The Genome Analysis Of Eucommia Ulmoides Oliver And Molecular Basis For The Adaptation And Eu-rubber Biosynthesis

Eucommia ulmoides Oliver(E.ulmoides)is an economically important plant.E.ulmoides is a tertiary relict species that is native to China and has extremely strong environmental adaptability.E.ulmoides is the only hardy rubber tree growing in and subtropic temperate regions.To date,knowledge of E.ulmoides genomics is very limited,which has significantly hindered molecular breeding and deep utilization of E.ulmoides.Therefore,we report a high-quality genome assembly of an E.ulmoides tree and show the comprehensive information of E.ulmoides genome.It will provide new insights into the environmental adaptability and Eu-rubber biosynthesis of E.ulmoides.The results of the research are as follows:1.A high-quality genome assembly of E.ulmoides was reported.The genome of E.ulmoide,which is the first member of the Garryales,the heterozygosis ratio and repeat sequences of the E.ulmoides genome was about 1.0% and 61.24%,respectively.Therefore,E.ulmoides genome was sequenced by employing complementary technologies including Illumina HiSeq and MiSeq(short-read)as well as Pacific Bioscience PacBio(long-read),we generated 156.24 Gb Raw data and 99.85 Gb Clean data,representing ~131.29 × and ~83.91 ×.Additional BioNano sequencing data were used to improve the assembly of the E.ulmoides genome,and then 1.18 Gb E.ulmoides genome was obtained,which 99.16% coverage of the predicted 1.19 Gb genome.The N50 s of contigs,scaffolds,and super scaffolds were 17.06 kb,1.03 Mb,and 1.88 Mb,respectively.Of 18 928 super scaffolds(>2 kb)covering 98.84% of the E.ulmoides genome.We aligned transcriptome sequences,expressed sequence tags(ESTs)and core eukaryotic genes(CEGs)with our assembled genome,and the mapping rates ranged from 87.07% to 95.09%,98.72%,and 93.55%,respectively.These results suggested that the E.ulmoides genome was properly assembled in this study.2.Gene annotation.Genome annotation was performed by combining the results from de novo predictions,homology information,and RNA-seq data.We finally annotated 26 723 protein-coding genes in the E.ulmoides genome.The functional annotation indicated that 24 902 of the predicted genes showed known homologous targets in at least one functional protein database.In addition,we predicted 1 281 transfer RNAs,526 microRNAs,275 ribosomal RNAs,1 119 small nuclear RNAs,and 72 transcription factor including 1 315 genes in the E.ulmoides genome.We identified ~61.24%(723 Mb)of the E.ulmoides genome as repeat sequences.Compared to other species,larger E.ulmoides genome might attribute to its higher proportion of repeat sequences.Two most abundant types of long terminal repeats,Gypsy and Copia,separately accounted for 16.70% and 13.22% of the E.ulmoides genome.Compared to other species,the Copia was preferential accumulation of Copia in the E.ulmoides genome.In addition,the complete chloroplast(cp)genome sequence of E.ulmoides was obtained base on the genome data.The cp genome of E.ulmoides was 163 341 bp long and contained 115 unique genes,including 80 protein-coding genes,31 transfer RNA(tRNAs),and four ribosomal RNA(rRNAs).Twenty-nine simple sequence repeats(SSRs)which exhibited almost A or T types,were identified in the E.ulmoides cp genome.Compared with the entire cp genome sequence,three unique genome rearrangements were observed in the LSC region.The E.ulmoides cp genome showed extreme expansion at the IR/SSC boundary owing to the integration of an additional complete gene,ycf1.3.Identified the evolution of the E.ulmoides genome.Based on the genomes and RNA-seq data,we found that E.ulmoides belonged to Garryales and a sister taxon to lamiids and campanulids,which are basal euasterids.Moreover,E.ulmoides probably diverged from Euasterids I and II 129 million years ago,suggestting that Eucommiaceae or Garryales can be traced back to the Cretaceous Period,which was earlier than inferred from the fossil record.E.ulmoides genome shows the ancient whole-genome duplication(WGD),the γ event,that is shared by core eudicots,and that no recent independent WGD occurred in the evolutionary history of E.ulmoides.The syntenic relationships that the E.ulmoides regions aligned with V.vinifera,S.lycopersicum,and A.chinensis,respectively further supporting the conclusion that E.ulmoides lacked a recent WGD event.4.Molecular basis of the environmental adaptability of E.ulmoides.The expanded genes were found to be closely associated with responses to stress and SM biosynthesis in E.ulmoides.Stress-related genes including PR17,callose synthases,and SYP12 were obviously expanded in the E.ulmoides genome.Interestingly,genes such as PIP1,HSP90,MT,and APX were highly expressed.In addition,we found that several important genes(CAD,STR,CAO,and CHI)involved in secondary metabolites(SMs)biosynthesis,such as phenylpropanoids,alkaloids,and flavonoids,were significantly expanded,which might explain the high SM content in E.ulmoides.Our analyses suggest that E.ulmoides may have increased its environmental adaptability and resistance to insects and pathogens through expansion and/or upregulation of multiple genes involved in stress responses and SMs biosynthesis.5.Rubber biosynthesis independently originated in E.ulmoides.The gene families,which involved in the upstream of Eu-rubber biosynthesis,were not expanded in the E.ulmoides genome.Wheseas,the FPS and REF/SRPP families were expanded,which lay in different clades from rubber tree.In addition,FPSs(Class II: EuFPS1,EuFPS3,and EuFPS5)evolved the ability to synthesize long-chain trans-polyisoprene in E.ulmoides,suggesting Eu-rubber biosynthesis in eudicots independently originated between H.brasiliensis and E.ulmoides.Combing the expression partterns of genes and accumulation rates of Eu-rubber showed that Eu-rubber was synthesized by clade II of EuFPS(EuFPS1,EuFPS3,and EuFPS5)and EuSRPP,in contrast,rubber particles biosynthesis need HbCPT and HbREFs.