The Draft Genome Of Arnebia Euchroma And The Transcriptome Of "Alkanet" Plants

Alkanets are a kind of plants whose roots are red and rich in naphthaquinone compounds(shikonin and its derivatives).Shikonin and its derivatives are not only famous natural pigment,but also important medicinal natural products.However,due to the lack of relevant genomes and transcriptomes,present studies about the molecular level of shikonin biosynthesis are not profound enough at home and abroad.Therefore,we performed the draft genome sequencing,assembly,annotation and preliminary analysis of the Arnebia euchroma using the Illumina sequencing technology.Moreover,we performed transcriptome sequencing,assembly and preliminary analysis of three alkanets including Arnebia euchroma,Lithospermum erythrorhizon and Echium plantagineum.The reults showed that Arnebia euchroma genome size is approximate 2.7 Gb,its genome heterozygosity is about 1.5-1.7%,its genome duplication rate is more than 50%.This means Arnebia euchroma genome is a large genome with a high degree of heterozygosity and duplication.Therefore,we only assembled a draft genome of Arnebia euchroma with 1.2 Gb genome size,whose Contig N50 is 1.9 kb and Scaffold N50 is 2.3 kb.In addition,its genome approximately contains 28157 protein-coding genes,and 542 miRNA were scanned in this draft genome.According to genome multiple comparison and evolution analysis,Arnebia euchroma and Solanum lycopersicum probably have an extreme close evolutionary relationship.This suggested that Boraginales might be closer to Solanales rather than Lamiales in the evolutionary distance scale.Furthermore,Boraginales might segregate from Solanales at approximate 75.3 Mya which is the junction between late Cretaceous period and early Tertiary period.Besides,the result of evolution analysis based on the chloroplast genome of Arnebia euchroma supported Boraginales closed to Solanales rather than Lamiales in the evolutionary distance scale.Though analyzing transcriptomes of three alkanets,we found that there were many highly significantly differentially expressed Unigenes(HDEGs)between their green stems/leaves(GL)and red roots(RR),in which we further selected some novel genes participating shikonin biosynthesis,such as geraniol 10-hydroxylase gene(G10H)related to the shikonin metabolism pathway,12-oxophytodienoate reductase gene(120PR)related to the methyl jasmonates metabolism pathway,S-adenosylmethionine decarboxylase gene(SAMDC)involved in the polyamine/ethylene metabolism pathway.Furthermore,transcriptome multiple comparison and evolution analysis also confirmed that Boraginales was closer to Solanales rather than Lamiales in the evolutionary distance scale,whose results were almostly in accordance with the evolutionary analysis results of Arnebia euchroma genome.Moreover,we also identified 145 single-copy orthologous genes were under positive selection in Lamiids evolution in the alkanet plants,in which 4-coumarate:CoA ligase gene(4CL)was directly involved in the shikonin biosynthesis pathway.In summary,this present study is able to lay a foundation for the alkanet plants origin,shikonin biosynthesis and metabolism regulation research areas,and applied a certain reference in shikonin metabolic engineering.