Comparative Chloroplast Genomics Of The Genus Lilium

Lily is a kind of ornamental flowers that has great commercial value,including ornamental,edible and medicinal value.After long-term study from traditional taxonomy morphology to modern molecular taxonomy,the origin and phylogeny of Lilium genus have a clear outline.However,there is still a series of arguments,such as systematic evolutionary process,the different classification methods of the same species in morphological taxonomy and molecular system taxonomy,the identification of near-species,the boundary of species and subspecies,whether Nomocharis can be divided into Lilium etc.At the same time there is not enough genetic data as theoritical support for conservation,domestication and breeding of endangered species and important germplasm resources in Lilium.At present,the chloroplast genomesr of more than 1000 species have been determined all over the world,providing important information for the study on photosynthetic plants.In this study,the structural characteristics,nucleotide polymorphisms,phylogenetic studies of Lilium chloroplast genome were analyzed by bioinformatics.This is a base for the studies of the conservation,breeding,population genetics,development of DNA barcode,phyletic evolution and diverse research of Lilium.Following are the major research conclusions:1.In this study,we present the ten complete chloroplast genomes(from 151,655 bp to 153,235 bp)of Lilium species through high-throughput sequencing techniques.The Lilium cp genome contains 113 individual genes,including 79 protein coding genes,30 tRNA genes and 4 rRNA genes.And the gene order is completely consistent,providing more genetic information of Lilium chloroplast genome.2.The structural characteristics of Lilium chloroplast genome were analyzed with 6 Lilium chloroplast genomes,which were published by NCBI(National Center of Biotechnology Information).According to the result,all gene order is completely consistent,without the appearance of gene rearrangement;the content of AT is high,especially in the third place of Protein-coding area codon;the proportion of sect.Martagon in Intron,IGS and Genes is obviously different from that in other regions of Lilium chloroplast genome.3.A total of 1043 SSR loci were identified in the analysis of 16 Lilium chloroplast genome by bioinformatics;According to the nucleotide polymorphism,it was revealed that the evolution velocity of Lilium chloroplast genome sequence is different in different regions and different species;in addition,basing on the degree of gene differentiation,10 hypervariable regions were identified and they can be used to mark Lilium chloroplast genome molecular.They are trnS-trnG,trnE-trnT-psbD,trnF-ndhJ,psbE-petL,trnP-psaJ-rpl33,psbB-psbH,petD-rpoA,ndhF-rpl32-trnL,ycf1 a and ycf1 b.4.Based on different regions in the chloroplast genome,phylogenetic trees were constructed.CpDNA phylogenetic tree,LSC phylogenetic tree,SSC phylogenetic tree and hypervariable region phylogenetic tree have highly similar topological structure with similar support rates;after the analysis with nucleotide diversity,L.sp.(from GenBank)and L.tsingtauense are most likely to be the same species;it is believed that chloroplast genome data of L.distichum(from GenBank)may not be accurate enough in species identification before sequencing.In summary,although Lilium chloroplast genome with the same gene order is not different in the length of the genome,it still provides very rich genetic information for the study of Lilium species in terms of sequence differentiation and structure.It can also be used to construct phylogenetic trees with high resolution,indentify SSR loci and SNP loci,develop the marker for the region of higher degree of differentiation.The information expands the researchers' horizon of the diversity of Lilium plants and enhances the understanding of phylogenetic relationships among Lilium species.It is of great value for analysing the climate adaptability of Lilium plants,promoting the germplasm innovation of Lilium species,authenticating closely related species and cultivar,protecting worthy hereditary phenotypic trait.