Genome Analysis Of Three Important Medicinal Plants

Research BackgroundIn this article,I mainly introduce the application of genomics method to analyze the genomes three medicinal plants,which are Andrographis paniculata,Gastrodia elata and Eleutherococcus senticosus.Gastrodia elata is a perennial,achlorophyllous orchid that displays distinctive evolutionary strategy of adaptation to the non-photosynthetic lifestyle.In this study,according to the characteristics of Gastrodia elata,photosynthesis-related genes and chlorophyll-related genes in Gastrodia elata were discovered and analyzed.Andrographis paniculata(Chinese name: Chuanxinlian)is an annual dicotyledonous medicinal plant that contains andrographolide and neoandrographolide.Its dry aerial parts have the effects of antipyretic,anti-inflammatory,and analgesic effects.This study mainly excavated the key genes in the pathway of andrographolide synthesis.Siberian ginseng(Eleutherococcus senticosus,also known as ciwujia)belongs to the Araliaceae family,which contains more than 1,500 species in 41 genera with diverse chromosome numbers and genome sizes.In an attempt to generate more genomic information for the Araliaceae family,this study studied the chromosome changes of Acanthopanax senticosus during the evolution process and the adaptive mechanism of Acanthopanax senticosus to the cold environment.Research MethodsUnder the technology of combining the third-generation single-molecule real-time sequencing and the second-generation pair-end sequencing,the genomes of the three plants are assembled,and the contigs are further assembled into chromosomes with the help of Hi-C technology.The repetitive sequences in G.elata,A.paniculata and E.senticosus were analyzed by gene annotation and repetitive sequence annotation.Through evolution analysis,ka/ks analysis,enrichment analysis and mass spectrometry analysis,the photosynthesis and chlorophyll related genes in G.elata were studied.Multiple sequence alignment and other technical means to mine key genes in the synthesis pathway of important compounds such as andrographolide.Collinearity analysis and chromosome analysis techniques are used to study the changes in chromosomes of E.senticosus during the evolution process and its adaptability to cold environments.Research ResultsHere in this study,the genome of G.elata was assembled to 1.12 Gb with a contig N50 size of 110 kb and a scaffold N50 size of 1.64 Mb.Based on the genomic data,key genes related to photosynthesis,leaf development,and plastid division pathways were found to be lost or under relaxed selection during the course of evolution.Thus,the genome sequence of G.elata provides a good resource for future investigations of the evolution of orchids and other achlorophyllous plants.In this study,the A.paniculata genome was assembled into a total size of 284 Mb with a contig N50 size of 5.14 Mb.The contigs were further assembled into 24pseudo-chromosomes by the Hi-C technique.The results showed that transposable factors accounted for 57.35% of the genome,and a total of 24,015 protein-coding genes were predicted.I also analyzed the gene families(eg.CPS,KSL and CYP450)whose protein products are essential for synthesizing bioactive compounds in A.paniculata.This study also assembled a 1.30 Gb high-quality draft genome of of E.senticosus(contig N50 = 309.43 kb).The results showed that transposable factors accounted for 72.82% of the genome.and a total of 36,372 protein-coding genes were predicted.Comparative analyses of the E.senticosus,Panax notoginseng and Daucus carota genomes revealed a burst expansion of Tekay chromoviral elements in Araliaceae after its divergence with Apiaceae.E.senticosus underwent a lineage-specific whole-genome duplication event Es-α and a whole-genome duplication event Araliaceae-β that was likely shared by all Araliaceae species was found.Pathway analyses showed that these two whole-genome duplication events may have contributed to the adaptation of E.senticosus to cold environment.Taken together,the high-quality genome assembly of E.senticosus provides a valuable genomic resource for future research on the evolution of Araliaceae.ConclusionsThe whole genome sequencing of these medicinal plants,the high-qaultiy assembly of medicinal plant genomes,and in-depth analysis based on the their uniq characteristics have greatly promoted the basic research of medicinal plants.It will provide some ideas for mining the key genes in the biosynthesis pathway of natural herbal products.It lays a strong foundation for revealing the genetic information of medicinal plants,analyzing the synthesis pathway of medicinal active ingredients and molecular breeding of medicinal plants.