Identification of DNA molecular markers by comparison of Pinus densiflora and Pinus sylvestris chloroplast genomes
- Published
- Accepted
- Subject Areas
- Genomics, Plant Science
- Keywords
- complete chloroplast genome, DNA molecular marker, Pinus densiflora, SNP, PCR-RFLP, Indels
- Copyright
- © 2018 Kim et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Identification of DNA molecular markers by comparison of Pinus densiflora and Pinus sylvestris chloroplast genomes. PeerJ Preprints 6:e26506v1 https://doi.org/10.7287/peerj.preprints.26506v1
Abstract
Background: Identifying and characterizing genetic variation can clarify the molecular basis of biological phenomena in plants. In particular, related or morphologically similar species can be distinguished by molecular markers. Pinus densiflora Siebold & Zucc. is a species that is distributed in the Korean peninsula, the Japanese archipelago, and China's Shandong and Manchu Provinces and has long been harvested for timber. However, it is difficult to distinguish P. densiflora from Pinus sylvestris L. both morphologically and phylogenetically. The complete chloroplast genome of P. densiflora has not yet been reported. In this study, we sequenced the P. densiflora chloroplast genome in order to identify the molecular markers that can be used to distinguish this species from P. sylvestris.
Methods: Genomic DNA was extracted from P. densiflora samples obtained from the clone bank of the National Forest Seed Variety Center and was sequenced on an Ion Torrent platform. Filtered sequences were assembled with P. sylvestris sequences used as a reference and gene annotation was performed. The chloroplast genome sequences of the two species were aligned and the number and location of forward, reverse, complement and palindromic matches were determined. Single nucleotide polymorphisms (SNPs) and insertion/deletion mutations (Indels) were identified and analyzed by PCR.
Results: The P. densiflora chloroplast genome consisted of circular double-stranded DNA with 119,835 bp compared to 119,758 bp for P. sylvestris. Between the two Pinus chloroplast genomes, we identified 73 SNPs and 171 Indels; two gene regions with amplification products ≤ 300 bp (rpoC1 and trnM-trnV) were validated as molecular markers.
Discussion: PCR restriction fragment length polymorphism analysis revealed differences between P. sylvestris and P. densiflora at the molecular level. These differences can be used to distinguish between these two species, which is not possible by microscopy-based morphological examination.
Author Comment
This is a submission to PeerJ for review.