Plastid Genome Comparative and Phylogenetic Analyses of the Key Genera in Fagaceae: Highlighting the Effect of Codon Composition Bias in Phylogenetic Inference

Frontiers in Plant Science

Guifang Zhao¹  Jia Yang¹  Yanci Yang¹  Juan Zhu²  Li Feng³  Tao Zhou³  Guoqing Bai⁴ 

[1] 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;School of Pharmacy, Xi'an Jiaotong University, Xi'an, China;Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Xi'an, China;

关键词: Fagaceae;    plastid genome;    topological incongruence;    codon composition bias;    phylogenomics;   

DOI  :  10.3389/fpls.2018.00082

来源: DOAJ

【 摘 要 】

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 (Fagus engleriana, Quercus spinosa, Quercus aquifolioides, and Quercus glauca) 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.

【 授权许可】

Unknown