Nuez, I. | Search bioRxiv

bioRxiv2026

The Illumina Stranded mRNA protocol is not strongly stranded for mRNA with low U content

The Illumina TruSeq Stranded and Illumina Stranded mRNA protocols are commonly used for strand-specific bulk RNA-seq and they typically yield >99% antisense reads. We show that these protocols can generate sense-oriented reads for transcripts with extremely low U content (<3%). Indeed, such regions can bypass the dUTP-based blockade of cDNA second strand amplification. A small number of genes are affected by this issue (three in Drosophila melanogaster, including the glue gene Sgs3, and 46 in Mus musculus). To prevent overestimation of expression levels, we recommend excluding sense reads for all genes.

genomics↗

bioRxiv2018

Correlated Evolution of two Sensory Organs via a Single Cis-Regulatory Nucleotide Change

Diverse traits often covary between species. The possibility that a single mutation could contribute to the evolution of several characters between species is rarely investigated as relatively few cases are dissected at the nucleotide level. Drosophila santomea has evolved additional sex comb sensory teeth on its legs and has lost two sensory bristles on its genitalia. We found that a single nucleotide substitution in an enhancer of the scute gene contributes to both changes. The mutation alters a binding site for the Hox protein Abdominal-B in the developing genitalia, leading to bristle loss, and for another factor in the developing leg, leading to bristle gain. Our study shows that morphological evolution between species can occur through a single nucleotide change affecting several sexually dimorphic traits.\n\nOne Sentence SummaryWe identify one nucleotide substitution in a gene regulatory region contributing to evolutionary change of two distinct organs.

evolutionary biology↗