Abstract
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.
Highlights
General features of the W. nobilis chloroplast genome
In the gymnosperm families Cycadaceae, Ephedraceae and Ginkgoaceae, protein-coding genes are duplicated in the inverted repeat regions (IR)
Wollemia is a monotypic genus, we observe a close similarity between the chloroplast genomes of A. dammara and W. nobilis in terms of genome size, organisation and sequence
Summary
W. nobilis is similar to fossil pines from the Cretaceous period (approximately 140 million years ago) and relatives of Wollemia were once widespread [2,3], but the living population consists of fewer than 100 individuals confined to a single canyon system. This critically endangered species belongs to the Araucariaceae, a conifer family containing 30 species and three extant genera (Agathis, Araucaria, Wollemia) [4,5,6,7]. Coppicing can occur in Agathis and Araucaria in response to trauma, but only Wollemia grows regularly in this manner
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