Carter, A. T. | Search bioRxiv

bioRxiv2026

The ivory:mir-193 non-coding RNA gene controls melanic camouflage in a polymorphic moth

A majority of moths use melanic pigmentation to blend into the visual environment, and some species display genetically controlled color polymorphisms that provide tractable systems for dissecting the genetic basis of camouflage. Here we leveraged the natural polymorphism of Anticarsia gemmatalis moths to map a major-effect gene that controls melanic variation, and study its developmental roles using expression and loss-of-function assays. A genome-wide association mapping identifies the ivory:mir-193 non-coding RNA locus as a major locus of melanic variation, with highly-divergent haplotypes differentiating the Light and Dark morphs. Second, the expression of ivory:mir-193 prefigures the melanic coloration of each morph, and suggests that cis-regulatory variation at this locus determines the difference in adult pattern. Finally, CRISPR disruption of the ivory promoter and mir-193 hairpin region each abolish melanic scale pigmentation, demonstrating that this lnc-pri-miRNA module is required for dark-scale differentiation. These findings corroborate the emerging role of ivory:mir-193 as a key factor in the development of melanic patterning, and highlight its unique propensity to repeatedly drive phenotypic variation of adaptive potential in butterflies and moths. HighlightsO_LIAnticarsia gemmatalis display striking variation in camouflage patterns C_LIO_LIDark vs. Light color polymorphism map to the ivory:mir-193 hotspot locus C_LIO_LIHighly-diverged haplotypes drive morph-specific expression of ivory:mir-193 C_LIO_LIThe miR-193 miRNA is required for melanic scale development C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/707733v2_ufig1.gif" ALT="Figure 1"> View larger version (80K): org.highwire.dtl.DTLVardef@8e491eorg.highwire.dtl.DTLVardef@1628425org.highwire.dtl.DTLVardef@d1b691org.highwire.dtl.DTLVardef@29247b_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2024

A long non-coding RNA at the cortex locus controls adaptive colouration in butterflies

Evolutionary variation in the wing pigmentation of butterflies and moths offers striking examples of adaptation by crypsis and mimicry. The cortex locus has been independently mapped as the locus controlling colour polymorphisms in 14 lepidopteran species, suggesting it acts as a genomic hotspot for the diversification of wing patterns, but functional validation through protein-coding knockouts has proven difficult to obtain. Our study unveils the role of a novel long non-coding RNA (lncRNA) which we name ivory, transcribed from the cortex locus, in modulating colour patterning in butterflies. Strikingly, ivory expression prefigures most melanic patterns during pupal development, suggesting an early developmental role in specifying scale identity. To test this, we generated CRISPR mosaic knock-outs in five nymphalid butterfly species and show that ivory mutagenesis yields transformations of dark pigmented scales into white or light-coloured scales. Genotyping of Vanessa cardui germline mutants associates these phenotypes to small on-target deletions at the conserved first exon of ivory. In contrast, cortex germline mutant butterflies with confirmed null alleles lack any wing phenotype, and exclude a colour patterning role for this adjacent gene. Overall, these results show that a lncRNA acts as a master switch of colour pattern specification, and played key roles in the adaptive diversification of colour patterns in butterflies. Significance statementDeciphering the genetic underpinnings of adaptive variation is fundamental for a comprehensive understanding of evolutionary processes. Long non-coding RNAs (lncRNAs) represent an emerging category of genetic modulators within the genome, yet they have been overlooked as a source of phenotypic diversity. In this study, we unveil the pivotal role of a lncRNA in orchestrating colour transitions between dark and light patterns during butterfly wing development. Remarkably, this lncRNA gene is nested within the cortex locus, a genetic region known to control multiple cases of adaptive variation in butterflies and moths, including iconic examples of natural selection. These findings highlight the significant influence of lncRNAs in developmental regulation, and also underscore their potential as key genetic players in the evolutionary process itself.

evolutionary biology↗