Structural Analysis Of Complete Chloroplast Genome Of Medicinal And Edible Original Plants Of Amomum,Chinese Wolfberry,Hawthorn And Ginger

Amomum,Chinese wolfberry,hawthorn and ginger are commonly used medicinal and edible Chinese herbal medicines recorded in the Chinese Pharmacopoeia and have high economic value.However,it is difficult to accurately identify their closely related species through morphology and traditional DNA barcodes.Chloroplast genome,as a plant specific genetic material independent of nuclear genome,plays an important role in species identification,phylogenetic evolution,and comparative genomics.In this study,the chloroplast genome of Amomum,Chinese wolfberry,hawthorn and ginger were sequenced and analyzed based on Illumina high-throughput sequencing platform.The chloroplast genomes of all the original plants were obtained,which were typical tetrad structures.The results are as follows:(1)The complete chloroplast genomes of eight samples of Amomum villosum,A.villosum var.xanthioides and A.longiligulare were determined to be 163,608-164,069 bp in size,encoding 113 different genes.The comparative analysis showed that the intraspecific sequences of the three species were highly conserved.Five highly variable regions,such as atpH-atpl,trnD-trnY,accD-psal,ycf4-cemA and trnl-ycf2 were screened by interspecific comparative analysis,which can be used as potential identification markers.The five highly variable regions were verified based on 32 samples from eight species in Amomum.The result showed that all of them showed low identification efficiency in Amomum species and none of them could distinguish these three species accurately.The ML phylogenetic tree based on 64 common protein-coding genes shows that the three species were clustered into one independent branch,which can accurately reflect the phylogenetic relationship between Amomum species,suggesting that the complete chloroplast genome can be used as a "super-barcode" to accurately identify the three Amomum species.(2)The complete chloroplast genome sequences of Lycium barbarum,L.chinense and L.ruthenicum spanned 155,656,155,745 and 154,869 bp in size,respectively.Each genome contains 113 unique genes.accD gene mutated in L.ruthenicum and was annotated as a pseudogene.The comparative analysis showed that three highly variable regions,namely atpH-atpI,accD-ycf4 and ndhF-trnL,were identified as potential molecular markers for species identification and phylogenetic analysis.The ML phylogenetic tree based on 54 common protein-coding genes showed that the chloroplast genome is expected to be a "ssuper-barcode" for the accurate identification of Lycium species.(3)The chloroplast genomes of Crataegus pinnatifida and C.pinnatifida var.major were 159,667 bp and 159,654 bp respectively,encoding 112 different genes.The ML phylogenetic tree based on 71 common protein-coding genes showed that C.pinnatifida and C.pinnatifida var.major could be distinguished obviously,and the support rate was high.Therefore,the chloroplast genome is expected to be used to accurately identify Crataegus species.(4)The Zingiber officinale chloroplast genome was 162,621 bp and encodes 113 unique genes.Five potential DNA barcodes(rps16-trnQ-UUG,atpH-atpI,trnT-UGU-trnL-UAA,ycfl and psaC-ndhE)were screened based on the global comparison of chloroplast genomes.At the same time,it was found that the SSC region was highly variable in Zingiberaceae.The results of ML phylogenetic tree based on 75 common protein-coding genes showed that Zingiber and Kaempferia were closely related.