The Chloroplast Genomes Of Four Quercus Species (Q.Wutaishanica,Q.Mongolica,Q.Dentata And Q.Fenchengensis)

Oaks(Quercus)are the main dietary plant for Chinese oak silkworm(Antheraea pernyi),and have important values in economic,ecological,cultural and scientific research.There are 450 species of oak trees,widely distributed in Asia,Europe,North America,and Africa in the northern hemisphere.Extensive crosses between species have caused many common morphological characteristics and intraspecific morphological variations,thus resulting in great difficulty in classifying this genus.Botanists have been studying the classification and evolution of this genus for a long time.The chloroplast genome sequence is highly conserved,making it an ideal marker for phylogenetic study of plants.So far,only 25 complete chloroplast genomes(including 4 determined in this study)are available in the public database for oak trees.New chloroplast genomes from known oak species and/or individuals from different regions would be helpful for understanding the classification and evolution of Quercus.In this study,the chloroplast genomes of four oak species including Q.wutaishanica,Q.mongolica,Q.dentata,and Q.fenchengensis of Section Quercus that were used as the dietary plant for A.pernyi were determined using Illumina nextgeneration sequencing technology.The four oaks are the dietary plants for Chinese oak silkworm in North China.The structural features of four chloroplast genomes were comparatively analyzed,and their phylogenetic relationships were reconstructed,together with the published chloroplast genomes of other Quercus species.The main results are as follows:1.The full chloroplast genomes of four Quercus species(Q.wutaishanica,Q.mongolica,Q.dentata,and Q.fenchengensis)were obtained for the first time.The chloroplast genomes of four oaks are 161,194-161,296 bp in size,and exhibit the quadripartite circular structure,including a large single copy region(LSC;90,504-90,584 bp),a small single copy region(SSC;19,036-19,058 bp),and a pair of inverted repeat regions(IRA and IRB;25,827-25,822 bp).All the four chloroplast genomes encode 134 functional genes,including 86 protein-coding genes,40 t RNA,and 8 r RNA genes.The GC content of four chloroplast genomes is highly similar,with the value of 36.8%,and their codons favor A and T,especially the second and third codons.Note that the chloroplast genome of Q.fengchengensis is identical to that of Q.wutaishanica,which is not in line with the morphological differences between them.2.The structural features of four chloroplast genomes were compared.The four chloroplast genomes are highly conserved,and the IR region exhibits more conservative than the LSC/SSC region.Comparison of the region boundaries showed that only the ycf1 gene in the IRB region and the SSC region changed.Analysis of the coding region and non-coding region of the nucleotide polymorphism(Pi)identified two regions with high variability,one in therbc L-acc D spacer(Pi = 0.01813)and the other in the gene acc D(Pi = 0.01875).All the four chloroplast genomes contain a large number of repeat sequences and simple sequence repeats(SSR).3.The phylogenetic relationships of four oaks were reconstructed based on chloroplast genome data.Based on the available 21 chloroplast genomes of oaks,two data sets(full chloroplast genome sequence and 77 common protein-coding gene sequences)and two treebuilt methods(maximum likelihood method and Bayesian statistical inference)were used to infer the phylogenetic relationships of four oaks.Four topologies obtained are generally consistent,with higher confidence support.In the phylogenetic tree,oak tree is divided into two clades,the sub-genus Quercus and the sub-genus Cerris.Quercus and Lobatae groups belong to the sub-genus Quercus,while Cyclobalanopsis,Ilex,and Cerris groups belong to the subgenus Cerris.Our study at the molecular level confirmed that the four oak species belonged to the Quercus group,and the phylogenetic relationship was((Q.wutaishanica/ Q.fenchengensis + Q.mongolica)+ Q.dentata).