TheivorylncRNA regulates seasonal color patterns in buckeye butterflies

Abstract

Long 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 butterfly Junonia coenia. ivory overlaps with cortex, a locus linked to multiple cases of crypsis and mimicry in Lepidoptera. Along with the Livraghi et. al companion paper, we argue that ivory, not cortex, is the color pattern gene of interest at this locus. In J. coenia a cluster of cis-regulatory elements (CREs) in the first intron of ivory are genetically associated with natural variation in seasonal color pattern plasticity, and targeted deletions of these CREs phenocopy seasonal phenotypes. Deletions of different ivory CREs 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 the ivory promoter during wing pattern development, suggesting that they directly regulate ivory. This case study demonstrates how cis-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.

Optix and cortex/ivory/mir-193 again: the repeated use of two mimicry hotspot loci

“…Here, we have used whole-genome analysis of 645 individual butterflies to demonstrate that putative Cortex is a cell cycle regulator that has been shown to determine scale identity, resulting in changes in pattern and coloration [16]. However, new evidence suggests that the wing patterning switch is in reality controlled by the ivory long non-coding RNA and the mir-193 microRNA sitting next to cortex [23][24][25]. Here we refer to the region implicated with colour pattern as the cortex/ ivory/mir-193 locus.…”

“…For example, a single TE insertion in an intron of cortex has been shown to cause the switch between the peppered and melanic morphs of the peppered moth, B. betularia [ 17 ], while in the Batesian mimic Papilio clytia, cortex/ivory/mir-193 has been associated with the differences between mimetic morphs: one with brown wings and reduced white elements in the apex mimicking Euploea models similarly to H. bolina, and another with melanic black and pigmented white scales in a pattern resembling toxic tiger butterflies [ 18 ]. Cortex/ivory/mir-193 has also been linked to changes in colour phenotypes in other moths, such as the silk moth Bombyx mori and some geometrids, and butterflies, such as Junonia coenia and Bicyclus anynana [ 20 , 22 , 23 , 25 , 56 , 57 ]. Crucially, in some of those cases, cis -regulatory variation around cortex has been suggested to be the cause of the phenotypic changes , with two cases in which TE insertions at regulatory regions have been implicated [ 16 , 17 , 20 ].…”

“…The ivory, mir-193 and mir2788 nucleotide sequences from Fandino et al . [ 23 , 24 ] were used to search (BLASTn [ 53 ] with E -value > 1 × 10 −10 ) for orthologous annotated genes in the HypBol_v1 and HypMisi_v2 genomes, but the results did not overlap with any annotated genes. To annotate them, we used the BLASTn results.…”

Synchronous seasonal plasticity in colouration, behaviour, and visual gene expression in a wild butterfly population

“…We aligned mRNA sequencing reads (∼33M-70M per sample) to a J. coenia transcriptome (Fandino et al, 2024) and genome ( Junonia coenia v2) on Lepbase (Challi et al, 2016) using the programs Salmon and STAR, respectively (Dobin et al, 2013; Patro et al, 2017). Pre and post alignment QC was performed with FastQC and MultiQC (Andrews, 2010; Ewels et al, 2016).…”

Lepidopteran scale cells derive from sensory organ precursors through a canonical lineage

“…Early competence in the undifferentiated SOP modulates scale colour fate Of note, the snRNAseq dataset revealed novel insights into the development of butterfly wing scales. We identified pattern-related genes restricted to the early SOP cells like WntA and fz2, and Ivory in the later scale-building cells, the latter specifically implicated in melanic patterns across Lepidoptera (Banerjee et al, 2023;Fandino et al, 2024;Hanly et al, 2023;Livraghi et al, 2024;Tian et al, 2024). Additionally, we identified a gene, pdm3, that contributes to scale cell development and differentiation, which is not found in analogous contexts in Drosophila.…”