Changes Of Genome And LncRNA In Early Stage Of Allotetraploid Cucumis×hytivus Formation

In the process of species formation,polyploidy played an important role and it is the main force to promote plant evolution.Commonly allopolyploidy is superior to diploid parent,which can be directly manifested in the increase of food or vegetative organs and the enhancement of stress resistance.Cucumis×hytivus(herein referred to as tetraploid new cucumber specie)is a successful attempt to artificially synthesize polyploid in cucumber breeding.One of its parents is from the wild cucumber species(C.hystrix),pickled cuke,and the other is cultivated cucumber from northern China.The early formation of allopolyploidy is often accompanied by genome and transcriptome shocks,that is,extensive genetic and epigenetic variations have occurred,and these variations have a significant impact on the phenotype.The tetraploid cucumber with stable phenotype obtained after multiple generations of selfing have a clear genetic relationship,which is an ideal model system for studying the speciation and phenotypic variation of allopolyploid.Although it has been clearly understood that distant hybridization,genome duplication,and continuous selfing are the three key steps to obtain tetraploid cucumber,the lack of genome data and transcriptome data has a great influence on the in-depth study of plant polyploidy.Long noncoding RNAs(lncRNAs)are a kind of noncoding RNAs that have been discovered in recent years and have received widespread attention.They play an important role in regulating the phenotypic variation of allopolyploidy.Therefore,this study first sequenced and assembled tetraploid cucumber,and tried to reveal the impact of allopolyploidization on cucumbers from the DNA and RNA levels.The main research results are as follows:1.Whole genome sequence of synthesized allopolyploid Cucumis reveals subgenome dominance,instant genomic changes initiated by hybridizationPacbio was used to sequence the whole genome of tetraploid cucumber(S14),combined with BioNano optical maps to assist assembly.The assembled scaffold N50 was 8.09Mb.And the final total assembly size was 540.74 Mb,which was 77%of the estimated size of Kmer.97.23%of the sequences were anchored on 19 chromosomes using Hi-C technique.After the integration of multiple methods,45,687 genes are predicted.The BUSCO data set has an estimated completeness of 90.9%.The average gene length is 3,846bp,and each gene has 5.26 exons.Tetraploid cucumber inherited repetitive resistance genes from wild species and cucumber,and enhanced resistance to nematodes.Collinearity analysis with the parental genes showed that the parental CC genome was better maintained in the polyploid C.×hytivus(S14)genome than the HH genome.The loss of 42 C.sativus and 177 C.hystrix gene confirmed by DNA sequence indicated that there was a biased inheritance of subgenomic DNA in Cucumis polyploidization.Analyzed the variation of nuclear genome and cytoplasmic genome from the three stages of distant hybridization,genome duplication,and continuous selfing(diploid hybrid F1 and C.×hytivus early selfed progeny S0,S4～S13).It shows that the loss of genome sequence mainly occurs immediately after interspecific hybridization.In the interspecific hybrid F1,29 and 124 parental genes have been lost.These results indicated that hybridization causes a greater degree of variation than genome duplication and diploidization.2.Global profiling of lncRNAs expression responsive to allopolyploidization in CucumisLong non-coding RNAs(lncRNAs)play critical regulatory roles in various biological processes.We examined the profile of novel lncRNAs in C.×hytivus(S14),its diploid parents and the F1 hybrid.Results showed that 2206 lncRNAs evenly transcribed from all 19 chromosomes were identified in allotetraploid C.×hytivus,44.6%of these were from intergenic regions.Like other model plants,C.×hytivus lncRNAs are shorter and have fewer exons than protein-coding genes.Base on the expression trend analysis of F1 hybrid,S14 and MPV(mid-parent value),we found that a high proportion of lncRNAs showed up-regulated expression to varying degrees following polyploidization.Compared to MPV,352 lncRNAs were nonadditively expressed in F1,of which 313 and 39 lncRNAs were significantly upregulated and down-regulated,respectively.In contrast,few lncRNAs were nonadditively expressed after genome duplication,suggesting the significant effect of hybridization on lncRNAs of polyploidization,rather than genome duplication.The accuracy of these differentially expressed genes was verified by using F-box as reference gene,which was selected by geNorm and NormFinder based on qPCR.In addition,253 cis-regulated proteincoding genes that predicted as potential target genes of the differentially expressed lncRNAs in S14 have participated in chloroplast biological regulation.A number of novel lncRNAs nonadditively expressed after polyploidization were involved in chlorophyll synthesis and light harvesting system,demonstrating the essential role of lncRNAs in the photosynthetic response of polyploidy.