Kloss-Schmidt, A. | bioRxiv Science

bioRxiv2026

Divergent regulatory impacts of endogenous siRNAs on host mRNAs in testis of closely related species

Invertebrates use RNAi to fight viruses that replicate via dsRNA intermediates, which serve as precursors for producing anti-viral siRNAs. In addition, siRNAs are produced from a broad range of endogenous dsRNAs in Drosophila melanogaster. However, beyond the impacts of siRNAs derived from a handful of hairpin RNAs, the regulatory potential of most endo-siRNAs has been unknown. Here, we report that RNAi is far more potent in the close sister species Drosophila simulans. Consequently, endo-siRNAs repress less than a dozen transcripts in D. melanogaster, but hundreds of mRNAs in D. simulans testis. These regulatory interactions occur in cis (between pairs of bidirectionally transcribed loci), as well as in trans (between genomically unlinked siRNA-target pairs). We establish the molecular determinants of productive gene repression by siRNAs in vivo, including cleavage in trans via >16-nt contiguous complementarity. Our data indicate that D. simulans spermatogenesis requires repression of numerous host mRNAs by endo-siRNAs. More generally, we reveal unexpectedly fast-evolving and broad regulatory impacts of endogenous RNAi in the male germline.

molecular biology↗

bioRxiv2025

Natural variation in expression of a plant immune receptor mediates elicitor sensitivity

Plant immune systems rely on pattern recognition receptors (PRRs) to specifically detect diverse pathogen/pest-associated molecular patterns (PAMPs). While many distinct receptors are known to mediate PAMP recognition, the role of transcriptional regulation of PRRs remains poorly understood. In legume plants, Inceptin Receptor (INR) senses an 11-amino acid peptide, In11, to activate direct and indirect defenses against caterpillar pests. Here we investigated the genetic basis of the rare In11 insensitivity phenotype found in common bean (Phaseolus vulgaris) landraces. Natural variation in the rapid In11-induced ethylene response corresponded with genetic variation at the locus encoding INR itself. Surprisingly, phenotypic variation corresponded with expression level of the INR receptor, rather than coding sequence variation. Promoter sequence variation across 21 accessions of Andean Phaseolus vulgaris, as well as near-isogenic lines (NILs) derived from crosses between an In11-sensitive and insensitive line, corresponded with strength of In11-induced ethylene response. Promoter alleles also corresponded with strength of activation of a luciferase reporter in the heterologous expression model, Nicotiana benthamiana, indicating that cis-element variation is sufficient to drive differences in leaf expression levels. Surprisingly, NILs encoding either WT or the lower expression inr-2 allele did not show differences in resistance to herbivory by beet armyworm (Spodoptera exigua), or in In11-pretreatment protection assays, suggesting that even low INR expression can still mediate effective responses against herbivores despite insensitivity to the In11 elicitor in laboratory assays. Our results demonstrate that natural variation in PRR expression can contribute to differential PAMP responses while not necessarily affecting downstream resistance phenotypes.

plant biology↗