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

Authors :
Yanci Yang
Juan Zhu
Li Feng
Tao Zhou
Guoqing Bai
Jia Yang
Guifang Zhao
Source :
Frontiers in Plant Science, Vol 9 (2018), Frontiers in Plant Science
Publication Year :
2018
Publisher :
Frontiers Media S.A., 2018.

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.

Details

Language :
English
Volume :
9
Database :
OpenAIRE
Journal :
Frontiers in Plant Science
Accession number :
edsair.doi.dedup.....aebab163c600cd53ddb7d643fdec0438
Full Text :
https://doi.org/10.3389/fpls.2018.00082/full