Genetic variation in central and peripheral populations of <i>O</i>. <i>rufipogon</i> across six microsatellite loci ^a.

Genetic variation in central and peripheral populations of O. rufipogon across six microsatellite loci a.</p

Lowered Diversity and Increased Inbreeding Depression within Peripheral Populations of Wild Rice <i>Oryza rufipogon</i> - Fig 2

Relationship between logarithm of population size and microsatellite diversity: allelic richness (a), and gene diversity (b). solid squares indicate the peripheral populations, while others are central populations.</p

Comparisons of population genetic parameters between maternal and seed samples from peripheral and central populations of <i>O</i>. <i>rufipogon</i> as detected by six microsatellite loci ^a.

Comparisons of population genetic parameters between maternal and seed samples from peripheral and central populations of O. rufipogon as detected by six microsatellite loci a.</p

Differences of <i>F</i>-statistics ^a between peripheral and central populations in <i>O</i>. <i>rufipogon</i> as detected by six microsatellite loci.

Differences of F-statistics a between peripheral and central populations in O. rufipogon as detected by six microsatellite loci.</p

Population codes, geographical origins and sample sizes of the 21 studied populations of <i>O</i>. <i>rufipogon</i>.

<p>Population codes, geographical origins and sample sizes of the 21 studied populations of <i>O</i>. <i>rufipogon</i>.</p

Allelic richness in central and peripheral populations of <i>O</i>. <i>rufipogon</i> across six microsatellite loci using rarefaction method.

<p>Allelic richness in central and peripheral populations of <i>O</i>. <i>rufipogon</i> across six microsatellite loci using rarefaction method.</p

Analysis of molecular variance (amova) to assess geographical partition between central and peripheral groups for 525 individual plants from 21 populations of <i>O</i>. <i>rufipogon</i> using six microsatellite loci.

<p>Analysis of molecular variance (amova) to assess geographical partition between central and peripheral groups for 525 individual plants from 21 populations of <i>O</i>. <i>rufipogon</i> using six microsatellite loci.</p

Gene map of the <i>P</i><i>. utilis</i> chloroplast genome.

<p>Genes lying outside of the outer circle are transcribed in the clockwise direction whereas genes inside are transcribed in the counterclockwise direction. Genes belonging to different functional groups are color coded. Area dashed darker gray in the inner circle indicates GC content while the lighter gray corresponds to AT content of the genome.</p

Plastid Genome Sequence of a Wild Woody Oil Species, <i>Prinsepia</i><i> utilis</i>, Provides Insights into Evolutionary and Mutational Patterns of Rosaceae Chloroplast Genomes

<div><p>Background</p><p><i>Prinsepia</i><i>utilis</i> Royle is a wild woody oil species of Rosaceae that yields edible oil which has been proved to possess particular benefits for human health and medical therapy. However, the lack of bred varieties has largely impeded exploiting immense potentials for high quality of its seed oil. It is urgently needed to enlarge the knowledge of genetic basis of the species and develop genetic markers to enhance modern breeding programs.</p> <p>Results</p><p>Here we reported the complete chloroplast (cp) genome of 156,328 bp. Comparative cp sequence analyses of <i>P</i><i>. utilis</i> along with other four Rosaceae species resulted in similar genome structures, gene orders, and gene contents. Contraction/expansion of inverted repeat regions (IRs) explained part of the length variation in the Rosaceae cp genomes. Genome sequence alignments revealed that nucleotide diversity was associated with AT content, and large single copy regions (LSC) and small single copy regions (SSC) harbored higher sequence variations in both coding and non-coding regions than IRs. Simple sequence repeats (SSRs) were detected in the <i>P</i><i>. utilis</i> and compared with those of the other four Rosaceae cp genomes. Almost all the SSR loci were composed of A or T, therefore it might contribute to the A-T richness of cp genomes and be associated with AT biased sequence variation. Among all the protein-coding genes, <i>ycf1</i> showed the highest sequence divergence, indicating that it could accomplish the discrimination of species within Rosaceae as well as within angiosperms better than other genes.</p> <p>Conclusions</p><p>With the addition of this new sequenced cp genome, high nucleotide substitution rate and abundant deletions/insertions were observed, suggesting a greater genomic dynamics than previously explored in Rosaceae. The availability of the complete cp genome of <i>P</i><i>. utilis</i> will provide chloroplast markers and genetic information to better enhance the conservation and utilization of this woody oil plant.</p> </div

Detailed view of the IR junctions among the five Rosaceae chloroplast genomes.

<p>Annotated genes or portions of genes are indicated by yellow boxes above or below the genome.</p