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Males and females share most of the genome, but many animals show different phenotypes between the sexes, known as sexual dimorphism. Many insect species show extreme sexual dimorphism, including beetles with "weapon traits" represented by extremely developed horns and mandibles. Existing studies of sex‐specific development of beetle weapon traits suggest that sex‐specific gene expression plays an important role. On the other hand, contributions of the Y‐chromosome, which may potentially carry genes necessary for male development, to weapon trait expression have not been examined. In holometabolous insects, including beetles, the feminizing gene transformer (tra) is roughly conserved in its feminizing function. Only females express a functional isoform of Tra, which causes female differentiation. Knocking down tra in females leads to male tissue differentiation, enabling us to analyze male phenotypes in individuals lacking a Y‐chromosome (XX‐males). In this study, we investigate whether the Y‐chromosome is necessary for stag beetles to express male‐specific weapon traits by comparing tra‐knockdown‐induced XX‐males with natural XY males. We show that XX‐males could express weapons (enlarged mandibles) as in XY‐males. These results suggest that the Y‐chromosome does not have a major role in weapon trait expression in this species. Research Highlights: Developmental roles of Y‐chromosome on male‐specific mandible growth in stag beetles were analyzed. "XX‐male" was induced from females by suppressing feminizer gene. These XX‐males had developed mandibles, indicating the Y‐chromosome's limited role. [ABSTRACT FROM AUTHOR]

Background: Cis-regulatory mutations often underlie phenotypic evolution. However, because identifying the locations of promoters and enhancers in non-coding regions is challenging, we have fewer examples of identified causative cis-regulatory mutations that underlie naturally occurring phenotypic variations than of causative amino acid-altering mutations. Because cis-regulatory elements have epigenetic marks of specific histone modifications, we can detect cis-regulatory elements by mapping and analyzing them. Here, we investigated histone modifications and chromatin accessibility with cleavage under targets and tagmentation (CUT&Tag) and assay for transposase-accessible chromatin-sequencing (ATAC-seq). Results: Using the threespine stickleback (Gasterosteus aculeatus) as a model, we confirmed that the genes for which nearby regions showed active marks, such as H3K4me1, H3K4me3, and high chromatin accessibility, were highly expressed. In contrast, the expression levels of genes for which nearby regions showed repressive marks, such as H3K27me3, were reduced, suggesting that our chromatin analysis protocols overall worked well. Genomic regions with peaks of histone modifications showed higher nucleotide diversity within and between populations. By comparing gene expression in the gills of the marine and stream ecotypes, we identified several insertions and deletions (indels) with transposable element fragments in the candidate cis-regulatory regions. Conclusions: Thus, mapping and analyzing histone modifications can help identify cis-regulatory elements and accelerate the identification of causative mutations in the non-coding regions underlying naturally occurring phenotypic variations. [ABSTRACT FROM AUTHOR]