Abstract Our main objective was to generate cost-effective chloroplast (cp) DNA markers that are easy to apply and to score. In combination with already published cpSSR markers they should increase haplotype resolution in populations. To discover new cpDNA markers, we sequenced 87-97 % of the entire chloroplast genome (except the second inverted repeat) of 8 trees representing different regions of the Quercus rubra L. natural range with 4,030X-6,297X coverage and assembled the genome sequences using the publicly available chloroplast genome of Quercus rubra L. as a reference. In total, 118 single nucleotide polymorphisms (SNPs) and 107 insertions or deletions (indels) were detected, and 15 cleaved amplified polymorphic sequence (CAPS) markers were developed for Q. rubra. Using these new markers together with five chloroplast microsatellite or simple sequence repeat (cpSSR) markers, we identified 10 haplotypes in our diversity panel of 19 Q. rubra populations. Specifically, two haplotypes based only on the cpSSR markers could now be separated in five haplotypes. These markers are useful to assess haplotype diversity with high resolution and are also transferable to a closely related species, Quercus ellipsoidalis E. J. Hill.

中文翻译：

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用于单倍型鉴定的新型红栎叶绿体基因组 CAPS 标记的开发

摘要 我们的主要目标是生成易于应用和评分的具有成本效益的叶绿体 (cp) DNA 标记。与已发表的 cpSSR 标记相结合，它们应该会增加群体中的单倍型分辨率。为了发现新的 cpDNA 标记，我们对代表红栎自然范围不同区域的 8 棵树的整个叶绿体基因组的 87-97%（除了第二个反向重复）进行了测序，覆盖率为 4,030X-6,297X，并组装了基因组序列使用公开可用的 Quercus rubra L. 叶绿体基因组作为参考。总共检测到 118 个单核苷酸多态性 (SNP) 和 107 个插入或缺失 (indel)，并为 Q. rubra 开发了 15 个切割的扩增多态性序列 (CAPS) 标记。将这些新标记与五个叶绿体微卫星或简单序列重复 (cpSSR) 标记一起使用，我们在 19 个 Q. rubra 种群的多样性面板中确定了 10 个单倍型。具体来说，现在可以将仅基于 cpSSR 标记的两个单倍型分成五个单倍型。这些标记可用于以高分辨率评估单倍型多样性，也可转移到密切相关的物种 Quercus ellipsoidalis EJ Hill。