| Asparagus officinalis L. is a typical dioecious plant and belongs to perennial herb plant of Asparagus.Asparagus officinalis can be served as not only a model dioecious species to study plant sex determinationand differentiation, but also a good experimental material for the study of the origin and evolution of plantsex chromosomes. However, so far, sex chromosome of asparagus the origin and evolution of sexdetermination mechanism still did not get direct genetic evidences. Plant genome contains a large portionof transposable elements which play an important role for chromosome instability and the evolution ofplant sex chromosome. Therefore, a comprehensive analysis of transposable elements in Asparagusofficinalis genome has an important place in sex determination and differentiation and the origin of the sexchromosome.In this paper, high throughput sequencing was used to perform sequencing of both male and femaleasparagus genomes followed by analyzing for types, distributions and copy number of transposons usingbioinformatics analysis, respectively. Sometimes, we cloned and identified two scaffolds sequences andcomparative analyzed between different varieties, different plants, male and female plants, differentmonoclones and relative plants. The main results are as follows:1. By high throughput sequencing, we generated17Gb of sequence (12×coverage) and assembledthem into163,406scaffolds with a total cumulated length of400Mbp, which represent about30%ofasparagus genome. Overall, TEs masked about53%of the A. officinalis assembly. The majority ofidentified TEs belonged to LTR-retrotransposons, constituting about28%of genomic DNA, with Ty1/copiaelements being more diverse and accumulated to higher copy numbers than Ty3/gypsy. In addition,comparison of the abundance of the TE families betwfeen male and female genomes showed that theoverall TE composition was highly similar, including Ty3-gypsy, LINE and SINE in retrotransposon typesand Ac/Ds, MULE, Mariner and ping/pong/SNOOPY in DNA transposon types, their concents differencesbetween male and female genomes range of0~0.261%; With only slight differences in the abundance ofseveral TE families, including Ty1-copia and CACTA, their percentages of concents differences are1.99%and0.50%, respectively, which is consistent with the relatively recent origin of asparagus sex chromosome.2. Sequence characteristics of asparagus109sequences were searched by Blastp, thereinto,25sequences in which52scaffold101366sequences belonged to conserved regions of Ty1-copia reversetranscripatase, and11sequences belonged to conserved regions of RNA enzymes, and17sequences notonly belonged to conserved regions of Ty1-copia reverse transcripatase, but also conserved regions of RNAenzymes. In addition,36sequences in which57scaffold107518sequences belonged to conserved regionsof Ty1-copia reverse transcripatase, and6sequences belonged to conserved regions of RNA enzymes, and15sequences not only belonged to conserved regions of Ty1-copia reverse transcripatase, but alsoconserved regions of RNA enzymes. Therefore, the above results indicated that the two scaffold sequencesgained were retrotransposons sequences. 3. According to analysis the PCR amplification results of scaffold101366and scaffold107518, itshowed that the consistency of109sequences amplificated was above95%. The consistency of52sequences of Asparagus officinalis in55scaffold101366sequences was92.44%, the results showed that326mutation sites in which had2082base transitions (80%) and508base transversions (20%) byanalyzing mutation sites, T C and G A accounted for51.28%and48.72%of the base transitions,respectively. In addition, the consistency of57sequences of Asparagus officinalis in59scaffold107518sequences was92.13%, the results showed that227mutation sites in which had3039base transitions (80%)and760base transversions (20%) by analyzing mutation sites, T C and G A accounted for50.89%and49.11%of the base transitions, respectively. The above results showed that the reasons of heterogeneity oftwo Ty1-copia retrotransposons mainly related to base transitions.4. The evolutionary tree of the55scaffold101366sequences was builded by using MEGA software,which showed that Ty1-copia sequences of asparagus were divided into two big groups (GroupⅠandGroupⅡ), however, through the analysis of the two groups of sequences found sequence clustering for thespecificity of gender and varieties; It also showed that intraspecific heterogeneity higher than interspecificheterogeneity comparing with Asparagus setaceus. The evolutionary tree of the59scaffold107518sequences indicated that Ty1-copia sequences all showed specificity between asparagus varieties andbetween genders and had no significant difference with Ty1-copia sequences of Asparagus setaceus. Theabove results responsed that Ty1-copia like retrotransposons had high consistency between differentvarieties, different plants, male and female plants, different monoclones and relative plants, and sometimesretrotransposons not only can vertical transmission between generations, but also can horizontal transferamong species, whatever, it also further confirmed that Ty1-copia like retrotransposons did not producelots of bases mutation or insertions or deletions during vertical transmission or horizontal transfer, this maybe lead to one of the reason for Ty1-copia sequences similarity. |
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