Populus-aligned plastome sequence alignments

WGS short reads were aligned to the Nisqually-1 chloroplast reference genome (GenBank: EF489041.1) using BWA version 0.6.2. For each position in the reference plastome, bases were called only if the coverage was greater than 1000 reads, as the average read depth for each base pair was 7000 or greater. To improve accuracy, bases were only called if the 1000+ calls agreed for either the reference or alternate base for at least 80% of the reads. Any position not meeting these criteria was called as missing data. Indels were excluded for all analyses.

将全基因组测序（Whole Genome Sequencing, WGS）短读段比对至Nisqually-1株的叶绿体参考基因组（GenBank：EF489041.1），比对工具采用BWA版本0.6.2。针对参考质体基因组的每个位点，仅当该位点的测序覆盖度大于1000条读段时方可进行碱基调用，因每个碱基对的平均测序深度可达7000及以上。为提升碱基调用的准确性，仅当1000条以上的读段中至少80%一致支持参考碱基或变异碱基时，方可完成碱基调用。未满足上述任一标准的位点均记为缺失数据。所有分析均排除插入缺失（indels）位点。