The chloroplast genome (CPG) of Pinus massoniana belonging to the genus Pinus (Pinaceae), which is a primary source of turpentine, was sequenced and analyzed in terms of gene rearrangements, ndh genes loss, and the contraction and expansion of short inverted repeats (IRs). P. massoniana CPG has a typical quadripartite structure that includes large single copy (LSC) (65,563 bp), small single copy (SSC) (53,230 bp) and two IRs (IRa and IRb, 485 bp). The 108 unique genes were identified, including 73 protein-coding genes, 31 tRNAs, and 4 rRNAs. Most of the 81 simple sequence repeats (SSRs) identified in CPG were mononucleotides motifs of A/T types and located in non-coding regions. Comparisons with related species revealed an inversion (21,556 bp) in the LSC region; P. massoniana CPG lacks all 11 intact ndh genes (four ndh genes lost completely; the five remained truncated as pseudogenes; and the other two ndh genes remain as pseudogenes because of short insertions or deletions). A pair of short IRs was found instead of large IRs, and size variations among pine species were observed, which resulted from short insertions or deletions and non-synchronized variations between “IRa” and “IRb”. The results of phylogenetic analyses based on whole CPG sequences of 16 conifers indicated that the whole CPG sequences could be used as a powerful tool in phylogenetic analyses.

Ginkgo biloba L. is a well-known relict tree species and an important medicinal plant. Ginkgo is rich in secondary metabolites (SMs), mainly including flavonoids, lactones, and ginkgolic acid. The aim of this study was to determine variations in the concentrations of these SMs in Ginkgo leaves from different geographical populations. The SMs in the leaves of 298 clones from 10 geographical populations grafted under the same conditions were extracted and measured by high performance liquid chromatography (HPLC). The results showed that there were significant differences in concentrations of SMs in leaves from different populations (p < 0.01). The concentrations of both flavonoids and lactones were significantly negatively correlated with that of ginkgolic acid. Altitude and annual rainfall were important factors influencing the concentrations of lactones, and the frost-free period influenced the concentration of isorhamnetin. Population Yingdianjie (YDJ) was ideal for the plantations from which medicinal flavonoids and lactones are extracted, followed by populations Xiaopu (XP), Anlu (AL) and Wuchuan (WC). As variations within each population were found, attention should be paid to selection within populations.