The ivory lncRNA regulates seasonal color patterns in buckeye butterflies
Data files
Sep 11, 2024 version files 102.10 MB
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JC_OGS3.beta_fixed.gtf
34.65 MB
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JC_OGS3.beta.gff
25.01 MB
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JC_OGS3.beta.gtf
27.54 MB
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jcgen_v2.OGS3.protein_geneID.txt
1.71 MB
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jcgen_v2.OGS3.protein.fasta
13.20 MB
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README.md
1.79 KB
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readme.txt
1.52 KB
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.
README: The ivory lncRNA regulates multiple aspects of butterfly wing patterning, including seasonal polyphenism and eyespot rings
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
robertreed@cornell.edu
|Results from dataset lepidoptera_odb10 |
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|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 |
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