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Background    Podocarpus lambertii  (Podocarpaceae) is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp) genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of  P. lambertii .    Methodology/Principal Findings  The  P. lambertii  cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR). It contains 118 unique genes and one duplicated tRNA ( trnN -GUU), which occurs as an inverted repeat sequence. The  rps16  gene was not found, which was previously reported for the plastid genome of another Podocarpaceae ( Nageia nagi ) and Araucariaceae ( Agathis dammara ). Structurally,  P. lambertii  shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the  Podocarpus totara  cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The  P. lambertii  cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency.    Conclusion  The complete cp genome sequence of  P. lambertii  revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the  P. lambertii  cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of this genus.

The Complete Chloroplast Genome Sequence of Podocarpus lambertii: Genome Structure, Evolutionary Aspects, Gene Content and SSR Detection