A high level of chloroplast genome sequence variability in the Sawtooth Oak Quercus acutissima
A high level of chloroplast genome sequence variability in the Sawtooth Oak Quercus acutissima
复制标题
锯齿橡栎叶绿体基因组序列的高水平变异
DOI：
10.1016/j.ijbiomac.2020.02.201
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发表时间：
2020-06-01
影响因子：
8.2
通讯作者：
Qin, Li
中科院分区：
文献类型：
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作者：
Zhang, Ru-Song;Yang, Jian;Qin, Li
锯齿橡树，麻栎，是壳斗科重要的经济和生态树种，在我国分布广泛。在这里，我们研究了其种内叶绿体（cp）基因组变异使用现有的和一个新测序的基因组。新的cp基因组来自Q. acutissima个体; acutissima Shenyang），并与最近发表的铜川（中国西北地区）和南京（中国东部地区）的cp基因组进行了比较。对Q. aculissima Shenyang的基因组大小略大于其他两个个体，但每个个体编码86个蛋白质编码基因、40个tRNA基因和8个rRNA基因。我们还发现了三个cp基因组之间的IR/SC边界区域的长度差异。序列比较显示了高的种内遗传分化：三个CP基因组不同的332个序列模式，包括77个单核苷酸多态性，和255个indel（每个缺口考虑）分散在67个区域。基于cp基因组的系统发育分析恢复了鱼藤亚属和栎亚属的分离，但发现3个Q。acutissima个体没有聚集在一起，表明即使是完整的cp基因组数据未能再现亚洲成员的种间界限。我们的研究结果表明，更完整的塑性体覆盖远程范围需要进行测序，为未来的populationscale的深入研究和系统发育分析的一个坚实的骨干。(C)2020由Elsevier B. V.出版
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. aculissima 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 populationscale in-depth studies and phylogenetic analysis of section Cerris. (C) 2020 Published by Elsevier B.V.