Comparation Of Chloroplast Genomes Of Different Leaf Habit Oak Species

Quercus contains about 500 species,which are important ecological species in the northern Hemisphere.Phenotypic similarity,reticulated evolution and frequent hybridization make the Quercus phylogeny studies full of challenges.Previous oak phylogenetic studies in East Asia either included section Quercus,section Ilex and section Cerris or only included section Cyclobalanopsis,and there was no phylogenetic studies including all the four sections in China.Different environments may have resulted in different adaptive evolution strategies in Quercus,such as two different leaf habits: evergreens and deciduous.The different habitat types and adaptation patterns of the Quercus groups make them ideal models to understand the role of natural selection in driving the evolution of chloroplast genome and identify key genes for the adaptive evolution of closely related species.In this study,high-throughput sequencing technology were used to sequence and assemble there chloroplast genome in 14 oak species of China: Seven evergreen oaks: Quercus semecarpifolia Smith,Quercus senescens Hand.-Mazz,Quercus baronii Skan,Quercus cocciferoides Hand.-Mazz,Quercus rehderiana Handel-Mazzetti,Quercus monimotricha Hand.-Mazz,and Quercus engleriana Seem;Seven deciduous oaks: Quercus serrata Murray,Quercus serrata var.brevipetiolata,Quercus yunnanensis Franchet,Quercus griffithii Hook.f.et Thoms.ex Miquel,Quercus stewardii Rehd,Quercus fabri Hance and Quercus mongolica Fischer ex Ledebour.Comparative analyses were conducted combining with other three plastid genomes obtained in our laboratory: Quercus aquifolioides Rehd.et Wils,Quercus spinosa David ex Franchet and Quercus aliena Blume.The results showed that lengths of these chloroplast genomes were rangeing from 160,415 bp to 161,415 bp,with a typical tetrad structure with small changes in CG content.Each chloroplast genome contains 86 proteincoding genes,40 transfer RNA genes and 4 ribosomal RNA genes.Repeat analysis showed that the number and distribution of various repeats in the chloroplast genomes of 17 oak species were conserved.Comparative analysis revealed that the single copy region(SC)region contained more loci with high nucleotide variation(Pi)values than that of the inverted repeat(IR)region.The phylogenetic tree constructed by the maximum likelihood method(ML),the neighbor-joining method(NJ)and the Bayesian method(BI)based on the whole choloroplast genomes and shared protein-coding genes of the selected 34 species showed almost the same topological structures.Consistent with the previous classification system for Quercus plants based on nuclear markers,34 Quercus species in East Asia were divided into two subgenres(subgenus Quercus,subgenus Cerris)and 4 groups(Sect.Quercus,Sect.Ilex,Sect.Cerris,Sect.Cyclobalanopsis).Manually screened out the 72 homologous genes of 34 East Asian oaks(including all of the four groups,with 18 evergreen oaks and 16 deciduous oaks),and used Codeml program in PAML to detect each homologous genes for positive selection analysis.In order to improve the accuracy of the results,we use both the site model and branch-site model.The two models simultaneously detect out the adaptive evolving genes: ndh F.Among them,the branch-site model detects positive selection sites from 15 evergreen oaks' ndh F genes,taking into account that most of the evergreen oaks live in the limestone matrix areas with higher altitudes,“adaptation to environmental stresses such as high ultraviolet radiation intensity,hypoxia,low temperature,drought,etc.” may be important genetic basis for the adaptive evolution of Quercus chloroplast.In this study I sequenced and assembled 14 Quercus chloroplast genomes,which further increased the number of chloroplast genomes in the genome database.Moreover,I also studied chloroplast genome structure,phylogenetic relationship and adaptive evolution of Quercus,and the results would help to understand the diversity and complexity of Quercus chloroplast genome,and provide new insights into understanding the role of natural selection in driving chloroplast gene evolution.