Analysis of transposable elements in the genome of Asparagus officinalis from high coverage sequence data

Abstract

Asparagus officinalis is an economically and nutritionally important vegetable crop that is widely cultivated and is used as a model dioecious species to study plant sex determination and sex chromosome evolution. To improve our understanding of its genome composition, especially with respect to transposable elements (TEs), which make up the majority of the genome, we performed Illumina HiSeq2000 sequencing of both male and female asparagus genomes followed by bioinformatics analysis. We generated 17 Gb of sequence (12×coverage) and assembled them into 163,406 scaffolds with a total cumulated length of 400 Mbp, which represent about 30% of asparagus genome. Overall, TEs masked about 53% of the A. officinalis assembly. Majority of the identified TEs belonged to LTR retrotransposons, which constitute about 28% of genomic DNA, with Ty1/copia elements being more diverse and accumulated to higher copy numbers than Ty3/gypsy. Compared with LTR retrotransposons, non-LTR retrotransposons and DNA transposons were relatively rare. In addition, comparison of the abundance of the TE groups between male and female genomes showed that the overall TE composition was highly similar, with only slight differences in the abundance of several TE groups, which is consistent with the relatively recent origin of asparagus sex chromosomes. This study greatly improves our knowledge of the repetitive sequence construction of asparagus, which facilitates the identification of TEs responsible for the early evolution of plant sex chromosomes and is helpful for further studies on this dioecious plant.

Figure 1. Histograms of the composition of transposable elements in A. officinalis.

A: Number of scaffolds; B: DNA fraction (in % of the whole TE fraction).

Figure 2. RPKM plot for retrotransposon sequences of A. officinalis.

The plot included 5506 Ty1/copia, 3160 Ty3/gypsy, 1621 LINE and 23 SINE assembled region. X axis stands for the RPKM value for per retrotransposons sequences from male DNA-sequencing library. Y axis stands for the RPKM value for female library.

Figure 3. RPKM plot for transposon sequences of A. officinalis.

There were 78 Ac/Ds; 1088 CACTA, En/Spm; 59 MULE; 50 Mariner (MLE); 22 ping/pong/SNOOPY sequences which were identified as transposons. X axis stand for the RPKM value for per transposons sequences from male DNA-sequencing library. Y axis stands for the RPKM value for female library.

Figure 4. Distinctly sex-biased sequences in the genome of Asparagus officinalis.

Let C1 and C2 denote the counts of reads mapped to a specific scaffold obtained from male and female samples, respectively. Then we define M = (C1+C2)/2, and A = C1–C2. Blue and green dots represent distinctly 248 male-biased and 553 female-biased sequences, respectively, while grey dots represent sequences which have similar abundance between male and female genomes.