Phylogeny And Molecular Evolution Of Chloroplast Genome In Camellia

The genus Camellia,belonging to Theaceae family,has the highest number of species and economic value,with its distribution only in Asia,primarily in subtropical evergreen broad-leaved forests.Nearly 280 Camellia species,comprising over 80% of all Camellia species,exist.Given the lateness of our study on Camellia,many of its plant resources are at risk and require urgent protection.Conducting phylogenetic studies on Camellia plants can facilitate the identification and isolation of Camellia species,thereby enabling us to analyze their genetic similarities and differences.This approach can provide scientific evidence and decision-making support for the conservation of Camellia resources.Selfincompatibility is common in Camellia species,which are cross-pollinated,and frequently hybridize with different species,leading to an ambiguous phylogenetic relationship.In our research,we integrated a high-throughput sequencing technique of 71 Camellia species with a comparative analysis of the plastid structure of Camellia utilizing bioinformatics.We utilized the chloroplast genome sequence to reconstruct the phylogenetic relationship of Camellia and estimate its differentiation time.Elucidating the inter-species relationship of Camellia can direct the conservation and utilization of Camellia resources.The following results were accomplished with this study:1.To acquire high-quality genome sequence data,Illumina Hi Seq 4000 platform was employed,sequencing 71 Camellia species from 13 groups.The chloroplast genome of Camellia showed a typical tetrad structure,with sequence length of 156390 bp-157147 bp and GC content of 37.29%-37.36%.131 genes were annotated for each species of Camellia,including 87 protein-coding genes,36 t RNA genes and 8 r RNA genes.No deletion or rearrangement of genes was observed.2.To analyze the characteristics of cp DNA sequences,13 representative Camellia species were chosen.911 SSR loci were detected,of which most were A/T-type single nucleotide repeat units.The analysis identified 536 long repeats,of which palindromic repeats represented the most substantial portion.Methionine(Met)and tryptophan(Trp)were the only codons with an A RSCU value of 1,denoting a lack of codon preference.Most codons preferred an A/U nucleotide as the final base.No inversion rearrangement of genes in the IR boundary was observed.The primary genes that underwent change were ndh F and ycf1.Compared to non-coding regions,coding regions had a higher degree of conservatism.Additionally,the IR region demonstrated greater conservatism than the LSC and SSC regions.3.The nucleotide polymorphisms and genetic distances of 71 self-measured chloroplast genome sequences of Camellia showed that the chloroplast genome sequence of Camellia was conservative.Eight hot spots of variation(trn S-trn R、pet N-psb M、trn Q-psb K、ndh Frpl32、psb K-psb I、ycf15-trn L、trn L-ndh B(exon2)、ycf1)were explored,which have the potential to be developed into molecular markers and DNA barcodes.The two species with the greatest distance between nucleic acid were C.weiningensis,C.pilosperma and C.assamica.4.This study used a total of 129 materials,including 71 sequenced assembly materials and 58 sequences downloaded from NCBI(including 106 species in 19 groups and 3outgroup).Based on the chloroplast sequence(LSC+SSC+IR)and CDS sequence,a maximum likelihood tree and a Bayesian tree were constructed.The results showed that the129 species of Camellia could be divided into 8 major clades,and the developmental relationships of each subgroup were as follows: 1)C.luteoflora is gathered into a single group,not combined with other combinations,independent group;2)Support the combination of Sect.Theopsis and Sect.Eriandria,merging of Sect.Paracamellia and Sect.Oleifera,but not supporting the merging of Sect.Lonissima and Sect.Longipedicellata,and merging of Sect.Thea and Sect.Glaberrima,and merging of Sect.Furfuracea and Sect.Pseudo Camellia;3)Sect.Chrysantha was a monophyletic group,while Sect.Archecamellia and Sect.Camellia were not monophyletic groups;4)assigning C.pilosperma to Sect.Thea,supporting the assignment of C.weiningensis to Sect.Camellia,and merging C.chungkingensis into Sect.Tubercula;5)Sect.Luteoflora,Sect.Theopsis,and Sect.Thea were relatively primitive groups,while Sect.Oleifera,Sect.Paracamellia,and Sect.Furfuracea were relatively evolved groups.5.The most recent common ancestor of the Camellia genus is estimated to be around25.21 million years ago(Mya),with the differentiation of Camellia occurring approximately20.99 Mya.The most primitive Camellia is the Sect.Stereocarpus(C.yunnanensis),and the differentiation time is about 8.05 Mya.The relatively evolved groups were Sect.Paracamellia,Sect.Oleifera,and Sect.Furfuracea,and the differentiation time was about4.97 Mya.The internal differentiation of Camellia was basically in Miocene.