Nupts Composition And Chromosome Location In Asparagus Officinalis Nuclear Genome

In plants,the transfer of plastid DNA to the nuclear genome is a widespread phenomenon of horizontal shift of genetic material,and the transferred plastid DNA is called NUPTs(nuclear plastid DNAs).The insertion of NUPTs into the nuclear genome can cause variation of nuclear genome and rearrangement of chromosome structure.It is one of the important factors of the evolution of genomes and genomes.Asparagus officinalis is a dioecious economic crop with 2n=20 chromosomes,with homotypic XY chromosomes determining its sextual type.The genome of A.officinalis is in an evolutionary unstable stage.However,it is still unclear which factors caused the instability of the A officinalis genome.Therefore,in this study,we used bioinformatics and molecular cytogenetics techniques to annotate and analyze NUPTs in the nuclear genome of A.officinalis,and investigate the distribution patterns on chromosomes.The main results are as follows:1.Bioinformatics analysis showed that a total of 2,239 NUPTs were found in the nuclear genome of A.officinalis,with a total length of 565,970 bp and accounting for 0.047% of the nuclear genome.NUPTs had different insertion lengths on different chromosomes,and the average length of Y chromosome insertion was the longest,significantly higher than the other chromosomes.There were 778 bp NUPTs sequences per Mb genome and there was an insertion hot spot.The number of NUPTs inserted on different chromosomes were also different significantly.The number of NUPTs on the Y chromosome is the highest,reaching to 272 NUPTs per 100 Mb of genome,indicating that NUTPs have more accumulation on the Y chromosome.The insertion of NUPTs on a given chromosome was uneven,with hot spot in some regions.Analysis of the colocalization patterns of genes,NUPTs,and transposons on 10 chromosomes showed that there was a significant co-localization relationship between NUPTs and transposons in the genomic DNA of A officinalis.Among the 2,239 NUPTs,1,690 NUPTs flanking sequences were transposon sequences,and the ratio of 75.5% was significantly higher than that of random sequences and transposon colocalization(51.6%).An analysis of the chloroplast genome source of NUPTs showed that the inverted repeat(IR)region,short single copy(SSC)region and large single copy(LSC)region in the chloroplast genome of A officinalis all can transfer to the nuclear genome,however,the transferring frequencies were different.The frequency of NUPTs derived from IR,LSC,and SSC regions was 27.9/Kb,14.6/Kb,and 15.9/Kb,respectively,indicating that the sequence of the IR region was transferred most frequently to the nuclear genome.2.In order to investigate the chromosomal location of NUPTs,we amplified the chloroplast genome in units of approximately 4,000 bp,and the recovered and purified sequences were probed to fluorescence in situ hybridization(FISH)analysis.The results showed that 23 out of a total of 28 probe sequences showed a stable interphase chromosome FISH signal.There were three localization patterns,four sequences were located in the centromere and the flanking regions,12 sequences were diffusely distributed on chromosomes,and 7 sequences were specifically distributed on a specific chromosome.According to the source of the NUPTs sequence,the LSC and SSC region sequences were mainly located on the chromosome arm and centromeres,and the IR region sequenceswere mainly located on the centromere of the chromosome.It is more important that we obtained three Y chromosome-specific NUPTs,which were mainly located in the centromeric region of the Y chromosome.The results indicated that the insertion of NUPTs may be involved in the evolution of sex chromosomes of A.officinalis.