Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China.
Center for Experimental Teaching, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
Int J Biol Macromol. 2020 Jun 1;152:340-348. doi: 10.1016/j.ijbiomac.2020.02.201. Epub 2020 Feb 25.
The Sawtooth Oak, Quercus acutissima Carruth., is an economically and ecologically important tree species in the family Fagaceae with a wide distribution in China. Here, we examined its intraspecific chloroplast (cp) genome variability using available and a newly sequenced genome. The new cp genome comes from a Q. acutissima individual collected from Shenyang (Northeast China; "Q. acutissima Shenyang" in the following), and then is compared with two recently published cp genomes from Tongchuan (Northwest China) and Nanjing (East China). The cp genome of Q. acutissima Shenyang exhibits a slightly larger genome size than the other two individuals, although each encodes 86 protein-coding genes, 40 tRNA genes and eight rRNA genes. We also found the length difference for the IR/SC boundary region among the three cp genomes. Sequence comparison revealed a high intraspecific genetic divergence: the three cp genomes differ by 332 sequence patterns including 77 single nucleotide polymorphisms, and 255 indels (each gap considered) scattering across 67 regions. Phylogenetic analyses based on the cp genome recovered the split between the subgenus Cerris and the subgenus Quercus, but revealed that three Q. acutissima individuals did not cluster together, indicating that even complete cp genome data fail to reproduce species boundaries in Asian members of section Cerris. Our results show that more complete plastomes covering remote ranges needs to be sequenced to provide a solid backbone for future population-scale in-depth studies and phylogenetic analysis of section Cerris.
锯齿栎（Quercus acutissima Carruth.）是壳斗科（Fagaceae）中一种具有广泛分布且经济和生态重要性的树种。本研究利用已发表和新测序的基因组，研究了其种内叶绿体（cp）基因组的变异性。新的 cp 基因组来自于在中国沈阳采集的一个锯齿栎个体（以下简称“沈阳锯齿栎”），然后与来自中国铜川和南京的两个最近发表的 cp 基因组进行比较。沈阳锯齿栎的 cp 基因组比其他两个个体稍大，尽管每个基因组都编码 86 个蛋白编码基因、40 个 tRNA 基因和 8 个 rRNA 基因。我们还发现了三个 cp 基因组中 IR/SC 边界区域的长度差异。序列比较显示了种内遗传分化很高：三个 cp 基因组在 67 个区域有 332 个序列模式差异，包括 77 个单核苷酸多态性和 255 个插入缺失（每个缺口视为一个）。基于 cp 基因组的系统发育分析恢复了 Cerris 亚属和 Quercus 亚属之间的分裂，但表明三个锯齿栎个体没有聚类在一起，表明即使是完整的 cp 基因组数据也无法重现亚洲 Cerris 节的物种边界。我们的结果表明，需要测序更多完整的质体基因组来覆盖更远的范围，为未来 Cerris 节的种群规模深入研究和系统发育分析提供坚实的基础。
