Ear phenotype of <i>P6z1RNAi/-</i> x IRLP (A) and <i>P6z1RNAi/-</i> x IHP (B).

<p>Vitreous and opaque kernels segregate as 1∶1 ratio in both crosses. Two representative kernels for each phenotype are indicated by white and black arrows, respectively.</p

Protein and amino acid composition analysis of seeds with genotype IHP/-; -/-, IHP/-; P6z1RNAi/-, IRLP/-; -/-, IRLP/-; P6z1RNAi/- and W64Ao2.

<p>AA_ab, absolute level of amino acid calculated by percentage of AA in total cornmeal; AA_rel, relative level of amino acid calculated by percentage of AA in total protein.</p

Protein and amino acid composition analysis of four Illinois Protein Strains (IHP, IRHP, ILP and IRLP) and B73.

<p>AA_ab, absolute level of amino acid calculated by percentage of AA in total cornmeal; AA_rel, relative level of amino acid calculated by percentage of AA in total protein.</p

Kernel phenotype and protein accumulation pattern of Illinois Protein Strains.

<p>(A) Kernel translucency and vitreousness of IHP, IRHP, ILP and IRLP. (B) Zein and non-zein accumulation pattern of B73, IHP, IRHP, ILP and IRLP analyzed by 15% SDS-PAGE. Protein from 500 µg of maize flour was loaded in each lane. M, protein markers from top to bottom being 250, 150, 100, 75, 50, 37, 25, 20, 15 and 10 kDa. The size of each zein band is indicated with numbers in the “kDa” column.</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

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

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

Pipeline of mitochondrial genome assembly.

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