Abstract
Research Highlights: The complete chloroplast genome for eight individuals of Japanese larch, including from the isolated population at the northern limit of the range (Manokami larch), revealed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed in Japanese larch. We detected intraspecific variation for possible candidate cpDNA markers in Japanese larch. Background and Objectives: The natural distribution of Japanese larch is limited to the mountainous range in the central part of Honshu Island, Japan, with an isolated northern limit population (Manokami larch). In this study, we determined the phylogenetic position of Manokami larch within Japanese larch, characterized the chloroplast genome of Japanese larch, detected intraspecific variation, and determined candidate cpDNA markers. Materials and Methods: The complete genome sequence was determined for eight individuals, including Manokami larch, in this study. The genetic position of the northern limit population was evaluated using phylogenetic analysis. The chloroplast genome of Japanese larch was characterized by comparison with eight individuals. Furthermore, intraspecific variations were extracted to find candidate cpDNA markers. Results: The phylogenetic tree showed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed, based on the complete chloroplast genome, with a bootstrap value of 100%. The value of nucleotide diversity (π) was calculated at 0.00004, based on SNP sites for Japanese larch, suggesting that sequences had low variation. However, we found three hyper-polymorphic regions within the cpDNA. Finally, we detected 31 intraspecific variations, including 19 single nucleotide polymorphisms, 8 simple sequence repeats, and 4 insertions or deletions. Conclusions: Using a distant genotype in a northern limit population (Manokami larch), we detected sufficient intraspecific variation for the possible candidates of cpDNA markers in Japanese larch.
Highlights
The chloroplast genome is highly conserved and has a much lower mutation rate than the nuclear genome [1]
Japanese larch is genetically close to L. decidua and L. gmelinii, but distant from L. sibirica and L. potaninii (Figure 1)
The chloroplast structure types were classified in Pinaceae according to their alignment order and the orientation of the F1, F2, T1, and T2 fragments in the large single-copy region (LSC) region, which can produce eight different Chloroplast DNA (cpDNA)
Summary
The chloroplast genome is highly conserved and has a much lower mutation rate than the nuclear genome [1]. Chloroplast DNA (cpDNA) has been widely used to clarify interspecific relationships, and to evaluate the magnitude of intraspecific variation [2,3]. The cpDNA of gymnosperms, of the conifers, is characterized by high levels of intraspecific variation [4,5] and paternal inheritance [6]. The chloroplast genome has a circular molecular structure, with a length ranging from 120 to 160 kbp in most plants. IRs are a crucial feature of the chloroplast genome in most plants, likely contributing to the maintenance of a conserved arrangement of cpDNA sequences. Previous studies have reported that the length of observed short IRs is roughly consistent among gymnosperm species [9]. Intraspecific variation in whole chloroplast genomes derived from multiple individuals can clarify the phylogenic lineage of target individuals [11]. Single nucleotide polymorphisms (SNPs) have been efficiently used in the fields of phylogeography and conservation biology [12]
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