Complete Chloroplast Genome Sequences And Evolution Analysis Of Eight Paulownia Species

Paulownia,one of the genus of Scrophulariaceae family,is a fast-growing timber tree species indigenous to China.It is widely distributed and planted in various provinces,municipalities and autonomous regions in China.Its system position and evolutionary relationship within genus maintain uncertain due to the potential hybridization and polyploidization.At the same time,the breeding of excellent varieties and the protection of germplasm resources also lack more genetic data as support.The sequence of the chloroplast genome is highly conserved and has a low base substitution rate,which is an ideal data source for studying plant phylogeny.With the development of high-throughput sequencing technology,the complete chloroplast genome sequence of most angiosperms has been sequenced and provide data support for the study of photosynthetic plants.In the present study,eight complete chloroplast genomes of Paulownia were sequenced by Illumina sequencing technology,and the bio-information technology was used to compare and analyze the basic characteristics,repeat sequences,simple sequence repeats and nucleotide variation of the chloroplast genome.Meanwhile,the phylogeny of order Tubiflorae,Malvales and Solanales was constructed based on the 23 cp DNA that had been published,revealing the evolutionary relationship between the various genera and species of Scrophulariaceae.These results provided important genetic data for the conservation of the germplasm resources,breeding of excellent varieties,development of molecular markers,and the relationship between the evolution and origin of the genera in the family Scrophulariaceae.The main contents and research results of this study were as follows:1.The complete cp genome sequences of eight species of Paulownia were sequenced and annotated for the first time.The length of their genomes ranged from 154,506 bp to 154,746 bp and had a typical quadripartite structure.That highly conserved quadripartite structure is composed of a couple of inverted repeats(IRs,25,761bp~25,797bp),a large single-copy region(LSC,85,262 bp ~85,371bp),and a small single-copy region(SSC,17,722 bp~17,786 bp).Among the obtained eight Paulownia cp genomes,114 functional genes were annotated,including 30 tRNA genes,4 rRNA genes and 80 protein-coding genes.The GC content of eight cp genomes was the same,both were 38.00%.Therefore,the content of AT base was rich.The codon usage was biased towards A and T.Besides,repeated sequence and SSR were also analyzed,and 431 simple sequence repeats loci(Paulownia fortunei)and 571 repeated sequences(Paulownia fortunei)were detected,which offered a research basis for the correlation analysis of Paulownia.2.For the first time,eight Paulownia species were compared with the published Paulownia coreana(KP 718622)and Paulownia tomentosa(KP 718624)in NCBI at the chloroplast genome level,and the highly variable regions of Paulownia were identified.The results showed that their sequence similarity was more than 99%;the analysis of IR region contraction and expansion indicated that there were differences in the size and distribution of the four regions genes(rps19,ndhF,ycf1 and trnH).For example,the distribution of rps19 gene in Pto,Pca,Pau and Pka was 237 bp in the LSC region and 42 bp in the IRb region,but the distribution length in the IRb region of other remaining Paulownia species was 30 bp.It showed that although the genome sequence of Paulownia species was highly similar,there were some differences in genome structure;the nucleotide variation values(PI)of the coding and non-coding regions of Paulownia plants were calculated to reflect the evolution rate of diverse regions between different species.Nine highly variable regions,such as trn H-psb A,trn S-trnG,trnG-trnT,accD-psaI,trnL-rps16,petN-trnA,psbZ-rps14,ccsA-ndhD and rpl22-rps9 were identified,as well as they could be used as candidate molecular markers of the chloroplast genome of Paulownia.3.Based on the whole genome sequences of Paulownia and other species,the phylogenetic trees were constructed with Maximum likelihood(ML),Maximum Parsimony(MP)and Bayesian inference(BI)methods for the first time at home and abroad.It more comprehensively uncovered the systematic status of Paulownia in Tubiflorae and the phylogenetic relationships between different species within the genus.