The ivory lncRNA regulates seasonal color patterns in buckeye butterflies

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 pig..., , , # The ivory lncRNA regulates multiple aspects of butterfly wing patterning, including seasonal polyphenism and eyespot rings

[https://doi.org/10.5061/dryad.qz612jmpb](https://doi.org/10.5061/dryad.qz612jmpb)

## Description of the data and file structure

Junonia coenia OGS3 Annotation Beta
Annotation models using BRAKER/TSEBRA were generated from both PacBio long read and short read mRNAseq
mRNAseq data was compiled from all developmental stages of wing bi-directional RNAseq data from VanderBurg et al 2019 and VanderBurg et al. 2020. PacBio long read transcriptome was compiled from all tissues and developmental stages, not yet published.

* Annotated files with gene prediction Drosophila melanogaster orthologs: `JC_OGS3.beta.gff`, `JC_OGS3.beta.gtf`
* Annotated file with gene id names, corrected for category errors: `JC_OGS3.beta_fixed.gtf`
* Fasta file of amino acid sequences with gene_id name: `jcgen_v2.OGS3.protein.fasta`
* gene_id names with drosophila orthologs: `jcgen_v2.OGS.pro...