Abstract
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 FindingsThe 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.ConclusionThe 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.
Highlights
Extant gymnosperms are considered the most ancient group of seed-bearing plants that first appeared approximately 300 million years ago [1]
P. lambertii cp genome size was determined to be 133,734 bp, which is very similar to P. totara (133,259 bp) (NC_020361.1) and larger than the sequenced cp genomes of Pinaceae species, which range from 116,479 bp in Pinus monophylla [14] to 124,168 bp in Picea morrisonicola [31]
P. lambertii cp genome size is smaller than the cp sequences in the cycads Cycas taitungensis (163,403 bp) [32]
Summary
Extant gymnosperms are considered the most ancient group of seed-bearing plants that first appeared approximately 300 million years ago [1] They consist of four major groups, including Gnetophytes, Conifers, Cycads and Ginkgo. P. lambertii is a native species from the Araucaria Forest, a subtropical moist forest ecoregion of the Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots of the world [8]. It is a dioecious evergreen tree of variable height, measuring 1–10 m, shade-tolerant, adapted to high frequency and density of undergrowth [9]. We present the complete cp genome sequence of P. lambertii
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