Comparative transcriptomics between Drosophila mojavensis and D. arizonae reveals transgressive gene expression and underexpression of spermatogenesis-related genes in hybrid testes

Abstract

Interspecific hybridization is a stressful condition that can lead to sterility and/or inviability through improper gene regulation in Drosophila species with a high divergence time. However, the extent of these abnormalities in hybrids of recently diverging species is not well known. Some studies have shown that in Drosophila, the mechanisms of postzygotic isolation may evolve more rapidly in males than in females and that the degree of viability and sterility is associated with the genetic distance between species. Here, we used transcriptomic comparisons between two Drosophila mojavensis subspecies and D. arizonae (repleta group, Drosophila) and identified greater differential gene expression in testes than in ovaries. We tested the hypothesis that the severity of the interspecies hybrid phenotype is associated with the degree of gene misregulation. We showed limited gene misregulation in fertile females and an increase in the amount of misregulation in males with more severe sterile phenotypes (motile vs. amotile sperm). In addition, for these hybrids, we identified candidate genes that were mostly associated with spermatogenesis dysfunction.

Figure 1

Crosses performed between D. arizonae and D. mojavensis subspecies and differential gene expression between parental lines and hybrids. Geographic distribution of D. m. wrigleyi, D. m. mojavensis and D. arizonae lines used in this study and their respective cross directions with offspring identifications (http://www.d-maps.com/carte.php?num_car=1404&lang=en). H♀m^wri♂ari and H♀ari♂m^wri are offspring from crosses between D. arizonae and D. m. wrigleyi, and H♀ari♂m^moj are hybrids from crosses between D. arizonae and D. m. mojavensis.

Figure 2

Differential gene expression between D. arizonae and D. mojavensis subspecies and between hybrids and their respective parental lines. Scatter plots representing differential gene expression in ovaries (left) and testes (right) between parental lines, as well as between hybrids and their respective parental lines. Genes were considered differentially expressed when they presented twofold differences and FDR-corrected p-values < 0.01. Red dots = overexpressed genes; blue dots = underexpressed genes; grey dots = not differentially expressed. (A) Differential expression in ovaries of D. m. mojavensis × D. arizonae and D. m. wrigleyi × D. arizonae hybrids. (B) Differential expression in ovaries of H♀m^wri♂ari × D. m. wrigleyi hybrids and D. arizonae. (C) Differential expression in ovaries of H♀ari♂m^wri × D. m. wrigleyi hybrids and D. arizonae. (D) Differential expression in ovaries of H♀ari♂m^moj × D. m. mojavensis hybrids and D. arizonae. (E) Differential expression in testes of D. m. mojavensis × D. arizonae and D. m. wrigleyi × D. arizonae hybrids. (F) Differential expression in testes of H♀m^wri♂ari × D. m. wrigleyi hybrids and D. arizonae. (G) Differential expression in testes of H♀ari♂m^wri × D. m. wrigleyi hybrids and D. arizonae. (H) Differential expression in testes of H♀ari♂m^moj × D. m. mojavensis hybrids and D. arizonae. The scatter plot was generated using the ggplot2 package (version 3.3.3) in R. O: overexpressed genes; U: underexpressed genes.

Figure 3

GO term enrichment analysis of DEGs between D. arizonae and D. mojavensis subspecies. Dot plot representing GO enrichment for the biological process category for DEGs in (A) ovaries and (B) testes between D. arizonae- D. m. mojavensis and D. arizonae- D. m. wrigleyi (FDR < 0.05). The dot plot was generated using the ggplot2 package (version 3.3.3) in R.

Figure 4

Shared DEGs between hybrids. (A) Number of shared overexpressed genes between H♀m^wri♂ari and H♀ari♂m^wri females. (B) Number of shared overexpressed genes between H♀m^wri♂ari, H♀ari♂m^wri and H♀ari♂m^moj males. (C) Number of shared underexpressed genes between H♀m^wri♂ari, H♀ari♂m^wri and H♀ari♂m^moj males. A Venn diagram was generated using the VennDiagram package (version 1.6.20) in R.

Figure 5

Functions of shared over- and underexpressed genes between H♀ari♂m^wri and H♀ari♂m^moj males. Dot plot representing GO enrichment for the biological process, cellular component and molecular function categories. The plot was generated using the ggplot2 package (version 3.3.3) in R.

Figure 6

Average viability and fertility of intraspecific and interspecific offspring. Average viability (%) of D. arizonae, D. m. wrigleyi and D. m. mojavensis and their respective hybrids, H♀m^wri♂ari, H♀ari♂m^wri and H♀ari♂m^moj. Sperm motility and fertility are represented by—and + signals. +/+: motile sperm/fertile, +/−: motile sperm/sterile, −/− amotile sperm/sterile. The boxplot was generated using the ggplot2 package (version 3.3.3) in R.

Figure 7

Inheritance of gene expression patterns in ovaries and testes of H♀m^wri♂ari, H♀ari♂m^wri and H♀ari♂m^moj. Gene expression patterns were classified into six categories of inheritance depending on the significance of the differential expression measured by performing pairwise comparisons in all conditions, according to McManus et al.. These categories are as follows: Conserved, when the level of gene expression in hybrids is similar to that of both parental lines (not show in the plot). Additive, when the expression levels are different between the two parental lines, but the hybrid expression level is intermediate. D. arizonae-dominant or D. mojavensis-dominant, when the hybrid expression level is similar to that of only one parental line. Overdominant, when the expression level in the hybrids is significantly higher than that in both parental lines. Underdominant, when the hybrid expression level is significantly lower than that in both parental lines. The bar plot was generated using the ggplot2 package (version 3.3.3) in R.