TheivorylncRNA regulates seasonal color patterns in buckeye butterflies

Abstract

AbstractLong non-coding RNAs (lncRNAs) are transcribed elements increasingly recognized for their roles in regulating gene expression. Thus far, however, we have little understanding of how lncRNAs contribute to evolution and adaptation. Here we show that a conserved lncRNA,ivory, is an important color patterning gene in the buckeye butterflyJunonia coenia.ivoryoverlaps withcortex, a locus linked to multiple cases of crypsis and mimicry in Lepidoptera. Along with a companion paper by Livraghi et. al., we argue thativory, notcortex, is the color pattern gene of interest at this locus. InJ. coeniaa cluster ofcis-regulatory elements (CREs) in the first intron ofivoryare genetically associated with natural variation in seasonal color pattern plasticity, and targeted deletions of these CREs phenocopy seasonal phenotypes. Deletions of differentivoryCREs produce other distinct phenotypes as well, including loss of melanic eyespot rings, and positive and negative changes in overall wing pigmentation. We show that the color pattern transcription factors Spineless, Bric-a-brac, and Ftz-f1 bind to theivorypromoter during wing pattern development, suggesting that they directly regulateivory. This case study demonstrates howcis-regulation of a single non-coding RNA can exert diverse and nuanced effects on the evolution and development of color patterns, including modulating seasonally plastic color patterns.SignificanceThe genomic locus hosting thecortexgene has been linked to numerous cases of color pattern adaptation in moths and butterflies, including crypsis, mimicry, and seasonal polyphenism. Here we show in buckeye butterflies that the actual color pattern gene at thecortexlocus is an evolutionarily conserved long non-coding RNA (lncRNA), dubbedivory, that overlaps withcortex. Compared with other wing pattern genes,ivorystands out because of the highly nuanced, quantitative changes in pigmentation that can be achieved by manipulating adjacentcis-regulatory sequences. This study highlights how lncRNAs can be important factors underlying morphological evolution, and emphasizes the importance of considering non-coding transcripts in comparative genomics.