Characterization of the complete chloroplast genome of <i>Abies sachalinensis</i> and its intraspecific variation hotspots

<i>Abies sachalinensis</i> 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 <i>A. sachalinensis</i> 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 <i>A. sachalinensis</i>.

萨哈林冷杉（Abies sachalinensis）是日本北海道地区的主要针叶树种，兼具生态与经济价值。本研究首次报道了萨哈林冷杉的完整叶绿体（cp）基因组序列，并鉴定了其种内基因组变异。研究采集了来自北海道三个地理隔离生境的植物样本：东部边缘区域、西部区域以及高海拔地带。通过高通量测序技术对富集得到的叶绿体DNA（cpDNA）进行完整序列组装，并鉴定叶绿体基因组中的变异位点。结果显示，完整环状叶绿体基因组序列的长度介于121265 bp至121337 bp之间。此外，本研究共鉴定到94个基因组变异位点，其中包括52个单核苷酸多态性位点（SNP，占比55%）、9个插入/缺失位点（In/Del，占比10%）以及33个简单序列重复位点（SSR，占比35%）。平均核苷酸多样性为0.00029，共鉴定出3个SNP热点区域。本研究所报道的全叶绿体DNA变异特征，将为未来萨哈林冷杉的系统发育研究提供重要参考价值。

搜集汇总

背景与挑战

背景概述

该数据集首次报道了日本北海道主要针叶树种“Abies sachalinensis”的完整叶绿体基因组序列，并识别了其种内基因组变异。研究基于三个地理分离的样本，通过高通量测序揭示了基因组长度范围（121,265-121,337 bp）、94个变异位点（包括SNP、In/Del和SSR）以及三个SNP热点区域，为未来该物种的系统发育研究提供了宝贵数据。