potential for various uses, such as novel multifunctional sensing and monitoring chips or devices

Using a Macroporous Silver Shell to Coat Sulfonic Acid Group-Functionalized Silica Spheres and Their Applications in Catalysis and Surface-Enhanced Raman Scattering

In this paper, novel organic sulfonic acid group-functionalized silica spheres (SiO₂–SO₃H) were chosen as a template for fabricating core–shell SiO₂–SO₃H@Ag composite spheres by the seed-mediated growth method. The SiO₂–SO₃H spheres could be obtained easily by oxidation of the thiol group-terminated silica spheres (SiO₂–SH) with H₂O₂. Due to the presence of sulfonic acid groups, the [Ag­(NH₃)₂]⁺ ions were captured on the surface of the silica spheres, followed by in-site reduction to silver nanoseeds for further growth of the silver shell. By this strategy, the complete silver shell could be obtained, and the surface morphologies and structures of the silver shell could be controlled by adjusting the number of sulfonic acid groups on the silica spheres. A large number of sulfonic acid groups on the SiO₂–SO₃H spheres favored the formation of the macroporous silver shell, which was unique and exhibited good catalytic performance and a high surface-enhanced Raman scattering (SERS) enhancement ability

RNA Editing in Chloroplasts of <i>Spirodela polyrhiza</i>, an Aquatic Monocotelydonous Species

<div><p>RNA editing is the post-transcriptional conversion from C to U before translation, providing a unique feature in the regulation of gene expression. Here, we used a robust and efficient method based on RNA-seq from non-ribosomal total RNA to simultaneously measure chloroplast-gene expression and RNA editing efficiency in the Greater Duckweed, <i>Spirodela polyrhiza</i>, a species that provides a new reference for the phylogenetic studies of monocotyledonous plants. We identified 66 editing sites at the genome-wide level, with an average editing efficiency of 76%. We found that the expression levels of chloroplast genes were relatively constant, but 11 RNA editing sites show significant changes in editing efficiency, when fronds turn into turions. Thus, RNA editing efficiency contributes more to the yield of translatable transcripts than steady state mRNA levels. Comparison of RNA editing sites in coconut, Spirodela, maize, and rice suggests that RNA editing originated from a common ancestor.</p></div