Whole Genome Sequencing And Gene Family Evolution Analysis Of Apocynum Venetum L.

Apocynum venetum L.,also known as kenaf,Apocynaceae perennial perennial root herb,is precious wild plant resources in our country.As an ecological and economic plant with strong resistance to stress,robinea officinalis can feed tea into its leaves,and its stem can be made into fiber.Roots,stems,leaves and flowers can be used as medicine.In 1977,it was listed in the pharmacopoeia of the People's Republic of China.The whole genome sequencing of plants is to analyze and solve the most basic information shortage of gene composition,component analysis,metabolic pathway and so on.It can provide scientific analysis and support for the information of genetic relationship,differentiation time and interspecific evolution relationship among species.However,there are few studies on the gene sequencing of Apocynum.There are only 89 sequences of Apocynum genome in NCBI database(as of June,14,2020),and a few of them hinder the genomic research of Apocynum,so the whole genome of Apocynum needs to be cracked.In this paper,the whole genome of A.venetum was sequenced,assembled and analyzed by using pacbio sequence platform,10x Gemonics sequencing technology,Hi-C assisted assembly and other methods.The results are as follows:1.The sequencing analysis results indicated that the preliminary estimated genome size of A.venetum was 254.40 Mbp,and its heterozygosity ratio and percentage of repeated sequences were 0.63%and 40.87%,respectively,indicating that it has a complex genome;We used k-mer=41 to carry out a preliminary assembly and obtained contig N50,which was 3,841 bp with a total length of 223,949,699 bp.We carried out further assembly to obtain scaffold N50,which was 6196 bp with a total length of 227,322,054 bp;We performed simple sequence repeat(SSR)molecular marker prediction based on the A.venetum genome data and identified a total of 101,918 SSRs.The differences between the different types of nucleotide repeats were great,with mononucleotide repeats being most numerous and hexanucleotide repeats being least numerous?2.This study successfully assembled the apocynum whole genome sketch(245 Mbp)for the first time,and determined that the number of chromosomes was 2n=22.The A.venetum genome super-scaffold was assembled with Hi-C assisted assembly technology,exhibited an N50 of 19.8 Mbp,and was anchored to 11 chromosomes.A total of 22,552 non-redundant protein-coding genes were predicted by annotation of the genome assembly,90.24%of which contained conserved protein domains,and 78.70%that were annotated within known metabolic pathways,95.9%of the genes had functional annotation,and 55.5%of the genes had GO functional annotation.A high-quality chromosome-level reference genome is described here for A.venetum after using long-read single-molecule sequencing and Hi-C based chromatin interaction maps.These results provide the foundation to explore the genetic basis of biological features of A.venetum that are of interest in several applications.3.Comparative genomic analysis reveals that Apocynum is most closely related to Calotropis gigantea.Through genome comparative analysis of A.venetum,a total of 43837 gene families were clustered,with a total of 3084 gene families,of which 405 gene families were expanded,including 1524 genes,342 gene families were contracted,including 167 genes.This may be due to the acquisition and loss of independent genes(families)in different degrees during the evolution of each species.Phylogenetic analysis of gene family shows that the differentiation time of Apocynum is about 35.9(26.7-46.8)million years,and the divergence time of A.venetum and Apocynum cannabinum is about 6.5(3.3-9.9)million years about.Gene family clustering found that A.venetum,A.cannabinum,Catharanthus roseus and C.gigantea were clustered into one group.Apocynum and C.gigantea are most closely related,which is highly consistent with the angiosperm classification ?(APG ?).4.A variety of genes related to the synthesis of flavonoids were identified based on the whole genome annotation of A.venetum.Genes related to flavonoid synthesis in the annotated results of A.venetum,including O-methyltransferase,anthocyanin reductase,colorless anthocyanin reductase,reductase,colorless anthocyanin plus dioxidase,Chalcone synthase,isoflavone reductase,and chalcone isomerase genes,etc.At the same time,79 AP2/ERF transcription factors related to the interaction of transcription regulation genes were also identified.