The Genome And Transcriptome Of Lithospermum Erythrorhizon

Gromwells,such as Lithospermum erythrorhizon,Arnebia euchroma,Onosma paniculatum,are a group of traditional Chinese herbs.Their roots produce shikonin(and its derivatives)which possessing high bioactivity;in addition,their seeds are rich in unsaturated fatty acid.Therefore,these plants have very high values in medicine and commerce.However,due to the lack of these plants' genome information,their research advances in molecular biology still fall further behind many other model plants and crops.In particular,many genes related to shikonin biosynthesis are still unclear,even if a few of genes have been identified and cloned in previous studies.Therefore,we performed the de novo genome sequencing,assembly,annotation and the preliminary analysis of the L.erythrorhizon whole genome.The results show that L.erythrorhizon genome size is approximately 727.38 Mb;its genome heterozygosity is about 0.6%;its genome duplication rate approximately about 56.26%;its assembled genome size is about 534.13 Mb,whose Contig N50 is 17.15 kb and Scaffold N50 is 337.88 kb;in addition,its genome approximately contains 26,717 protein-coding genes.Therefore,compared with other sequenced plant genomes,L.erythrorhizon genome has three features:medium size,high duplication,medium heterozygosity.According to genome multiple comparison and evolution analysis,L.erythrorhizon and Solanum lycopersicum have a extreme close evolutionary relationship,probably.This suggested that Boraginales might be closer to Solanales rather than Lamiales in the evolutionary distance scale.Furthermore,after segregate from S.lycopersicum in evolution,L.erythrorhizon occurred whole-genome duplication at 30-40 million years ago.Moreover,there was a LTR insertion event in L.erythrorhizon genome at approximately 3 million years ago.These two factors possibly was the main determinant for the size and duplication rate of the L.erythrorhizon genome.Through gene families expansion and contraction analysis,we found that the expansion rate of HMGR(hydroxymethylglutaryl-CoA reductase)gene,which is a key enzyme gene in the shikonin biosynthesis,was at a significance level.Additionlly,this project further carried out the transcriptome sequencing and analysis of the six different organizations from L.erythrorhizon,in order to detect the expression profile of the genes related to shikonin biosynthesis.The results implied that in the shikonin biosynthesis the gene expression regulation of the MVA(mevalonate pathway)might have greater influence than the gene expression of the PP(phenylpropanoid pathway).In addition,some identified and cloned enzyme genes related to shikonin biosynthesis have more copys than previously reported.To sum up,this project could be expected to improve the identification of the genes related to shikonin biosynthesis;also is advantageous to shikonin metabolic engineering and its development;and could make a substantial contribution to genome researches in gromwells,even Chinese medicinal plants.