Yang Yanci, Zhu Juan, Feng Li, Zhou Tao, Bai Guoqing, Yang Jia, Zhao Guifang
Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China.
Middle School of Xi'an Electronic Science and Technology, Xi'an, China.
Front Plant Sci. 2018 Feb 1;9:82. doi: 10.3389/fpls.2018.00082. eCollection 2018.
Fagaceae is one of the largest and economically important taxa within Fagales. Considering the incongruence among inferences from plastid and nuclear genes in the previous Fagaceae phylogeny studies, we assess the performance of plastid phylogenomics in this complex family. We sequenced and assembled four complete plastid genomes (, and ) using reference-guided assembly approach. All of the other 12 published plastid genomes in Fagaceae were retrieved for genomic analyses (including repeats, sequence divergence and codon usage) and phylogenetic inference. The genomic analyses reveal that plastid genomes in Fagaceae are conserved. Comparing the phylogenetic relationships of the key genera in Fagaceae inferred from different codon positions and gene function datasets, we found that the first two codon sites dataset recovered nearly all relationships and received high support. Thus, the result suggested that codon composition bias had great influence on Fagaceae phylogenetic inference. Our study not only provides basic understanding of Fagaceae plastid genomes, but also illuminates the effectiveness of plastid phylogenomics in resolving relationships of this intractable family.
壳斗科是壳斗目中最大且具有重要经济意义的类群之一。鉴于先前壳斗科系统发育研究中质体基因和核基因推断结果不一致，我们评估了质体系统发育基因组学在这个复杂科中的表现。我们采用参考引导组装方法对四个完整的质体基因组（ 、 和 ）进行了测序和组装。检索了壳斗科已发表的其他12个质体基因组用于基因组分析（包括重复序列、序列分歧和密码子使用情况）以及系统发育推断。基因组分析表明壳斗科的质体基因组是保守的。比较从不同密码子位置和基因功能数据集推断出的壳斗科关键属的系统发育关系，我们发现前两个密码子位点数据集恢复了几乎所有关系并获得了高度支持。因此，结果表明密码子组成偏差对壳斗科系统发育推断有很大影响。我们的研究不仅提供了对壳斗科质体基因组的基本认识，还阐明了质体系统发育基因组学在解决这个难处理科的关系方面的有效性。
