Drosophila Interspecific Hybridization Causes a Deregulation of the piRNA Pathway Genes

Abstract

Almost all eukaryotes have transposable elements (TEs) against which they have developed defense mechanisms. In the Drosophila germline, the main transposable element (TE) regulation pathway is mediated by specific Piwi-interacting small RNAs (piRNAs). Nonetheless, for unknown reasons, TEs sometimes escape cellular control during interspecific hybridization processes. Because the piRNA pathway genes are involved in piRNA biogenesis and TE control, we sequenced and characterized nine key genes from this pathway in Drosophila buzzatii and Drosophila koepferae species and studied their expression pattern in ovaries of both species and their F1 hybrids. We found that gene structure is, in general, maintained between both species and that two genes—armitage and aubergine—are under positive selection. Three genes—krimper, methyltransferase 2, and zucchini—displayed higher expression values in hybrids than both parental species, while others had RNA levels similar to the parental species with the highest expression. This suggests that the overexpression of some piRNA pathway genes can be a primary response to hybrid stress. Therefore, these results reinforce the hypothesis that TE deregulation may be due to the protein incompatibility caused by the rapid evolution of these genes, leading to a TE silencing failure, rather than to an underexpression of piRNA pathway genes.

High Stability of the Epigenome inDrosophilaInterspecific Hybrids

“…Results of expression of these genes showed the same general trend as observed in a previous study with these species using a different analysis approach of RNAseq data ( Romero-Soriano et al 2017 ). Nevertheless, overexpression of three additional piwi pathway genes in the same hybrids was detected by RT-qPCR in our previous work ( Gámez-Visairas et al 2020 ), suggesting that the activation of these genes could be a primary response to the hybridization stress. Discrepancies found between RT-qPCR and RNAseq results highlight the different sensibilities of these two techniques.…”

“…Gene and TE deregulation in D. buzzatii and koepferae hybrids were previously described in the literature ( Soto et al 2008 ; Vela et al 2014 ; García Guerreiro 2015 ; Romero-Soriano and Garcia Guerreiro 2016 ; Romero-Soriano et al 2017 ; Gámez-Visairas et al 2020 ), as well as in other hybrids of Drosophila ( Moehring et al 2007 ; Ortíz-Barrientos et al 2007 ; Satyaki et al 2014 ) and of other organisms ( De Araujo et al 2005 ; He et al 2013 ; Zhu, Greaves, et al 2017 ). To get insight about these genomic deregulation mechanisms, we studied the epigenomic landscape of a euchromatic mark (H3K4me3) and two heterochromatic marks (H3K9me3 and H3K27me3) in D. buzzatii , D. koepferae , and their F 1 hybrids, and we found a high similarity across these species.…”

“…For example, the misexpression of genes involved in spermatogenesis in Drosophila male hybrids ( Michalak and Noor 2003 ; Moehring et al 2007 ) has been related with their sterility. Deregulation of gene expression was also observed in hybrid females of Drosophila buzzatii and Drosophila koepferae ( Romero-Soriano et al 2017 ; Gámez-Visairas et al 2020 ) and in other Drosophila hybrids ( Ranz et al 2004 ). Gene expression in Drosophila is controlled at different levels, including epigenetic modifications ( Yin et al 2011 ) and cis- and trans- regulatory elements, among others.…”

“…A total of 31 proteins were detected and associated with D. buzzatti genes. The Argonaute 3 gene ( ago3 ), not included in the reference genes, was manually included in the list from our previous results ( Gámez-Visairas et al 2020 ).…”

“…These phenomena are induced by the fusion of two different parental genomes and epigenomes, which act as a genomic stressful factor in the hybrid genome ( García Guerreiro 2012 ). This integration leads to deregulation of gene expression in hybrids, which has been described in Drosophila ( Michalak and Noor 2003 ; Ranz et al 2004 ; Moehring et al 2007 ; Romero-Soriano et al 2017 ; Gámez-Visairas et al 2020 ) and other organisms ( Malone and Michalak 2008 ; Zhu, Hu, et al 2017 ). For example, the misexpression of genes involved in spermatogenesis in Drosophila male hybrids ( Michalak and Noor 2003 ; Moehring et al 2007 ) has been related with their sterility.…”