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Molecular identification of plant species may be highly related to the geographic isolation and speciation stages among species. In this study, we examined these possibilities in a group of white pines in China. We sampled 449 individuals from 60 natural populations of seven species from sect. Quinquefoliae subsect. Strobus. We sequenced four chloroplast DNA regions (around 3100 bp in length) and two mitochondrial DNAs (around 1000 bp in length). We identified 21 chlorotypes and 10 mitotypes. Both chlorotypes and mitotypes recovered from four species with long disjunction and restricted distributions in northern or northwestern China, Pinus sibirica, Pinus koraiensis, Pinus wallichiana and Pinus pumila are species-specific, suggesting that these cytoplasmic DNAs can distinguish them from the close relatives. Allopatric isolations should have contributed greatly to their genetic divergences. However, both chlorotypes and mitotypes recovered for Pinus dabeshanensis and Pinus fenzeliana distributed in southeastern and southern China are shared or closely related to those found in the widely distributed Pinus armandii. These two species may have diverged or derived from P. armandii recently. All of our findings together suggest that the discrimination power of the molecular identifications based on the cytoplasmic DNA barcodes may show variable discriminability depending on geographic isolation and speciation stages among the sampled species.

The complete nucleotide sequence of the Taiwan red pine Pinus taiwanensis Hayata chloroplast genome (cpDNA) is determined in this study. The genome is composed of 119,741 bp in length, containing a pair of very short inverted repeat (IRa and IRb) regions of 495 bp, which was divided by a large single-copy (LSC) region of 65,670 bp and a small single-copy (SSC) region of 53,080 bp in length. The cpDNA contained 115 genes, including 74 protein-coding genes (73 PCG species), 4 ribosomal RNA genes (four rRNA species) and 37 tRNA genes (22 tRNA species). Out of these genes, 12 harbored a single intron, and one (rps12) contained a couple of introns. The overall AT content of the Taiwan red pine cpDNA is 61.5%, while the corresponding values of the LSC, SSC and IR regions are 62.2%, 60.6% and 63.6%, respectively. A maximum parsimony phylogenetic analysis suggested that the genus Pinus, Picea, Abies and Larix were strongly supported as monophyletic, and the cpDNA of P. taiwanensis is closely related to that of P. thunbergii.

The complete chloroplast genome (cpDNA) sequence of an endemic conifer species, Armand pine Pinus armandii Franch., is determined in this study. The cpDNA was 117,265 bp in length, containing a pair of 475 bp inverted repeat (IR) regions those distinguished in large and small single copy (LSC and SSC) regions of 64,548 and 51,767 bp in length, respectively. The cpDNA contained 114 genes, including 74 protein-coding genes (74 PCG species), 4 ribosomal RNA genes (four rRNA species) and 36 transfer RNA genes (33 tRNA species). Out of these genes, 12 harbor a single intron and most of the genes occurred in a single copy. The overall AT content of the Armand pine cpDNA was 61.2%, while the corresponding values of the LSC, SSC and IR regions were 62.0%, 60.2% and 62.7%, respectively. A phylogenetic analysis revealed that P. armandii chloroplast genome is closely related to that of the P. koraiensis within the genus Pinus.