Transposable Element Expression and Regulation Profile in Gonads of Interspecific Hybrids of Drosophila  arizonae and Drosophila mojavensis wrigleyi

Abstract

Interspecific hybridization may lead to sterility and/or inviability through differential expression of genes and transposable elements (TEs). In Drosophila, studies have reported massive TE mobilization in hybrids from interspecific crosses of species presenting high divergence times. However, few studies have examined the consequences of TE mobilization upon hybridization in recently diverged species, such as Drosophila arizonae and D. mojavensis. We have sequenced transcriptomes of D. arizonae and the subspecies D. m. wrigleyi and their reciprocal hybrids, as well as piRNAs, to analyze the impact of genomic stress on TE regulation. Our results revealed that the differential expression in both gonadal tissues of parental species was similar. Globally, ovaries and testes showed few deregulated TEs compared with both parental lines. Analyses of small RNA data showed that in ovaries, the TE upregulation is likely due to divergence of copies inherited from parental genomes and lack of piRNAs mapping to them. Nevertheless, in testes, the divergent expression of genes associated with chromatin state and piRNA pathway potentially indicates that TE differential expression is related to the divergence of regulatory genes that play a role in modulating transcriptional and post-transcriptional mechanisms.

Keywords: expression; hybrids; repleta group; transposable elements.

Figure 1

Expression profile of TEs in gonads of D. arizonae compared with D. m. wrigleyi subspecies. Scatter plots representing differential TE expression in (a) ovaries and (b) testes between D. arizonae and D. m. wrigleyi. TE families were considered as DE when they presented Log2(FoldChange) ≥ |1| and p-value adjusted (corrected by FDR) < 0.01. (c) Percentage of DE TEs families between parental lines classified by TE order. Transposable elements from TIR and RC orders belong to Class II elements, known as DNA transposons. Transposable elements from LTR (long terminal repeat) and LINE (long interspersed nuclear element) orders belong to Class I elements, known as retrotransposons. DE TEs: deregulated TEs; O: overexpressed TEs; U: underexpressed TEs.

Figure 2

TE expression in hybrids gonads. (a) The total number of TE families in hybrid ovaries and testes classified in different categories of expression. (b) Global expression of TEs orders according to Log2(FoldChange), between parental lines and between hybrids and parental lines. Dotted lines represent Log2(FoldChange) > |1| and p-value adjusted < 0.05.

Figure 3

TE expression in ovaries of hybrids vs. parental lines. (a) log2 of the ratio (counts in H♀m^wri♂ari/counts in parental lines (D. arizonae and D. m. wrigleyi)); (b) log2 of the ratio (counts in H♀ari♂m^wri/counts in parental lines (D. arizonae and D. m. wrigleyi)). Dotted lines represent Log2(FoldChange) > |1| and p-value adjusted < 0.05. DE TEs: deregulated TEs; O: overexpressed TEs; U: underexpressed TEs.

Figure 4

TE expression in testes of hybrids vs. parental lines. (a) log2 of the ratio (counts in H♀m^wri♂ari/counts in parental lines (D. arizonae and D. m. wrigleyi)); (b) log2 of the ratio (counts in H♀ari♂m^wri/counts in parental lines (D. arizonae and D. m. wrigleyi)). Dotted lines represent Log2(FoldChange) > |1| and p-value adjusted < 0.05. DE TEs: deregulated TEs; O: overexpressed TEs; U: underexpressed TEs.

Figure 5

Small RNA abundance in gonads of hybrid and parental lines. (a) TE-derived small RNA production for ovaries (left) and testes (right) of D. arizonae, D. m. wrigleyi, and their reciprocal hybrids; (b) TE-derived 23 to 30 nt small RNA modulation upon interspecific hybridization in female gonadal tissues; (c) TE-specific piRNA abundance for upregulated TEs found in ovaries; (d) TE-derived 23 to 30 nt small RNA modulation upon interspecific hybridization in male gonadal tissues; (e) TE-specific piRNA abundance for upregulated TEs identified in testes. Small RNA amounts were normalized relative to miRNAs. Dotted lines represent Log2(FoldChange) = |1|.

Figure 6

TE transcripts and TE-derived piRNAs in females assessed from RNA-Seq. (a) Expression level of TEs found upregulated in H♀m^wri♂ari and H♀ari♂m^wri ovaries. (b) Ping-pong signatures for 23–30 nt RNAs in D. H♀m^wri♂ari and H♀ari♂m^wri ovaries. Significant enrichment in 10-nt overlaps (i.e., ping-pong signatures) is considered when z-score > 2.58.

Figure 7

TE transcripts and TE-derived piRNAs in males assessed from RNA-Seq. (a) Expression level of TEs found upregulated in H♀m^wri♂ari and H♀ari♂m^wri testes. (b) Ping-pong signatures for 23–30 nt RNAs in D. H♀m^wri♂ari and H♀ari♂m^wri testes. Significant enrichment in 10-nt overlaps (i.e., ping-pong signatures) is considered when z-score > 2.58.

Figure 8

piRNA pathway genes that act in the biogenesis of primary and secondary via piRNAs. (a) Heatmap representing gene expression in ovaries (left) and testes (right) of D. arizonae, D. m. wrigleyi, H♀m^wri♂ari and in H♀ari♂m^wri. Colors indicate the level of expression according to log2 of normalized counts (NC). (b) d_N/d_S ratio for the 33 genes involved in the piRNA pathway between parental species. The genes under negative relaxed selection (d_N/d_S > 0.3) for each comparison are identified in the plot.