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
Yanci YangGuifang Zhao

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, andQuercus 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 intr...Continue Reading

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Citations

Apr 13, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Xia LiuBoyang Zhou
Aug 22, 2018·International Journal of Molecular Sciences·Xuan LiYanming Fang
Aug 30, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Xiao ZhangGuifang Zhao
Jun 5, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Hai-Ying LiuSong-Dong Zhou

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Datasets Mentioned

BETA
KX852398

Software Mentioned

MEGA
Tandem Repeats Finder ( TRF )
GENEIOUS
Modeltest
DOGMA
MrBayes
RAxML
REPuter
MIRA
MAFFT

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