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

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.

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

“…Higher nucleotide diversity has been found in SCs compared with IRs and in noncoding regions compared with coding regions, which is in accordance with the results found for other taxa [43][44][45]63,68], although exceptions have been identified [32,69]. A cp genome has a copy-dependent repair mechanism that ensures the uniformity and stability of two IR regions in sequence and enhances the stability and conservation of the genome [70,71], which might explain the lower sequence divergence in the IRs compared with the LSC or SSC regions, because natural selection coding regions are more conserved than non-coding regions [72].…”

“…Q. bawanglingensis and Q. tarokoensis have a close relationship, and in accordance with their morphological features, both of these species belong to section Engleriana in group Ilex [73,100]. Importantly, the Quercus species were not shown to form a clade, similar to the findings in other research [44][45][46]. Group Ilex within group Cerris forms a Cerris-Ilex clade, which is identified by inferences from primarily chloroplast haplotypes between group Cerris and its sister group, Ilex [39].…”

“…In general, the complete cp genome of Q. bawanglingensis has a strong resemblance to those of other Quercus species in the aspects of genome size and structure, GC content, genes and gene order, which illustrates that the cp genomes are conserved in Quercus [43][44][45]62,63]. Nonetheless, changes in the border of LSC/IRb and the nucleotide variability were detected, which are relatively common in plants [15,46,64].…”

“…Thus, a high-resolution and supported molecular phylogenetic tree is necessary. Obtaining cp genome information is necessary due to the lack of data on Q. bawanglingensis, and the importance and availability of information on the plastid genomes of oaks for detailed comparisons are increasing [40,[43][44][45][46]. Polymorphic chloroplast microsatellite markers designed based on a cp genome analysis can be utilised to comprehend the levels and patterns of the geographical structure and genetic diversity of Q. bawanglingensis, and this information can subsequently be used formulate an effective protection strategy.…”

Complete chloroplast genome of Fagus multinervis, a beech species endemic to Ulleung Island in South Korea

“…This genomic DNA was sequenced with the Illumina MiSeq platform (Macrogen, Seoul, Korea). The 10,007,240 paired reads were then assembled using the cp of F. engleriana from China as our reference genome (GenBank: KX852398) (Yang et al 2018). For the draft genome, we employed Sanger sequencing to validate four junctions between the large single copy (LSC) region, small single copy (SSC) region, and two inverted repeats (IRs), and regions showing low coverage (<100).…”