Structural genomic variation and behavioral interactions underpin a balanced sexual mimicry polymorphism
Data files
Oct 02, 2024 version files 10.62 GB
-
README.md
1.10 KB
-
xbir-BEJU-S231-3-IV-23-M01-FGS_Assembly-Phased.fasta.gz
318.47 MB
-
xbir-BEJU-S231-9-VIII-23-M01-WT_Assembly-Phased.fasta.gz
311.39 MB
-
xbir-BEJU-S231-9-VIII-23-M02-FGS_Assembly-Phased.fasta.gz
356.69 MB
-
xbir-COAC-19-IX-23-M.q20.bp.p_utg.fa.gz
445.69 MB
-
xbir-COAC-otolith_processing.tar.gz
6.46 GB
-
xbir-COAC-S217-22-VI-23-M01-WT_Assembly-Phased.fasta.gz
376.89 MB
-
xbir-COAC-S217-22-VI-23-M03-WT_Assembly-Phased.fasta.gz
378.17 MB
-
xbir-COAC-S217-9-VIII-23-M01-WT_Assembly-Phased.fasta.gz
370.84 MB
-
xbir-COAC-S217-9-VIII-23-M02-FGS_Assembly-Phased.fasta.gz
383.71 MB
-
xbir-COAC-S217-9-VIII-23-M03-FGS_Assembly-Phased.fasta.gz
373.30 MB
-
xbir-IZAP-S234-9-VIII-23-M01-FGS_Assembly-Phased.fasta.gz
202.92 MB
-
xbir-IZAP-S234-9-VIII-23-M02-WT_Assembly-Phased.fasta.gz
210.49 MB
-
xbir-IZAP-S234-9-VIII-23-M03-FGS_Assembly-Phased.fasta.gz
208.79 MB
-
xmal-CHIC-XI-20-M_v2023.2.fa.gz
220.81 MB
Abstract
Here, we uncover the genetic architecture of a balanced sexual mimicry polymorphism and identify behavioral mechanisms that may be involved in its maintenance in the swordtail fish Xiphophorus birchmanni. We find that ~40% of X. birchmanni males develop a “false gravid spot”, a melanic pigmentation pattern that mimics the “pregnancy spot” associated with sexual maturity in female live-bearing fish. Using genome-wide association mapping, we detect a single intergenic region associated with variation in the false gravid spot, which is upstream of kitlga, a gene involved in melanophore patterning. By performing long-read sequencing within and across populations, we identify complex structural rearrangements between alternate alleles at this locus. The false gravid spot haplotype drives increased allele-specific expression of kitlga, which provides a mechanistic explanation for the increased melanophore abundance that causes the spot. We speculate that structural variants affecting gene regulation may be an underappreciated driver of balanced polymorphisms across diverse species.
README: Complex structural variation and behavioral interactions underpin a balanced sexual mimicry polymorphism
https://doi.org/10.5061/dryad.w6m905qxc
The following data relating to this project have been deposited: X. malinche genome assembly, X. birchmanni nanopore and hifi assemblies, RNAseq kallisto h5 abundance files, images from X. birchmanni otoliths
Description of the data and file structure
Haploid genome assembly for X. malinche:
- xmal-CHIC-XI-20-M_v2023.2.fa.gz
Diploid assemblies for X. birchmanni using ONT (shasta) or PacBio HiFi (hifiasm). Naming conventions are as follows: species-population-date_sampled-sex. Corresponding individual IDs can be found at https://zenodo.org/doi/10.5281/zenodo.13329118.
- xbir-*_Assembly-Phased.fasta.gz
- xbir-COAC-19-IX-23-M.q20.bp.p_utg.fa.gz
Images of otoliths from juvenile X. birchmanni. Naming conventions are as follows: number-leftright. Number denotes individual sampled, and leftright which side of the fish the otolith was taken from.
- xbir-COAC-otolith_processing.tar.gz