MAUVE alignment of <i>W</i>. <i>nobilis</i> and <i>A</i>. <i>dammara</i> chloroplast genomes.

<p>The <i>W</i>. <i>nobilis</i> genome is shown at top as the reference genome. Within each of the alignments, local collinear blocks are represented by blocks of the same colour connected by lines. Note that the two LCBs in the <i>A</i>. <i>dammara</i> genome are both inverted relative to the <i>W</i>. <i>nobilis</i> genome.</p

Comparison of chloroplast genome characteristics in different species of Araucariaceae and Podocarpaceae.

<p>^<i>A</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128126#pone.0128126.ref025" target="_blank">25</a>]</p><p>^<i>B</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128126#pone.0128126.ref023" target="_blank">23</a>]</p><p>^<i>C</i> In parentheses is the value observed after these published chloroplast genomes were re-annotated using tRNAscan-SE [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128126#pone.0128126.ref039" target="_blank">39</a>] and reference to the <i>Cedrus deodara</i> (NC_014575) plastome.</p><p>Comparison of chloroplast genome characteristics in different species of Araucariaceae and Podocarpaceae.</p

Characteristics of simple sequence repeats identified in the chloroplast genomes of <i>W</i>. <i>nobilis</i>, <i>A</i>. <i>dammara</i> and <i>P</i>. <i>lambertii</i>.

<p>Characteristics of simple sequence repeats identified in the chloroplast genomes of <i>W</i>. <i>nobilis</i>, <i>A</i>. <i>dammara</i> and <i>P</i>. <i>lambertii</i>.</p

Sequence map of the <i>Wollemia nobilis</i> chloroplast genome.

<p>Genes drawn outside of the circle are transcribed clockwise, while genes shown on the inside of the circle are transcribed counter-clockwise. Genes belonging to different functional groups are colour-coded. The darker gray in the inner circle indicates GC content, while the lighter gray corresponds to AT content.</p

Distribution of tandem repeats in the <i>W</i>. <i>nobilis</i> chloroplast genome.

<p>Distribution of tandem repeats in the <i>W</i>. <i>nobilis</i> chloroplast genome.</p

Complete Chloroplast Genome of the Wollemi Pine (Wollemia nobilis): Structure and Evolution

The Wollemi pine (Wollemia nobilis) is a rare Southern conifer with striking morphological similarity to fossil pines. A small population of W. nobilis was discovered in 1994 in a remote canyon system in the Wollemi National Park (near Sydney, Australia). This population contains fewer than 100 individuals and is critically endangered. Previous genetic studies of the Wollemi pine have investigated its evolutionary relationship with other pines in the family Araucariaceae, and have suggested that the Wollemi pine genome contains little or no variation. However, these studies were performed prior to the widespread use of genome sequencing, and their conclusions were based on a limited fraction of the Wollemi pine genome. In this study, we address this problem by determining the entire sequence of the W. nobilis chloroplast genome. A detailed analysis of the structure of the genome is presented, and the evolution of the genome is inferred by comparison with the chloroplast sequences of other members of the Araucariaceae and the related family Podocarpaceae. Pairwise alignments of whole genome sequences, and the presence of unique pseudogenes, gene duplications and insertions in W. nobilis and Araucariaceae, indicate that the W. nobilis chloroplast genome is most similar to that of its sister taxon Agathis. However, the W. nobilis genome contains an unusually high number of repetitive sequences, and these could be used in future studies to investigate and conserve any remnant genetic diversity in the Wollemi pine