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Abies sachalinensis  is a major coniferous species in Hokkaido, Japan, with both ecological and economic importance. This study is the first to report the complete chloroplast (cp) genome sequence of  A. sachalinensis  and to identify its intraspecific genomic variants. Plant samples were collected from three geographically separated origins (the eastern margin, western region, and high-altitude zone of Hokkaido). High-throughput sequencing was used to reconstruct the complete sequences from enriched cpDNAs and to identify variations in the cp genome. The length of the complete circular cp genome sequence was found to range from 121,265 to 121,337 bp. Furthermore, 94 genomic variants were detected, which were composed of 52 single nucleotide polymorphism sites (SNP; 55%), nine insertion/deletion sites (In/Del; 10%), and 33 simple sequence repeat sites (SSR; 35%). Nucleotide diversity was 0.00029 on average, representing three SNP hotspot regions. The characterization of the cpDNA-wide variation reported in this study will be valuable for future phylogenetic studies of  A. sachalinensis .

Characterization of the complete chloroplast genome of Abies sachalinensis and its intraspecific variation hotspots