Comparative Chloroplast Genome Analysis And Phylogenetic Of Wikstroemia

The genus Wikstroemia belongs to the Thymelaeaceae family,which is divided into Sect.Diplomorpha Meisn.and Sect.Wikstroemia,comprises of about 70 known species.Members of Wikstroemia are distributed in the southeastern Asia,Oceania,and Pacific islands.In China,there are about 51 species recorded,and 45 species are endemic to China;while most of them are distributed in the southern region of China.Some species of Wikstroemia have extremely high economic and medicinal value.At present,the researches on Wikstroemia mainly focus on the chemical constituents,pharmacological properties,and palynology;while there is a lack of comprehensive molecular systematic studies.There are only a few reports on the nuclear DNA and chloroplast DNA of Wikstroemia that are publicly available.The phylogenetic position of Wikstroemia within the Thymelaeaceae family and its phylogenetics relationship with relative genera,as well as the division of species within the genus and the relationship between species have been controversial.Based on the fact that the chloroplast complete genome sequence is a useful genetic data to study species identification and phylogenetics,this study used high-throughput sequencing technology to obtain the chloroplast genome sequence of 23 species and 1 variety of the Wikstroemia.Annotation and comparative genomics analysis were performed.Based on the existing 52 chloroplast genome sequences and 49 nuclear DNA sequences of Thymelaeaceae,phylogenetic trees were reconstructed using the maximum likelihood and Bayesian inference methods,analyzed separately.The main contents and final results of our study are as follows:The chloroplast genomes of the Wikstroemia exhibited a typical quadripartite structure,the genome length is between 148-173 Kb,the lengths of LSC,SSC,and IR are 85,490-86,816 bp,2,639-12,384 bp,26,378-42,059 bp,respectively.The GC content of the whole chloroplast genome,LSC,SSC,and IR region is 36.4-37.5%,34.6-34.9%,28.3-32.5%,38.8-42.9%,respectively.A total of 946 long repeat sequences of four types were detected,and the number,proportion and distribution of each repeat sequence in each species were analyzed.In addition,a total of 2,456 simple sequence repeatsrepeats(SSRs)loci were detected in the 23 species 1 variety of Wikstroemia.Through the detection and analysis of the codon usage of the protein,the number of codons encoded by the protein is found to be between 22,622-30,120.The relative synonymous codon usage(RSCU)value of 30 codons was greater than 1,indicating a strong preference,while the RSCU value of 32 codons was less than 1,indicating a weak preference.The stop codon UAA had the most occurrence when compared to stop codons UAG and UGA.Most of the preferred codons ended with the amino acid A or U,except for the leucine(Leu)encoding codon UUG.The results of the m VISTA and nucleotide polymorphism analysis of the Wikstroemia showed that the 24 chloroplast sequences of Wikstroemia contain variations.In general,the IR is more conservative than the LSC and the SSC regions,and the variations mainly occurs in the non-coding region.The collinearity analysis showed that the chloroplast DNA of the Wikstroemia was highly collinear,and there was no rearrangement or inversion of large gene segments observed.The IR boundary analysis of the Wikstroemia showed that there is contraction/expansion of the IR region in Wikstroemia,and the gene species present adjacent to the JSB(IRb/SSC)border can be categorized into two types,in which they are either the trn L and ndh F genes,or trn L and ycf1 genes.Based on 6 datasets of chloroplast genome(complete chloroplast genome sequence,protein coding sequence,LSC region,SSC region,IR region)and nuclear DNA,species of Thymelaeaceae were phylogenetically reconstructed.The phylogenetic trees were well-resolved,and the following conclusions were obtained:(1)Based on the current generic circumscription,Daphne and Wikstroemia are independent genera;Wikstroemia is not monophyletic,and is closely related to Stellera.(2)The 4 species of Daphne(D.aurantiaca,D.genkwa,D.holosericea,and,D.rosmarinifolia)should be transferred into Wikstroemia.(3)The traditional sectioning of Wikstroemia is not supported by the molecular phylogenetic tree.In this study,the phylogenetic placement of member of Wikstroemia based on the chloroplast genome sequences showed distinct sectioning event.However,further investigation is required to verify its association towards taxonomic classification chloroplast genome characteristics of the genus Wikstroemia have obvious sect phenomenon.Whether the sect of the genus Wikstroemia can adopt molecular methods is also considered in future research direction.(4)Wikstroemia micrantha var.paniculata should be treated as a distinct species,but not as a variety of W.micrantha.It is therefore suggested that W.micrantha var.paniculata remains under the name W.paniculata that was originally proposed published by Li Huilin in 1934.