| As an important component of the eukaryotic genome,transposable elements(TEs)can cause rearrangement of the chromosome structure and therefore play an important role in chromosome evolution.Asparagus officinalis,also known as asparagus,is a perennial dioecious herbaceous plant belonging to genus Asparagus.Its sexual type is determined by a pair of homotypic XY sex chromosomes and is one of the model plant species for studying the origin and evolution of sex chromosomes in plants.The draft genome has been sequenced and assembled..However,it is still unclear about the composition and characteristics of the TEs in the genome of Asparagus officinalis,especially its chromosome distribution pattern.Therefore,bioinformatics techniques were used to annotate TEs in the genome of Asparagus officinalis,and its composition types and proportions in the genome were analyzed.Furthermore,metaphase chromosome fluorescence in situ hybridization(FISH)was used to investigate the distribution patterns of the major types of TEs on chromosomes.The main findings are as follows:1.Based on a series of repeat sequence analysis tools,we performed repeat sequence annotation of the published genome sequence of Asparagus officinalis.The results showed that the proportion of TEs in the genome of Asparagus officinalis was 60.92%,which was mainly composed of Ty1-copia and Ty3-gypsy retrotransposons,with the proportion of 18.13% and 37.82% of the genome,respectively.The DNA transposon content is relatively low,with a ratio of 1.28%.The analysis of gene density and transposon length on 10 chromosomes showed that TEs mainly distributed in the middle of the chromosomes,and less distributed at the end of the chromosome,which showed a nenative correlation with gene distribution.Analysis of the TEs in the MSY region of the Y chromosome revealed that the percentage of TEs reached to 86.95%,which was significantly higher than the proportion of 69.38% in the genome.Furthermore,the TEs of the MSY region was mainly constituted by LTR retrotransposons,indicating that the LTR retrotransposons may be involved in the origin and evolution of sex chromosomes of Asparagus officinalis.In order to understand the transposon composition characteristics of different dioecious plant genomes,we compared the TE content of 11 dioecious plant genomes that were sequenced,and found that the content of the retrotransposons was significantly higher than that of the DNA transposons in all the 11 dioecious plant genomes.The retrotransposons were mainly constituted by Ty1-copia and Ty3-gypsy.However,the variation of TE content in the 11 dioecious plant genomes ranged from 17.70% in Morus alba to 67.84% in Spinacia oleracea and there was also a significant difference in genome size and transposon content,which is is consistent with the ideal that dioecious plants are origined independently.2.In order to investigate the chromosome distribution pattern of the TEs,,51 transposons were cloned from the genome of Asparagus officinalis,including 14 Ty1-copia etrotransposons and 17 Ty3-gypsy retrotransposons,8 other types of retrotransposons and 12 DNA transposons.The FISH results demonstrated that 51 transposon sequences showed clear and stable hybridization signals.In the retrotransposons,the distribution patterns of the LTR retrotransposons mainly include four modes,including specific distribution in centromeres,distribution mainly in centromeres and their flanking regions,distrubition in chromosome arms except for centromeres and telomeres,and diffuse distrubion on the whole chromosome.The LINE retrotransposons mainly distributed in centromeres and their flanking regions on the chromosome.The signals of DNA transposons mainly occur in centromeres and their flanking regions and chromosome arms.The results indicated that there were differences in the distribution of chromosomes between the retrotransposons and the DNA transposons.Although the distribution of different types of retrotransposons on chromosomes is also specific for certain locations,their hybridization signals are extensive in the centromeres and their flanking heterochromatin regions.We speculated that the heterochromatin region of the centromere and its flank regions are the hot spots of the transposon distribution.Comparative study of transposon distribution on different chromosomes showed that the TE contents of the first seven pairs of larger chromosomes were obviously higher than that of the last three pairs of small chromosomes,indicating that the continuous insertion of the retrotransposons may be a main contributor for the expansion of chromosomes. |
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