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

Yanci Yang,Li Feng,Jia Yang,Tao Zhou,Guoqing Bai,Juan Zhu,Guifang Zhao

doi:10.3389/fpls.2018.00082

Abstract

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.

Highlights

Due to the rapid development of next-generation sequencing (NGS) technology, genomic data have been increasingly used to explore plant phylogeny
Considering the performances of the few molecular markers in Fagaceae phylogenetic inferences and the ability of plastid phylogenomics in the earlier studies, we explore whether plastid genome-scale data have the ability to infer strongly supported phylogenetic relationships for Fagaceae, especially for the monophyletic genus Quercus
The size, gene content and gene order are similar among the plastid genomes, which reveal that plastid genomes are highly conserved in Fagaceae

Summary

Introduction

Due to the rapid development of next-generation sequencing (NGS) technology, genomic data have been increasingly used to explore plant phylogeny. With respect to genomic complexity, sequencing cost, analysis methods and the degree of recombination of different genomes (organelle genomes and nuclear genome), the plastid genome presents obvious advantages (e.g., generally recombination-free, uniparental inheritance, highly conserved structure) (Birky et al, 1983; Jansen and Ruhlman, 2012). The structure of the plastid genome is generally highly conserved, different levels of genomic upheaval (such as gene or IR losses, largescale rearrangements) have been detected in Campanulaceae, Fabaceae, Geraniaceae, Oleaceae and many other families (Cosner et al, 2004; Lee et al, 2007; Cai et al, 2008; Guisinger et al, 2010, 2011; Martin et al, 2014)

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