Genome Survey Of Rehmannia Chingii,a Rare And Medicinal Herb In China

Genome technology is composed of bioinformatics,molecular biology,chemistry and materials science,which helps researchers to understand gene structure and their function in organisms.Genome sequencing technology has developed rapidly in recent years.High-throughput sequencing technology(next generation sequencing technology)provides a new opportunity for the genomic works.Rehmannia chingii,a perennial herb belonging to Orobanchaceae(Lamiales),is mainly distributed in Tianmushan area of Zhejiang province.This species is used as a traditional Chinese herbal medicine for nourishing Yin and kidney.Nowadays Rehmannia chingii is in the list of the rare species in China.In this study,we carried out the preliminary genomics research on Rehmannia chingii using the Illumina Hiseq X sequencing platform,to obtain sequence resource,reveal its genetic characteristics,and to establish a platform for their genomic study.The main results are followed:(1)A total of 69.70 Gb data were generated.The estimated genome size was 1.14 Gb,with the GC content of 40.64%.After assembly,there are 2,353,003 Contigs with the total base of 947 Mb.6,135,032 Scaffolds were obtained with the total base of 953 Mb.In addition,the total gap length was 5.9Mb.We found 200 Mb TE intron,covering 21.09% of the genome.419,207 simple sequence repeats(SSR)were found in Rehmannia chingii survey sequences,among which,mononucleotide(68.50%)were the most frequent,followed by dinucleotide(22.32%)and trinucleotide(7.78%).These three types of repeats account for 98.6% of all SSRs.(2)Comparing with the six public gene databases,32,372 genes were generated with genome analysis.The average length of genes,exons and introns was 1,250.33 bp,251.03 bp,and 161.59 bp,respectively.12,753 genes were shared between Rehmannia chingii and its related species.And1,597 genes were unique to Rehmannia chingii,which weremuch higher than that of sesame(130)and monkey flower(409),but close to Boea hygrometrica(1,169)and rice(1,221).(3)Catalpol is the main medicinal ingredient in Rehmannia chingii,which could be used as hypoglycemic drugs.In order to investigate metabolic pathway of catalpol,we identified the terpenoid biosynthetic pathway framework(KO00900)by searching KEGG database.30 genes are unique to Rehmannia chingii,which may have some relation with catalpol biosynthesis.Two pathways were involved in the synthesis of terpenoids,one is mevalerate(MVA)pathway,and the other is 2-C-methyl-D-erythritol-4-phosphate(MEP)pathway.