Abstract
Pinus densiflora (Korean red pine) is widely distributed in East Asia and considered one of the most important species in Korea. In this study, the complete chloroplast genome of P. densiflora was sequenced by combining the advantages of Oxford Nanopore MinION and Illumina MiSeq. The sequenced genome was then compared with that of a previously published conifer plastome. The chloroplast genome was found to be circular and comprised of a quadripartite structure, including 113 genes encoding 73 proteins, 36 tRNAs and 4 rRNAs. It had short inverted repeat regions and lacked ndh gene family genes, which is consistent with other Pinaceae species. The gene content of P. densiflora was found to be most similar to that of P. sylvestris. The newly attempted sequencing method could be considered an alternative method for obtaining accurate genetic information, and the chloroplast genome sequence of P. densiflora revealed in this study can be used in the phylogenetic analysis of Pinus species.
Highlights
Pinaceae is the largest gymnosperm family, consisting of 10 genera and more than 230 species.Most of Pinaceae species are classified as forest and timber species, and they are mainly distributed in the northern hemisphere [1]
The complete chloroplast genome of Pinus densiflora was sequenced using an Oxford Nanopore MinION (ONM) sequencer and error corrected by Illumina MiSeq short reads
After mapping the ONM reads of the completed chloroplast genome sequence, the sequencing error rate for each base position was calculated to be about 9.29% (Figure S3)
Summary
Pinaceae is the largest gymnosperm family, consisting of 10 genera and more than 230 species.Most of Pinaceae species are classified as forest and timber species, and they are mainly distributed in the northern hemisphere [1]. Pinus densiflora Siebold & Zucc., called Korean red pine, is a species widely distributed in East Asia, including the Korean Peninsula, Japan and China [2]. This species occupies more than 23% of forest land in South Korea, and is the most important and popular coniferous species in Korea [3]. The chloroplast genome is a valuable resource in molecular phylogenetic studies [4,5]. It usually exhibits uniparental inheritance and contains conserved sequences as a result of its slower evolutionary rate of change compared to nuclear genomes. Most land plants have 110–130 genes in their chloroplast genome [8]
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