DOI: 10.5061/dryad.qz612jmpb
title: The ivory lncRNA regulates seasonal color patterns in buckeye butterflies

description: 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.
description: # 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.protein_geneID.txt` Post-processing annotations are still required before publishing. Please contact Richard A. Fandino or Robert D. Reed for any questions: [rfandino81@gmail.com](mailto:rfandino81@gmail.com) [robertreed@cornell.edu](mailto:robertreed@cornell.edu) ``` |Results from dataset lepidoptera_odb10 | \-------------------------------------------------- |C:97.9%[S:91.1%,D:6.8%],F:0.9%,M:1.2%,n:5286 | |5173 Complete BUSCOs (C) | |4814 Complete and single-copy BUSCOs (S) | |359 Complete and duplicated BUSCOs (D) | |50 Fragmented BUSCOs (F) | |63 Missing BUSCOs (M) | |5286 Total BUSCO groups searched | \-------------------------------------------------- ```